Rapid development of medical imaging tools with open-source libraries.

Science.gov (United States)

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

BAT: An open-source, web-based audio events annotation tool

OpenAIRE

Blai Meléndez-Catalan, Emilio Molina, Emilia Gómez

2017-01-01

In this paper we present BAT (BMAT Annotation Tool), an open-source, web-based tool for the manual annotation of events in audio recordings developed at BMAT (Barcelona Music and Audio Technologies). The main feature of the tool is that it provides an easy way to annotate the salience of simultaneous sound sources. Additionally, it allows to define multiple ontologies to adapt to multiple tasks and offers the possibility to cross-annotate audio data. Moreover, it is easy to install and deploy...

iPhone Open Application Development Write Native Applications Using the Open Source Tool Chain

CERN Document Server

Zdziarski, Jonathan

2008-01-01

Developers everywhere are eager to create applications for the iPhone, and many of them prefer the open source, community-developed tool chain to Apple's own toolkit. This new edition of iPhone Open Application Development covers the latest version of the open toolkit -- now updated for Apple's iPhone 2.x software and iPhone 3G -- and explains in clear language how to create applications using Objective-C and the iPhone API.

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.

From Open Source Software to Open Source Hardware

OpenAIRE

Viseur , Robert

2012-01-01

Part 2: Lightning Talks; International audience; The open source software principles progressively give rise to new initiatives for culture (free culture), data (open data) or hardware (open hardware). The open hardware is experiencing a significant growth but the business models and legal aspects are not well known. This paper is dedicated to the economics of open hardware. We define the open hardware concept and determine intellectual property tools we can apply to open hardware, with a str...

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…

Open-Source Colorimeter

OpenAIRE

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 porta...

Tools for open geospatial science

Science.gov (United States)

Petras, V.; Petrasova, A.; Mitasova, H.

2017-12-01

Open science uses open source to deal with reproducibility challenges in data and computational sciences. However, just using open source software or making the code public does not make the research reproducible. Moreover, the scientists face the challenge of learning new unfamiliar tools and workflows. In this contribution, we will look at a graduate-level course syllabus covering several software tools which make validation and reuse by a wider professional community possible. For the novices in the open science arena, we will look at how scripting languages such as Python and Bash help us reproduce research (starting with our own work). Jupyter Notebook will be introduced as a code editor, data exploration tool, and a lab notebook. We will see how Git helps us not to get lost in revisions and how Docker is used to wrap all the parts together using a single text file so that figures for a scientific paper or a technical report can be generated with a single command. We will look at examples of software and publications in the geospatial domain which use these tools and principles. Scientific contributions to GRASS GIS, a powerful open source desktop GIS and geoprocessing backend, will serve as an example of why and how to publish new algorithms and tools as part of a bigger open source project.

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). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Demonstrating High-Accuracy Orbital Access Using Open-Source Tools

Science.gov (United States)

Gilbertson, Christian; Welch, Bryan

2017-01-01

Orbit propagation is fundamental to almost every space-based analysis. Currently, many system analysts use commercial software to predict the future positions of orbiting satellites. This is one of many capabilities that can replicated, with great accuracy, without using expensive, proprietary software. NASAs SCaN (Space Communication and Navigation) Center for Engineering, Networks, Integration, and Communications (SCENIC) project plans to provide its analysis capabilities using a combination of internal and open-source software, allowing for a much greater measure of customization and flexibility, while reducing recurring software license costs. MATLAB and the open-source Orbit Determination Toolbox created by Goddard Space Flight Center (GSFC) were utilized to develop tools with the capability to propagate orbits, perform line-of-sight (LOS) availability analyses, and visualize the results. The developed programs are modular and can be applied for mission planning and viability analysis in a variety of Solar System applications. The tools can perform 2 and N-body orbit propagation, find inter-satellite and satellite to ground station LOS access (accounting for intermediate oblate spheroid body blocking, geometric restrictions of the antenna field-of-view (FOV), and relativistic corrections), and create animations of planetary movement, satellite orbits, and LOS accesses. The code is the basis for SCENICs broad analysis capabilities including dynamic link analysis, dilution-of-precision navigation analysis, and orbital availability calculations.

VSEARCH: a versatile open source tool for metagenomics.

Science.gov (United States)

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

2016-01-01

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. 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. 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 with USEARCH for paired

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.

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.

An open-source optimization tool for solar home systems: A case study in Namibia

International Nuclear Information System (INIS)

Campana, Pietro Elia; Holmberg, Aksel; Pettersson, Oscar; Klintenberg, Patrik; Hangula, Abraham; Araoz, Fabian Benavente; Zhang, Yang; Stridh, Bengt; Yan, Jinyue

2016-01-01

Highlights: • An open-source optimization tool for solar home systems (SHSs) design is developed. • The optimization tool is written in MS Excel-VBA. • The optimization tool is validated with a commercial and open-source software. • The optimization tool has the potential of improving future SHS installations. - Abstract: Solar home systems (SHSs) represent a viable technical solution for providing electricity to households and improving standard of living conditions in areas not reached by the national grid or local grids. For this reason, several rural electrification programmes in developing countries, including Namibia, have been relying on SHSs to electrify rural off-grid communities. However, the limited technical know-how of service providers, often resulting in over- or under-sized SHSs, is an issue that has to be solved to avoid dissatisfaction of SHSs’ users. The solution presented here is to develop an open-source software that service providers can use to optimally design SHSs components based on the specific electricity requirements of the end-user. The aim of this study is to develop and validate an optimization model written in MS Excel-VBA which calculates the optimal SHSs components capacities guaranteeing the minimum costs and the maximum system reliability. The results obtained with the developed tool showed good agreement with a commercial software and a computational code used in research activities. When applying the developed optimization tool to existing systems, the results identified that several components were incorrectly sized. The tool has thus the potentials of improving future SHSs installations, contributing to increasing satisfaction of end-users.

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

VSEARCH: a versatile open source tool for metagenomics

Directory of Open Access Journals (Sweden)

Torbjørn Rognes

2016-10-01

Full Text Available 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

Online characterization of planetary surfaces: PlanetServer, an open-source analysis and visualization tool

Science.gov (United States)

Marco Figuera, R.; Pham Huu, B.; Rossi, A. P.; Minin, M.; Flahaut, J.; Halder, A.

2018-01-01

The lack of open-source tools for hyperspectral data visualization and analysis creates a demand for new tools. In this paper we present the new PlanetServer, a set of tools comprising a web Geographic Information System (GIS) and a recently developed Python Application Programming Interface (API) capable of visualizing and analyzing a wide variety of hyperspectral data from different planetary bodies. Current WebGIS open-source tools are evaluated in order to give an overview and contextualize how PlanetServer can help in this matters. The web client is thoroughly described as well as the datasets available in PlanetServer. Also, the Python API is described and exposed the reason of its development. Two different examples of mineral characterization of different hydrosilicates such as chlorites, prehnites and kaolinites in the Nili Fossae area on Mars are presented. As the obtained results show positive outcome in hyperspectral analysis and visualization compared to previous literature, we suggest using the PlanetServer approach for such investigations.

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).

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.

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

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.

Open source tools for the information theoretic analysis of neural data

Directory of Open Access Journals (Sweden)

Robin A. A Ince

2010-05-01

Full Text Available The recent and rapid development of open-source software tools for the analysis of neurophysiological datasets consisting of multiple simultaneous 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 integrate the 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.

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.

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.

WannierTools: An open-source software package for novel topological materials

Science.gov (United States)

Wu, QuanSheng; Zhang, ShengNan; Song, Hai-Feng; Troyer, Matthias; Soluyanov, Alexey A.

2018-03-01

We present an open-source software package WannierTools, a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 (Mostofi et al., 2008). It can help to classify the topological phase of a given material by calculating the Wilson loop, and can get the surface state spectrum, which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone (BZ).

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

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

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.

M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.

Science.gov (United States)

Aiyetan, Paul; Zhang, Bai; Chen, Lily; Zhang, Zhen; Zhang, Hui

2014-04-28

Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Here we present M2Lite, an open-source, light-weight, easily pluggable and fast conversion tool. M2Lite converts proteome discoverer derived MSF files to the proteomics community defined standard - the mzIdentML file format. M2Lite's source code is available as open-source at https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/m2lite/downloads.

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!

CellProfiler and KNIME: open source tools for high content screening.

Science.gov (United States)

Stöter, Martin; Niederlein, Antje; Barsacchi, Rico; Meyenhofer, Felix; Brandl, Holger; Bickle, Marc

2013-01-01

High content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using Open Source software. We present and discuss the Open Source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions which increase flexibility and keep costs low.

Openly Published Environmental Sensing (OPEnS) | Advancing Open-Source Research, Instrumentation, and Dissemination

Science.gov (United States)

Udell, C.; Selker, J. S.

2017-12-01

The increasing availability and functionality of Open-Source software and hardware along with 3D printing, low-cost electronics, and proliferation of open-access resources for learning rapid prototyping are contributing to fundamental transformations and new technologies in environmental sensing. These tools invite reevaluation of time-tested methodologies and devices toward more efficient, reusable, and inexpensive alternatives. Building upon Open-Source design facilitates community engagement and invites a Do-It-Together (DIT) collaborative framework for research where solutions to complex problems may be crowd-sourced. However, barriers persist that prevent researchers from taking advantage of the capabilities afforded by open-source software, hardware, and rapid prototyping. Some of these include: requisite technical skillsets, knowledge of equipment capabilities, identifying inexpensive sources for materials, money, space, and time. A university MAKER space staffed by engineering students to assist researchers is one proposed solution to overcome many of these obstacles. This presentation investigates the unique capabilities the USDA-funded Openly Published Environmental Sensing (OPEnS) Lab affords researchers, within Oregon State and internationally, and the unique functions these types of initiatives support at the intersection of MAKER spaces, Open-Source academic research, and open-access dissemination.

Tools for Trade Analysis and Open Source Information Monitoring for Non-proliferation

International Nuclear Information System (INIS)

Cojazzi, G.G.M.; Versino, C.; Wolfart, E.; Renda, G.; Janssens, W.A.M.; )

2015-01-01

The new state level approach being proposed by IAEA envisions an objective based and information driven safeguards approach utilizing all relevant information to improve the effectiveness and efficiency of safeguards. To this goal the IAEA makes also use of open source information, here broadly defined as any information that is neither classified nor proprietary. It includes, but is not limited to: media sources, government and non-governmental reports and analyzes, commercial data, and scientific/technical literature, including trade data. Within the EC support programme to IAEA, JRC has surveyed and catalogued open sources on import-export customs trade data and developed tools for supporting the use of the related databases in safeguards. The JRC software The Big Table, (TBT), supports i.a.: a) the search through a collection of reference documents relevant to trade analysis (legal/regulatory documents, technical handbooks); b) the selection of items of interests to specific verifications and c) the mapping of these items to customs commodities searchable in trade databases. In the field of open source monitoring, JRC is developing and operating a ''Nuclear Security Media Monitor'' (NSMM), which is a web-based multilingual news aggregation system that automatically collects news articles from pre-defined web sites. NSMM is a domain specific version of the general JRC-Europe Media Monitor (EMM). NSMM has been established within the EC support programme with the aim, i.e., to streamline IAEA's process of open source information monitoring. In the first part, the paper will recall the trade data sources relevant for non-proliferation and will then illustrate the main features of TBT, recently coupled with the IAEA Physical Model, and new visualization techniques applied to trade data. In the second part it will present the main aspects of the NSMM also by illustrating some of uses done at JRC. (author)

Open-source colorimeter.

Science.gov (United States)

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

2013-04-19

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.

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

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.

Pika: A snow science simulation tool built using the open-source framework MOOSE

Science.gov (United States)

Slaughter, A.; Johnson, M.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase-field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture and crack propagation (via the extended finite-element method), flow in porous media, and others. The heat conduction, tensor mechanics, and phase-field modules, in particular, are well-suited for snow science problems. Pika--an open-source MOOSE-based application--is capable of simulating both 3D, coupled nonlinear continuum heat transfer and large-deformation mechanics applications (such as settlement) and phase-field based micro-structure applications. Additionally, these types of problems may be coupled tightly in a single solve or across length and time scales using a loosely coupled Picard iteration approach. In addition to the wide range of physics capabilities, MOOSE-based applications also inherit an extensible testing framework, graphical user interface, and documentation system; tools that allow MOOSE and other applications to adhere to nuclear software quality standards. The snow science community can learn from the nuclear industry and harness the existing effort to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The snow science community should build on existing tools to enable collaboration between researchers and practitioners throughout the world, and advance the

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

ProteoWizard: open source software for rapid proteomics tools development.

Science.gov (United States)

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome.

Science.gov (United States)

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the "connectome". Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/.

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.

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.

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

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

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

Open-Source tools: Incidence in the wireless security of the Technical University of Babahoyo

Directory of Open Access Journals (Sweden)

Joffre León-Acurio

2018-02-01

Full Text Available Computer security is a fundamental part of an organization, especially in Higher Education institutions, where there is very sensitive information, capable of being vulnerable by diffeerent methods of intrusion, the most common being free access through wireless points. The main objective of this research is to analyze the impact of the open source tools in charge of managing the security information of the wireless network, such as OSSIM, a set of active and passive components used to manage events that generate tra c within the network. net. This research exposes the use of free software as a viable option of low cost to solve the problems that a ict student sta , such as lack of access to academic services, problems of wireless interconnectivity, with the purpose to restore confidence in students in the Use of the services offered by the institution for research-related development, guaranteeing free and free access to the internet. The level of dissatisfaction on the part of the students con rms the problem presented at the Technical University of Babahoyo, thus confirming the positive influence of the Open-Source tools for the institution’s wireless security.

Code Forking, Governance, and Sustainability in Open Source Software

OpenAIRE

Juho Lindman; Linus Nyman

2013-01-01

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 possibilit...

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. ...

A Benchmarking Analysis of Open-Source Business Intelligence Tools in Healthcare Environments

Directory of Open Access Journals (Sweden)

Andreia Brandão

2016-10-01

Full Text Available In recent years, a wide range of Business Intelligence (BI technologies have been applied to different areas in order to support the decision-making process. BI enables the extraction of knowledge from the data stored. The healthcare industry is no exception, and so BI applications have been under investigation across multiple units of different institutions. Thus, in this article, we intend to analyze some open-source/free BI tools on the market and their applicability in the clinical sphere, taking into consideration the general characteristics of the clinical environment. For this purpose, six BI tools were selected, analyzed, and tested in a practical environment. Then, a comparison metric and a ranking were defined for the tested applications in order to choose the one that best applies to the extraction of useful knowledge and clinical data in a healthcare environment. Finally, a pervasive BI platform was developed using a real case in order to prove the tool viability.

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.

Open Source Information in Support of Safeguards

International Nuclear Information System (INIS)

Christopher, G.

2015-01-01

Open source techniques are an increasingly important tool for in safeguards. From social networking sites, such as Linkedin, to B2B portals like Alibaba, there are large open source databases that touch all aspects of the nuclear fuel cycle, from goods to scientists. This is in addition to the wealth of more traditional open source tools such as search engines. In this paper we focus on the potential of B2B sites to provide dual use goods for use in the nuclear fuel cycle. We will discuss the availability of these items as well as the frequency and content of tenders. As many of the largest sites—by traffic and content—are in Asia we will examine the potential of these sites to provide goods used in the nuclear fuel cycle. (author)

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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Science.gov (United States)

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

An Open-Source Web-Based Tool for Resource-Agnostic Interactive Translation Prediction

Directory of Open Access Journals (Sweden)

Daniel Torregrosa

2014-09-01

Full Text Available We present a web-based open-source tool for interactive translation prediction (ITP and describe its underlying architecture. ITP systems assist human translators by making context-based computer-generated suggestions as they type. Most of the ITP systems in literature are strongly coupled with a statistical machine translation system that is conveniently adapted to provide the suggestions. Our system, however, follows a resource-agnostic approach and suggestions are obtained from any unmodified black-box bilingual resource. This paper reviews our ITP method and describes the architecture of Forecat, a web tool, partly based on the recent technology of web components, that eases the use of our ITP approach in any web application requiring this kind of translation assistance. We also evaluate the performance of our method when using an unmodified Moses-based statistical machine translation system as the bilingual resource.

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.

MASTODON: A geosciences simulation tool built using the open-source framework MOOSE

Science.gov (United States)

Slaughter, A.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture (extended finite-element method), and porous media, among others. The tensor mechanics and contact modules, in particular, are well suited for nonlinear geosciences problems. Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON; https://seismic-research.inl.gov/SitePages/Mastodon.aspx)--a MOOSE-based application--is capable of analyzing the response of 3D soil-structure systems to external hazards with current development focused on earthquakes. It is capable of simulating seismic events and can perform extensive "source-to-site" simulations including earthquake fault rupture, nonlinear wave propagation, and nonlinear soil-structure interaction analysis. MASTODON also includes a dynamic probabilistic risk assessment capability that enables analysts to not only perform deterministic analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk assessment. Although MASTODON has been developed for the nuclear industry, it can be used to assess the risk for any structure subjected to earthquakes.The geosciences community can learn from the nuclear industry and harness the enormous effort underway to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other

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

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

Open source tools for large-scale neuroscience.

Science.gov (United States)

Freeman, Jeremy

2015-06-01

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

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.

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

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...

Advances in the use of open-source information

International Nuclear Information System (INIS)

Horak, K.; Bleakly, D.; McDaniel, M.

2013-01-01

Great advances have been made in the application of open-source information for Safeguards. However, the open-source 'ecosystem' is rapidly evolving. Recently, the combination of powerful smart-phones and the World Wide Web have led to novel developments for mapping the impact of natural and man-made disasters. Researchers are learning to harness online volunteers as citizen scientists. Online social media such as Facebook, LinkedIn, and Twitter are becoming accepted channels of credible information. Geo-spatially-aware applications (augmented reality applications) are capable of overlaying data upon a smart-phone's view screen. The authors review available open-source tools and technologies. These and other developments will have a significant effect on the collection, evaluation, structuring, analysis, and dissemination of safeguards-relevant information. In addition, the modern, open Internet is posing new security threats.not just viruses and their ilk, but threats based on digital traces left by browsing the open Web. The authors present a case study of the disastrous toxic flood near Devecser, Hungary in October 2010 for which we get 621,000 results for everything related to search terms, 68,000 blog posts on the topic, 43,300 images available and then give recommendations for the future use of open-source information and software tools. (authors)

Advances in the use of open-source information

Energy Technology Data Exchange (ETDEWEB)

Horak, K.; Bleakly, D.; McDaniel, M. [Sandia National Laboratories, Albuquerque, NM (United States)

2013-07-01

Great advances have been made in the application of open-source information for Safeguards. However, the open-source 'ecosystem' is rapidly evolving. Recently, the combination of powerful smart-phones and the World Wide Web have led to novel developments for mapping the impact of natural and man-made disasters. Researchers are learning to harness online volunteers as citizen scientists. Online social media such as Facebook, LinkedIn, and Twitter are becoming accepted channels of credible information. Geo-spatially-aware applications (augmented reality applications) are capable of overlaying data upon a smart-phone's view screen. The authors review available open-source tools and technologies. These and other developments will have a significant effect on the collection, evaluation, structuring, analysis, and dissemination of safeguards-relevant information. In addition, the modern, open Internet is posing new security threats.not just viruses and their ilk, but threats based on digital traces left by browsing the open Web. The authors present a case study of the disastrous toxic flood near Devecser, Hungary in October 2010 for which we get 621,000 results for everything related to search terms, 68,000 blog posts on the topic, 43,300 images available and then give recommendations for the future use of open-source information and software tools. (authors)

SedInConnect: a stand-alone, free and open source tool for the assessment of sediment connectivity

Science.gov (United States)

Crema, Stefano; Cavalli, Marco

2018-02-01

There is a growing call, within the scientific community, for solid theoretic frameworks and usable indices/models to assess sediment connectivity. Connectivity plays a significant role in characterizing structural properties of the landscape and, when considered in combination with forcing processes (e.g., rainfall-runoff modelling), can represent a valuable analysis for an improved landscape management. In this work, the authors present the development and application of SedInConnect: a free, open source and stand-alone application for the computation of the Index of Connectivity (IC), as expressed in Cavalli et al. (2013) with the addition of specific innovative features. The tool is intended to have a wide variety of users, both from the scientific community and from the authorities involved in the environmental planning. Thanks to its open source nature, the tool can be adapted and/or integrated according to the users' requirements. Furthermore, presenting an easy-to-use interface and being a stand-alone application, the tool can help management experts in the quantitative assessment of sediment connectivity in the context of hazard and risk assessment. An application to a sample dataset and an overview on up-to-date applications of the approach and of the tool shows the development potential of such analyses. The modelled connectivity, in fact, appears suitable not only to characterize sediment dynamics at the catchment scale but also to integrate prediction models and as a tool for helping geomorphological interpretation.

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.

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.

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

International Nuclear Information System (INIS)

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

2011-01-01

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. 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.

Role of Open Source Tools and Resources in Virtual Screening for Drug Discovery.

Science.gov (United States)

Karthikeyan, Muthukumarasamy; Vyas, Renu

2015-01-01

Advancement in chemoinformatics research in parallel with availability of high performance computing platform has made handling of large scale multi-dimensional scientific data for high throughput drug discovery easier. In this study we have explored publicly available molecular databases with the help of open-source based integrated in-house molecular informatics tools for virtual screening. The virtual screening literature for past decade has been extensively investigated and thoroughly analyzed to reveal interesting patterns with respect to the drug, target, scaffold and disease space. The review also focuses on the integrated chemoinformatics tools that are capable of harvesting chemical data from textual literature information and transform them into truly computable chemical structures, identification of unique fragments and scaffolds from a class of compounds, automatic generation of focused virtual libraries, computation of molecular descriptors for structure-activity relationship studies, application of conventional filters used in lead discovery along with in-house developed exhaustive PTC (Pharmacophore, Toxicophores and Chemophores) filters and machine learning tools for the design of potential disease specific inhibitors. A case study on kinase inhibitors is provided as an example.

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.

Survivability as a Tool for Evaluating Open Source Software

Science.gov (United States)

2015-06-01

tremendously successful in certain applications such as the Mozilla Firefox web browser and the Apache web server [10]. Open source software is often...source versions (such as Internet Explorer compared to Mozilla Firefox ), which typically conclude that vulnerabilities are, in fact, much more...for radios M. Smith ACS ACS ROS autonomous functionality (none) ACS PX4 Firmware PX4 FMU driver BSD 3-clause ACS PX4 Nuttx real time OS BSD ACS

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.

BlueSky ATC Simulator Project : An Open Data and Open Source Approach

NARCIS (Netherlands)

Hoekstra, J.M.; Ellerbroek, J.

2016-01-01

To advance ATM research as a science, ATM research results should be made more comparable. A possible way to do this is to share tools and data. This paper presents a project that investigates the feasibility of a fully open-source and open-data approach to air traffic simulation. Here, the first of

Open Source Tools for Assessment of Global Water Availability, Demands, and Scarcity

Science.gov (United States)

Li, X.; Vernon, C. R.; Hejazi, M. I.; Link, R. P.; Liu, Y.; Feng, L.; Huang, Z.; Liu, L.

2017-12-01

Water availability and water demands are essential factors for estimating water scarcity conditions. To reproduce historical observations and to quantify future changes in water availability and water demand, two open source tools have been developed by the JGCRI (Joint Global Change Research Institute): Xanthos and GCAM-STWD. Xanthos is a gridded global hydrologic model, designed to quantify and analyze water availability in 235 river basins. Xanthos uses a runoff generation and a river routing modules to simulate both historical and future estimates of total runoff and streamflows on a monthly time step at a spatial resolution of 0.5 degrees. GCAM-STWD is a spatiotemporal water disaggregation model used with the Global Change Assessment Model (GCAM) to spatially downscale global water demands for six major enduse sectors (irrigation, domestic, electricity generation, mining, and manufacturing) from the region scale to the scale of 0.5 degrees. GCAM-STWD then temporally downscales the gridded annual global water demands to monthly results. These two tools, written in Python, can be integrated to assess global, regional or basin-scale water scarcity or water stress. Both of the tools are extensible to ensure flexibility and promote contribution from researchers that utilize GCAM and study global water use and supply.

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…

Sharing Lessons-Learned on Effective Open Data, Open-Source Practices from OpenAQ, a Global Open Air Quality Community.

Science.gov (United States)

Hasenkopf, C. A.

2017-12-01

Increasingly, open data, open-source projects are unearthing rich datasets and tools, previously impossible for more traditional avenues to generate. These projects are possible, in part, because of the emergence of online collaborative and code-sharing tools, decreasing costs of cloud-based services to fetch, store, and serve data, and increasing interest of individuals to contribute their time and skills to 'open projects.' While such projects have generated palpable enthusiasm from many sectors, many of these projects face uncharted paths for sustainability, visibility, and acceptance. Our project, OpenAQ, is an example of an open-source, open data community that is currently forging its own uncharted path. OpenAQ is an open air quality data platform that aggregates and universally formats government and research-grade air quality data from 50 countries across the world. To date, we make available more than 76 million air quality (PM2.5, PM10, SO2, NO2, O3, CO and black carbon) data points through an open Application Programming Interface (API) and a user-customizable download interface at https://openaq.org. The goal of the platform is to enable an ecosystem of users to advance air pollution efforts from science to policy to the private sector. The platform is also an open-source project (https://github.com/openaq) and has only been made possible through the coding and data contributions of individuals around the world. In our first two years of existence, we have seen requests for data to our API skyrocket to more than 6 million datapoints per month, and use-cases as varied as ingesting data aggregated from our system into real-time models of wildfires to building open-source statistical packages (e.g. ropenaq and py-openaq) on top of the platform to creating public-friendly apps and chatbots. We will share a whirl-wind trip through our evolution and the many lessons learned so far related to platform structure, community engagement, organizational model type

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. PMID:23544104

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.

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.

TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

Energy Technology Data Exchange (ETDEWEB)

Mishra, P [Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Varian Medical Systems, Palo Alto, CA (United States); Lewis, J [Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Etmektzoglou, T; Svatos, M [Varian Medical Systems, Palo Alto, CA (United States)

2014-06-15

Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slots mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future

TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

International Nuclear Information System (INIS)

Mishra, P; Lewis, J; Etmektzoglou, T; Svatos, M

2014-01-01

Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slots mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future

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.

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

Educatie en open-source software: meer dan gratis tools.

NARCIS (Netherlands)

Bakker, de G.M.

2008-01-01

In het onderwijs wordt steeds meer open source software gebruikt, zo merkt ook Gijs de Bakker*. In de regel moet daar niet al te veel achtergezocht worden. 'Het is in de regel niet meer dan een slimme manier om aan gratis en doorgaans kwalitatief goede software te komen'. Wat De Bakker betreft een

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

Science.gov (United States)

Gupta, Rishi R; Gifford, Eric M; Liston, Ted; Waller, Chris L; Hohman, Moses; Bunin, Barry A; Ekins, Sean

2010-11-01

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

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.

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…

42: An Open-Source Simulation Tool for Study and Design of Spacecraft Attitude Control Systems

Science.gov (United States)

Stoneking, Eric

2018-01-01

Simulation is an important tool in the analysis and design of spacecraft attitude control systems. The speaker will discuss the simulation tool, called simply 42, that he has developed over the years to support his own work as an engineer in the Attitude Control Systems Engineering Branch at NASA Goddard Space Flight Center. 42 was intended from the outset to be high-fidelity and powerful, but also fast and easy to use. 42 is publicly available as open source since 2014. The speaker will describe some of 42's models and features, and discuss its applicability to studies ranging from early concept studies through the design cycle, integration, and operations. He will outline 42's architecture and share some thoughts on simulation development as a long-term project.

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.

ImTK: an open source multi-center information management toolkit

Science.gov (United States)

Alaoui, Adil; Ingeholm, Mary Lou; Padh, Shilpa; Dorobantu, Mihai; Desai, Mihir; Cleary, Kevin; Mun, Seong K.

2008-03-01

The Information Management Toolkit (ImTK) Consortium is an open source initiative to develop robust, freely available tools related to the information management needs of basic, clinical, and translational research. An open source framework and agile programming methodology can enable distributed software development while an open architecture will encourage interoperability across different environments. The ISIS Center has conceptualized a prototype data sharing network that simulates a multi-center environment based on a federated data access model. This model includes the development of software tools to enable efficient exchange, sharing, management, and analysis of multimedia medical information such as clinical information, images, and bioinformatics data from multiple data sources. The envisioned ImTK data environment will include an open architecture and data model implementation that complies with existing standards such as Digital Imaging and Communications (DICOM), Health Level 7 (HL7), and the technical framework and workflow defined by the Integrating the Healthcare Enterprise (IHE) Information Technology Infrastructure initiative, mainly the Cross Enterprise Document Sharing (XDS) specifications.

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

OPEN SOURCE APPROACH TO URBAN GROWTH SIMULATION

Directory of Open Access Journals (Sweden)

A. Petrasova

2016-06-01

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

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.

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,

OMPC: an Open-Source MATLAB?-to-Python Compiler

OpenAIRE

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...

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

OpenAIRE

Evviva Weinraub Lajoie; Trey Terrell; Susan McEvoy; Eva Kaplan; Ariel Schwartz; Esther Ajambo

2014-01-01

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 multipl...

From Open Source to Open Collaboration

CERN Multimedia

CERN. Geneva

2015-01-01

Open source is the right to modify, not the right to contribute. Are external contributions absent from your project? Have you ever thought about what is it like to be a new contributor on your project? I challenge you to transform your project from Open Source to an Open Collaboration.

Open-source web-enabled data management, analyses, and visualization of very large data in geosciences using Jupyter, Apache Spark, and community tools

Science.gov (United States)

Chaudhary, A.

2017-12-01

Current simulation models and sensors are producing high-resolution, high-velocity data in geosciences domain. Knowledge discovery from these complex and large size datasets require tools that are capable of handling very large data and providing interactive data analytics features to researchers. To this end, Kitware and its collaborators are producing open-source tools GeoNotebook, GeoJS, Gaia, and Minerva for geosciences that are using hardware accelerated graphics and advancements in parallel and distributed processing (Celery and Apache Spark) and can be loosely coupled to solve real-world use-cases. GeoNotebook (https://github.com/OpenGeoscience/geonotebook) is co-developed by Kitware and NASA-Ames and is an extension to the Jupyter Notebook. It provides interactive visualization and python-based analysis of geospatial data and depending the backend (KTile or GeoPySpark) can handle data sizes of Hundreds of Gigabytes to Terabytes. GeoNotebook uses GeoJS (https://github.com/OpenGeoscience/geojs) to render very large geospatial data on the map using WebGL and Canvas2D API. GeoJS is more than just a GIS library as users can create scientific plots such as vector and contour and can embed InfoVis plots using D3.js. GeoJS aims for high-performance visualization and interactive data exploration of scientific and geospatial location aware datasets and supports features such as Point, Line, Polygon, and advanced features such as Pixelmap, Contour, Heatmap, and Choropleth. Our another open-source tool Minerva ((https://github.com/kitware/minerva) is a geospatial application that is built on top of open-source web-based data management system Girder (https://github.com/girder/girder) which provides an ability to access data from HDFS or Amazon S3 buckets and provides capabilities to perform visualization and analyses on geosciences data in a web environment using GDAL and GeoPandas wrapped in a unified API provided by Gaia (https://github.com/Open

VR WebGIS: an OpenSource approach to 3D real-time landscape management

OpenAIRE

Calori, Luigi; Camporesi, Carlo; Forte, Maurizio; Pescarin, Sofia

2005-01-01

OpenSource philosophy has reached to unexpected goals. The diffusion of OpenSource tools is increased quite a lot, but also the quality of the tools is improving. Their usability is slowing going even towards communities not exactly skilled in advanced programming. Open movement is penetrated in many sectors, often subverting, thank to its social impact, the traditional rules of companies and research institutions, pulling down sometimes hierarchies and pushin...

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools.

Science.gov (United States)

Dutta, Priyanka; Lehmann, Christina; Odedra, Devang; Singh, Deepika; Pohl, Christian

2015-12-16

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.

Open Source, Openness, and Higher Education

Science.gov (United States)

Wiley, David

2006-01-01

In this article David Wiley provides an overview of how the general expansion of open source software has affected the world of education in particular. In doing so, Wiley not only addresses the development of open source software applications for teachers and administrators, he also discusses how the fundamental philosophy of the open source…

The Systems Biology Research Tool: evolvable open-source software

OpenAIRE

Wright, J; Wagner, A

2008-01-01

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 calle...

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

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

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.

Swan: A tool for porting CUDA programs to OpenCL

Science.gov (United States)

Harvey, M. J.; De Fabritiis, G.

2011-04-01

The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source translation tool, "Swan" for facilitating the conversion of an existing CUDA code to use the OpenCL model, as a means to aid programmers experienced with CUDA in evaluating OpenCL and alternative hardware. While the performance of equivalent OpenCL and CUDA code on fixed hardware should be comparable, we find that a real-world CUDA application ported to OpenCL exhibits an overall 50% increase in runtime, a reduction in performance attributable to the immaturity of contemporary compilers. The ported application is shown to have platform independence, running on both NVIDIA and AMD GPUs without modification. We conclude that OpenCL is a viable platform for developing portable GPU applications but that the more mature CUDA tools continue to provide best performance. Program summaryProgram title: Swan Catalogue identifier: AEIH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License version 2 No. of lines in distributed program, including test data, etc.: 17 736 No. of bytes in distributed program, including test data, etc.: 131 177 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Linux RAM: 256 Mbytes Classification: 6.5 External routines: NVIDIA CUDA, OpenCL Nature of problem: Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An

Evaluation and Testing of Several Free/Open Source Web Vulnerability Scanners

OpenAIRE

Suteva, Natasa; Zlatkovski, Dragi; Mileva, Aleksandra

2013-01-01

Web Vulnerability Scanners (WVSs) are software tools for identifying vulnerabilities in web applications. There are commercial WVSs, free/open source WVSs, and some companies offer them as a Software-as-a-Service. In this paper, we test and evaluate six free/open source WVSs using the web application WackoPicko with many known vulnerabilities, primary for false negative rates.

Nástroje Business Intelligence jako Open Source

OpenAIRE

Filipčík, Zdeněk

2011-01-01

This master's thesis focuses on the issues of selecting the Business Intelligence tools distributed under open source licenses. The main objective of this work is to compare the different instruments in all layers of the Business Intelligence architecture. The first part is focused on the definition of key concepts of the main topic. Provides necessary theoretical basis for understanding the context used in the practical part, which is dedicated to comparison tools realized according to the e...

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.

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

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

International Nuclear Information System (INIS)

Messroghli, Daniel R; Rudolph, Andre; Abdel-Aty, Hassan; Wassmuth, Ralf; Kühne, Titus; Dietz, Rainer; Schulz-Menger, Jeanette

2010-01-01

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. 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. 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

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.

The OpenPMU Platform for Open Source Phasor Measurements

OpenAIRE

Laverty, David M.; Best, Robert J.; Brogan, Paul; Al-Khatib, Iyad; Vanfretti, Luigi; Morrow, D John

2013-01-01

OpenPMU is an open platform for the development of phasor measurement unit (PMU) technology. A need has been identified for an open-source alternative to commercial PMU devices tailored to the needs of the university researcher and for enabling the development of new synchrophasor instruments from this foundation. OpenPMU achieves this through open-source hardware design specifications and software source code, allowing duplicates of the OpenPMU to be fabricated under open-source licenses. Th...

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.

Open Source Cloud-Based Technologies for Bim

Science.gov (United States)

Logothetis, S.; Karachaliou, E.; Valari, E.; Stylianidis, E.

2018-05-01

This paper presents a Cloud-based open source system for storing and processing data from a 3D survey approach. More specifically, we provide an online service for viewing, storing and analysing BIM. Cloud technologies were used to develop a web interface as a BIM data centre, which can handle large BIM data using a server. The server can be accessed by many users through various electronic devices anytime and anywhere so they can view online 3D models using browsers. Nowadays, the Cloud computing is engaged progressively in facilitating BIM-based collaboration between the multiple stakeholders and disciplinary groups for complicated Architectural, Engineering and Construction (AEC) projects. Besides, the development of Open Source Software (OSS) has been rapidly growing and their use tends to be united. Although BIM and Cloud technologies are extensively known and used, there is a lack of integrated open source Cloud-based platforms able to support all stages of BIM processes. The present research aims to create an open source Cloud-based BIM system that is able to handle geospatial data. In this effort, only open source tools will be used; from the starting point of creating the 3D model with FreeCAD to its online presentation through BIMserver. Python plug-ins will be developed to link the two software which will be distributed and freely available to a large community of professional for their use. The research work will be completed by benchmarking four Cloud-based BIM systems: Autodesk BIM 360, BIMserver, Graphisoft BIMcloud and Onuma System, which present remarkable results.

OPEN SOURCE CLOUD-BASED TECHNOLOGIES FOR BIM

Directory of Open Access Journals (Sweden)

S. Logothetis

2018-05-01

Full Text Available This paper presents a Cloud-based open source system for storing and processing data from a 3D survey approach. More specifically, we provide an online service for viewing, storing and analysing BIM. Cloud technologies were used to develop a web interface as a BIM data centre, which can handle large BIM data using a server. The server can be accessed by many users through various electronic devices anytime and anywhere so they can view online 3D models using browsers. Nowadays, the Cloud computing is engaged progressively in facilitating BIM-based collaboration between the multiple stakeholders and disciplinary groups for complicated Architectural, Engineering and Construction (AEC projects. Besides, the development of Open Source Software (OSS has been rapidly growing and their use tends to be united. Although BIM and Cloud technologies are extensively known and used, there is a lack of integrated open source Cloud-based platforms able to support all stages of BIM processes. The present research aims to create an open source Cloud-based BIM system that is able to handle geospatial data. In this effort, only open source tools will be used; from the starting point of creating the 3D model with FreeCAD to its online presentation through BIMserver. Python plug-ins will be developed to link the two software which will be distributed and freely available to a large community of professional for their use. The research work will be completed by benchmarking four Cloud-based BIM systems: Autodesk BIM 360, BIMserver, Graphisoft BIMcloud and Onuma System, which present remarkable results.

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.

Python Open source Waveform ExtractoR (POWER): an open source, Python package to monitor and post-process numerical relativity simulations

Science.gov (United States)

Johnson, Daniel; Huerta, E. A.; Haas, Roland

2018-01-01

Numerical simulations of Einstein’s field equations provide unique insights into the physics of compact objects moving at relativistic speeds, and which are driven by strong gravitational interactions. Numerical relativity has played a key role to firmly establish gravitational wave astrophysics as a new field of research, and it is now paving the way to establish whether gravitational wave radiation emitted from compact binary mergers is accompanied by electromagnetic and astro-particle counterparts. As numerical relativity continues to blend in with routine gravitational wave data analyses to validate the discovery of gravitational wave events, it is essential to develop open source tools to streamline these studies. Motivated by our own experience as users and developers of the open source, community software, the Einstein Toolkit, we present an open source, Python package that is ideally suited to monitor and post-process the data products of numerical relativity simulations, and compute the gravitational wave strain at future null infinity in high performance environments. We showcase the application of this new package to post-process a large numerical relativity catalog and extract higher-order waveform modes from numerical relativity simulations of eccentric binary black hole mergers and neutron star mergers. This new software fills a critical void in the arsenal of tools provided by the Einstein Toolkit consortium to the numerical relativity community.

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.

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

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

2017-04-01

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.

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 reasons...... for not regarding open source innovations as anomalies. The paper is based on three sectorial and 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. In closing...

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.

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.

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.

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

DEFF Research Database (Denmark)

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

2010-01-01

to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results: OptFlux is an open-source and modular...... available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network...

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

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.

Open Source Hbim for Cultural Heritage: a Project Proposal

Science.gov (United States)

Diara, F.; Rinaudo, F.

2018-05-01

Actual technologies are changing Cultural Heritage research, analysis, conservation and development ways, allowing new innovative approaches. The possibility of integrating Cultural Heritage data, like archaeological information, inside a three-dimensional environment system (like a Building Information Modelling) involve huge benefits for its management, monitoring and valorisation. Nowadays there are many commercial BIM solutions. However, these tools are thought and developed mostly for architecture design or technical installations. An example of better solution could be a dynamic and open platform that might consider Cultural Heritage needs as priority. Suitable solution for better and complete data usability and accessibility could be guaranteed by open source protocols. This choice would allow adapting software to Cultural Heritage needs and not the opposite, thus avoiding methodological stretches. This work will focus exactly on analysis and experimentations about specific characteristics of these kind of open source software (DBMS, CAD, Servers) applied to a Cultural Heritage example, in order to verifying their flexibility, reliability and then creating a dynamic HBIM open source prototype. Indeed, it might be a starting point for a future creation of a complete HBIM open source solution that we could adapt to others Cultural Heritage researches and analysis.

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.

Neural ensemble communities: Open-source approaches to hardware for large-scale electrophysiology

Science.gov (United States)

Siegle, Joshua H.; Hale, Gregory J.; Newman, Jonathan P.; Voigts, Jakob

2014-01-01

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is “open” or “closed”: that is, whether or not the system’s schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. PMID:25528614

Sharing clinical decisions for multimorbidity case management using social network and open-source tools.

Science.gov (United States)

Martínez-García, Alicia; Moreno-Conde, Alberto; Jódar-Sánchez, Francisco; Leal, Sandra; Parra, Carlos

2013-12-01

. The professionals valued positively all the items in the questionnaire. As part of the SCP, opensource tools for CDS will be incorporated to provide recommendations for medication and problem interactions, as well as to calculate indexes or scales from validated questionnaires. They will receive the patient summary information provided by the regional Electronic Health Record system through a web service with the information defined according to the virtual Medical Record specification. Clinical Wall has been developed to allow communication and coordination between the healthcare professionals involved in multimorbidity patient care. Agreed decisions were about coordination for appointment changing, patient conditions, diagnosis tests, and prescription changes and renewal. The application of interoperability standards and open source software can bridge the gap between knowledge and clinical practice, while enabling interoperability and scalability. Open source with the social network encourages adoption and facilitates collaboration. Although the results obtained for use indicators are still not as high as it was expected, based on the promising results obtained in the acceptance questionnaire of SMP, we expect that the new CDS tools will increase the use by the health professionals. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

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.

Managing research and surveillance projects in real-time with a novel open-source eManagement tool designed for under-resourced countries.

Science.gov (United States)

Steiner, Andreas; Hella, Jerry; Grüninger, Servan; Mhalu, Grace; Mhimbira, Francis; Cercamondi, Colin I; Doulla, Basra; Maire, Nicolas; Fenner, Lukas

2016-09-01

A software tool is developed to facilitate data entry and to monitor research projects in under-resourced countries in real-time. The eManagement tool "odk_planner" is written in the scripting languages PHP and Python. The odk_planner is lightweight and uses minimal internet resources. It was designed to be used with the open source software Open Data Kit (ODK). The users can easily configure odk_planner to meet their needs, and the online interface displays data collected from ODK forms in a graphically informative way. The odk_planner also allows users to upload pictures and laboratory results and sends text messages automatically. User-defined access rights protect data and privacy. We present examples from four field applications in Tanzania successfully using the eManagement tool: 1) clinical trial; 2) longitudinal Tuberculosis (TB) Cohort Study with a complex visit schedule, where it was used to graphically display missing case report forms, upload digitalized X-rays, and send text message reminders to patients; 3) intervention study to improve TB case detection, carried out at pharmacies: a tablet-based electronic referral system monitored referred patients, and sent automated messages to remind pharmacy clients to visit a TB Clinic; and 4) TB retreatment case monitoring designed to improve drug resistance surveillance: clinicians at four public TB clinics and lab technicians at the TB reference laboratory used a smartphone-based application that tracked sputum samples, and collected clinical and laboratory data. The user friendly, open source odk_planner is a simple, but multi-functional, Web-based eManagement tool with add-ons that helps researchers conduct studies in under-resourced countries. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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).

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.

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

Open Educational Resources in Support of Science Learning: Tools for Inquiry and Observation

Science.gov (United States)

Scanlon, Eileen

2012-01-01

This article focuses on the potential of free tools, particularly inquiry tools for influencing participation in twenty-first-century learning in science, as well as influencing the development of communities around tools. Two examples are presented: one on the development of an open source tool for structured inquiry learning that can bridge the…

An Open-Source Toolbox for PEM Fuel Cell Simulation

Directory of Open Access Journals (Sweden)

Jean-Paul Kone

2018-05-01

Full Text Available In this paper, an open-source toolbox that can be used to accurately predict the distribution of the major physical quantities that are transported within a proton exchange membrane (PEM fuel cell is presented. The toolbox has been developed using the Open Source Field Operation and Manipulation (OpenFOAM platform, which is an open-source computational fluid dynamics (CFD code. The base case results for the distribution of velocity, pressure, chemical species, Nernst potential, current density, and temperature are as expected. The plotted polarization curve was compared to the results from a numerical model and experimental data taken from the literature. The conducted simulations have generated a significant amount of data and information about the transport processes that are involved in the operation of a PEM fuel cell. The key role played by the concentration constant in shaping the cell polarization curve has been explored. The development of the present toolbox is in line with the objectives outlined in the International Energy Agency (IEA, Paris, France Advanced Fuel Cell Annex 37 that is devoted to developing open-source computational tools to facilitate fuel cell technologies. The work therefore serves as a basis for devising additional features that are not always feasible with a commercial code.

osni.info-Using free/libre/open source software to build a virtual international community for open source nursing informatics.

Science.gov (United States)

Oyri, Karl; Murray, Peter J

2005-12-01

Many health informatics organizations seem to be slow to take up the advantages of dynamic, web-based technologies for providing services to, and interaction with, their members; these are often the very technologies they promote for use within healthcare environments. This paper aims to introduce some of the many free/libre/open source (FLOSS) applications that are now available to develop interactive websites and dynamic online communities as part of the structure of health informatics organizations, and to show how the Open Source Nursing Informatics Working Group (OSNI) of the special interest group in nursing informatics of the International Medical Informatics Association (IMIA-NI) is using some of these tools to develop an online community of nurse informaticians through their website, at . Some background introduction to FLOSS applications is used for the benefit of those less familiar with such tools, and examples of some of the FLOSS content management systems (CMS) being used by OSNI are described. The experiences of the OSNI will facilitate a knowledgeable nursing contribution to the wider discussions on the applications of FLOSS within health and healthcare, and provides a model that many other groups could adopt.

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…

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

nDPI: Open-Source High-Speed Deep Packet Inspection

DEFF Research Database (Denmark)

Deri, Luca; Martinelli, Maurizio; Bujlow, Tomasz

2014-01-01

protocols became increasingly challenging, thus creating a motivation for creating tools and libraries for network protocol classification. This paper covers the design and implementation of nDPI, an open-source library for protocol classification using both packet header and payload. nDPI was extensively...

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.

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.

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.

A framework for air quality monitoring based on free public data and open source tools

Science.gov (United States)

Nikolov, Hristo; Borisova, Denitsa

2014-10-01

In the recent years more and more widely accepted by the Space agencies (e.g. NASA, ESA) is the policy toward provision of Earth observation (EO) data and end products concerning air quality especially in large urban areas without cost to researchers and SMEs. Those EO data are complemented by increasing amount of in-situ data also provided at no cost either from national authorities or having crowdsourced origin. This accessibility together with the increased processing capabilities of the free and open source software is a prerequisite for creation of solid framework for air modeling in support of decision making at medium and large scale. Essential part of this framework is web-based GIS mapping tool responsible for dissemination of the output generated. In this research an attempt is made to establish a running framework based solely on openly accessible data on air quality and on set of freely available software tools for processing and modeling taking into account the present status quo in Bulgaria. Among the primary sources of data, especially for bigger urban areas, for different types of gases and dust particles, noted should be the National Institute of Meteorology and Hydrology of Bulgaria (NIMH) and National System for Environmental Monitoring managed by Bulgarian Executive Environmental Agency (ExEA). Both authorities provide data for concentration of several gases just to mention CO, CO2, NO2, SO2, and fine suspended dust (PM10, PM2.5) on monthly (for some data on daily) basis. In the framework proposed these data will complement the data from satellite-based sensors such as OMI instrument aboard EOS-Aura satellite and from TROPOMI instrument payload for future ESA Sentinel-5P mission. Integral part of the framework is the modern map for the land use/land cover which is provided from EEA by initiative GIO Land CORINE. This map is also a product from EO data distributed at European level. First and above all, our effort is focused on provision to the

compomics-utilities: an open-source Java library for computational proteomics.

Science.gov (United States)

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

compomics-utilities: an open-source Java library for computational proteomics

Directory of Open Access Journals (Sweden)

Helsens Kenny

2011-03-01

Full Text Available Abstract Background The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. Results In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. Conclusions As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

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

Open source data assimilation framework for hydrological modeling

Science.gov (United States)

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

2013-04-01

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

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

International Nuclear Information System (INIS)

Minelli, Annalisa; Marchesini, Ivan; Taylor, Faith E.; De Rosa, Pierluigi; Casagrande, Luca; Cenci, Michele

2014-01-01

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

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.

Mitigating Spreadsheet Model Risk with Python Open Source Infrastructure

OpenAIRE

Beavers, Oliver

2018-01-01

Across an aggregation of EuSpRIG presentation papers, two maxims hold true: spreadsheets models are akin to software, yet spreadsheet developers are not software engineers. As such, the lack of traditional software engineering tools and protocols invites a higher rate of error in the end result. This paper lays ground work for spreadsheet modelling professionals to develop reproducible audit tools using freely available, open source packages built with the Python programming language, enablin...

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...

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…

Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for chromatographic alignment and internal calibration.

Science.gov (United States)

Palmblad, Magnus; van der Burgt, Yuri E M; Dalebout, Hans; Derks, Rico J E; Schoenmaker, Bart; Deelder, André M

2009-05-02

Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.

An Open-source Meteorological Operational System and its Installation in Portuguese- speaking Countries

Science.gov (United States)

Almeida, W. G.; Ferreira, A. L.; Mendes, M. V.; Ribeiro, A.; Yoksas, T.

2007-05-01

CPTEC, a division of Brazil’s INPE, has been using several open-source software packages for a variety of tasks in its Data Division. Among these tools are ones traditionally used in research and educational communities such as GrADs (Grid Analysis and Display System from the Center for Ocean-Land-Atmosphere Studies (COLA)), the Local Data Manager (LDM) and GEMPAK (from Unidata), andl operational tools such the Automatic File Distributor (AFD) that are popular among National Meteorological Services. In addition, some tools developed locally at CPTEC are also being made available as open-source packages. One package is being used to manage the data from Automatic Weather Stations that INPE operates. This system uses only open- source tools such as MySQL database, PERL scripts and Java programs for web access, and Unidata’s Internet Data Distribution (IDD) system and AFD for data delivery. All of these packages are get bundled into a low-cost and easy to install and package called the Meteorological Data Operational System. Recently, in a cooperation with the SICLIMAD project, this system has been modified for use by Portuguese- speaking countries in Africa to manage data from many Automatic Weather Stations that are being installed in these countries under SICLIMAD sponsorship. In this presentation we describe the tools included-in and and architecture-of the Meteorological Data Operational System.

OSeMOSYS: The Open Source Energy Modeling System

International Nuclear Information System (INIS)

Howells, Mark; Rogner, Holger; Strachan, Neil; Heaps, Charles; Huntington, Hillard; Kypreos, Socrates; Hughes, Alison; Silveira, Semida; DeCarolis, Joe; Bazillian, Morgan; Roehrl, Alexander

2011-01-01

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.

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.

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.

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

Science.gov (United States)

Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

2017-08-01

Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

Open-Source Sequence Clustering Methods Improve the State Of the Art.

Science.gov (United States)

Kopylova, Evguenia; Navas-Molina, Jose A; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric; He, Yan; Zhou, Hong-Wei; Rognes, Torbjørn; Caporaso, J Gregory; Knight, Rob

2016-01-01

Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http

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.

Open source Matrix Product States: Opening ways to simulate entangled many-body quantum systems in one dimension

Science.gov (United States)

Jaschke, Daniel; Wall, Michael L.; Carr, Lincoln D.

2018-04-01

Numerical simulations are a powerful tool to study quantum systems beyond exactly solvable systems lacking an analytic expression. For one-dimensional entangled quantum systems, tensor network methods, amongst them Matrix Product States (MPSs), have attracted interest from different fields of quantum physics ranging from solid state systems to quantum simulators and quantum computing. Our open source MPS code provides the community with a toolset to analyze the statics and dynamics of one-dimensional quantum systems. Here, we present our open source library, Open Source Matrix Product States (OSMPS), of MPS methods implemented in Python and Fortran2003. The library includes tools for ground state calculation and excited states via the variational ansatz. We also support ground states for infinite systems with translational invariance. Dynamics are simulated with different algorithms, including three algorithms with support for long-range interactions. Convenient features include built-in support for fermionic systems and number conservation with rotational U(1) and discrete Z2 symmetries for finite systems, as well as data parallelism with MPI. We explain the principles and techniques used in this library along with examples of how to efficiently use the general interfaces to analyze the Ising and Bose-Hubbard models. This description includes the preparation of simulations as well as dispatching and post-processing of them.

Close connections between open science and open-source software

Directory of Open Access Journals (Sweden)

YouHua Chen

2014-09-01

Full Text Available Open science is increasingly gaining attention in recent years. In this mini-review, we briefly discuss and summarize the reasons of introducing open science into academic publications for scientists. We argue that open-source software (like R and Python software can be the universal and important platforms for doing open science because of their appealing features: open source, easy-reading document, commonly used in various scientific disciplines like statistics, chemistry and biology. At last, the challenges and future perspectives of performing open science are discussed.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

Science.gov (United States)

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

Directory of Open Access Journals (Sweden)

Michael D M Dryden

Full Text Available Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat, an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously, and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

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.

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.

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…

Open source in Finnish software companies

OpenAIRE

Seppä, Arto

2006-01-01

This paper explores survey data focusing on open source software supply collected from 170 Finnish software firms using descriptive statistical analysis. The first half of the report contains general data about software companies and the differences between proprietary and open source firms. The second half focuses on open source firms. A subject of analysis are copyrights, products and services supply, the firms’ relationships with the open source community, and their views on opportunities ...

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

An Open Source Computational Framework for Uncertainty Quantification of Plasma Chemistry Models

OpenAIRE

Zaheri Sarabi, Shadi

2017-01-01

The current thesis deals with the development of a computational framework for performing plasma chemistry simulations and their uncertainty quantification analysis by suitably combining and extending existing open source computational tools. A plasma chemistry solver is implemented in the OpenFOAM C++ solver suite. The OpenFOAM plasma chemistry application solves the species conservation equations and the electron energy equation by accounting suitably for various production and loss terms b...

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 ...

Open source software and libraries

OpenAIRE

Randhawa, Sukhwinder

2008-01-01

Open source software is, software that users have the ability to run, copy, distribute, study, change, share and improve for any purpose. Open source library software’s does not need the initial cost of commercial software and enables libraries to have greater control over their working environment. Library professionals should be aware of the advantages of open source software and should involve in their development. They should have basic knowledge about the selection, installation and main...

The use of open source bioinformatics tools to dissect transcriptomic data.

Science.gov (United States)

Nitsche, Benjamin M; Ram, Arthur F J; Meyer, Vera

2012-01-01

Microarrays are a valuable technology to study fungal physiology on a transcriptomic level. Various microarray platforms are available comprising both single and two channel arrays. Despite different technologies, preprocessing of microarray data generally includes quality control, background correction, normalization, and summarization of probe level data. Subsequently, depending on the experimental design, diverse statistical analysis can be performed, including the identification of differentially expressed genes and the construction of gene coexpression networks.We describe how Bioconductor, a collection of open source and open development packages for the statistical programming language R, can be used for dissecting microarray data. We provide fundamental details that facilitate the process of getting started with R and Bioconductor. Using two publicly available microarray datasets from Aspergillus niger, we give detailed protocols on how to identify differentially expressed genes and how to construct gene coexpression networks.

DNA - An integrated open-source optimization platform for thermo-fluid systems

DEFF Research Database (Denmark)

Pierobon, Leonardo; Wronski, Jorrit; Elmegaard, Brian

2014-01-01

This paper presents developments and new features added to the simulation tool Dynamic Network Analysis. This open-source software is the result of ongoing development at the Department of Mechanical Engineering, Technical University of Denmark since 1988. Ever since, it has been employed to model...... to extend the capabilities of the software, while at the same time decreasing computational time. Dynamic Network Analysis can now solve non-convex optimization problems by virtue of the fully-embedded genetic algorithm. Moreover, the thermophysical fluid property library has been extended with more than...... 110 fluids by interfacing CoolProp, a high-accuracy open-source property package for pure and pseudo-pure fluids, as well as humid air. Furthermore, the use as time integrator for other tools is demonstrated. The new features are unveiled in two case studies. The first example covers the optimization...

FREEWAT: FREE and open source software tools for WATer resource management

OpenAIRE

Rossetto, Rudy; Borsi, Iacopo; Foglia, Laura

2015-01-01

FREEWAT is an HORIZON 2020 project financed by the EU Commission under the call WATER INNOVATION: BOOSTING ITS VALUE FOR EUROPE. 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 other EU wa...

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

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.

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.

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.

Development of a Modular Laboratory Information Management System (LIMS) for NAA Laboratories Using Open-Source Developing Tools

International Nuclear Information System (INIS)

Bounakhla, Moussa; Amsil, Hamid; Embarch, K.; Bounouira, Hamid

2018-01-01

CNESTEN designed and developed a modular Laboratory Information Management System (LIMS) for the NAA Laboratory using open-source developing tools. This LIMS ensures a personalized management web space for sample acquisition and preparation, spectra processing and for final analysis of the sample. The system helps also dematerializing process for irradiation requests and for the acquisition of new equipments and samples. It allows managing circulating documents between different actors of the LIMS. Modules for concentration determination, facilities characterization are also included in this LIMS. New modules such as spectra fitting, true coincidence and attenuation corrections can be developed and integrated individually in this system. All data, including nuclear data libraries, are stored in a unique distant database via intranet network to allow instantaneous multi-user access. (author)

ATLAS OpenData and OpenKey: using low tech computational tools for students training in High Energy Physics

CERN Document Server

Sanchez Pineda, Arturos; The ATLAS collaboration

2018-01-01

One of the big challenges in High Energy Physics development is the fact that many potential -and very valuable- students and young researchers live in countries where internet access and computational infrastructure are poor compared to institutions already participating. In order to accelerate the process, the ATLAS Open Data project releases useful and meaningful data and tools using standard and easy-to-deploy computational means, such as custom and light Linux Virtual Machines, open source technologies, web and desktop applications. The ATLAS Open Key, a simple USB pen, allows transporting all those resources around the globe. As simple as it sounds, this approach is helping to train students that are now PhD candidates and to integrate HEP educational programs at Master level in universities where did not exist before. The software tools and resources used will be presented, as well as results and stories, ideas and next steps of the ATLAS Open Data project.

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...

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.

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.

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.

OSGeo - Open Source Geospatial Foundation

Directory of Open Access Journals (Sweden)

Margherita Di Leo

2012-09-01

Full Text Available L'esigenza nata verso la fine del 2005 di selezionare ed organizzare più di 200 progetti FOSS4G porta alla nascita nel Febbraio2006 di OSGeo (the Open Source Geospatial Foundation, organizzazione internazionale la cui mission è promuovere lo sviluppo collaborativo di software libero focalizzato sull'informazione geografica (FOSS4G.Open   Source   Geospatial   Foundation (OSGeoThe Open Source Geospatial Foundation (OSGeo  is  a  not-for-profit  organization, created  in  early  2006  to  the  aim  at  sup-porting   the   collaborative   development of  geospatial  open  source  software,  and promote its widespread use. The founda-tion provides financial, organizational and legal support to the broader open source geospatial community. It also serves as an independent  legal  entity  to  which  com-munity  members  can  contribute  code, funding  and  other  resources,  secure  in the knowledge that their contributions will be maintained for public benefit. OSGeo also  serves  as  an  outreach  and  advocacy organization for the open source geospa-tial  community,  and  provides  a  common forum  and  shared  infrastructure  for  im-proving  cross-project  collaboration.  The foundation's projects are all freely available and  useable  under  an  OSI-certified  open source license. The Italian OSGeo local chapter is named GFOSS.it     (Associazione     Italiana     per l'informazione Geografica Libera.

OpenMeetings as a browser-based teleconferencing tool for EFDA laboratories

Energy Technology Data Exchange (ETDEWEB)

Santos, B., E-mail: bsantos@ipfn.ist.utl.pt [Associacao EURATOM/IST, Instituto de Plasmas e Fusao Nuclear - Laboratorio Associado, Instituto Superior Tecnico, P-1049-001 Lisboa (Portugal); Castro, R. [Asociacion EURATOM/CIEMAT Para Fusion, 28040 Madrid (Spain); Santos, J.H.; Gomes, D.; Fernandes, H.; Sousa, J.; Varandas, C.A.F. [Associacao EURATOM/IST, Instituto de Plasmas e Fusao Nuclear - Laboratorio Associado, Instituto Superior Tecnico, P-1049-001 Lisboa (Portugal)

2011-10-15

Remote participation is a key success factor for worldwide organizations and video-conference is an important aspect when laboratory collaborators are geographically dispersed. Several tools for video-conference are available worldwide. However, there is a need for a default integrated set of tools which provide all the needed features for remote participation between cooperating laboratories. Moreover, laboratories currently use different video-conference tools to communicate leading to a non-compatible method among them. OpenMeetings is open source software which provides video-conferences through web-browsing. It is operating system independent, requires no computer installation providing easy integration with already existing tools and customization of requirements. This paper intends to give an OpenMeetings overview as a video-conference application between worldwide laboratories and to demonstrate its integration with the European Fusion Development Agreement (EFDA) Federation authentication and authorization features. EFDA Federation is a multi-organization security infrastructure, whose purpose is to provide sharing and provision of a wide set of resources so that authenticated users may access them in a transparent and secure mode. This infrastructure is based on a distributed security technology called PAPI (Point of Access to Providers of Information). OpenMeetings can be a valuable EFDA Federation resource and a good approach as a method to provide a worldwide laboratory video-conferencing application, based on standard browsers.

OpenMeetings as a browser-based teleconferencing tool for EFDA laboratories

International Nuclear Information System (INIS)

Santos, B.; Castro, R.; Santos, J.H.; Gomes, D.; Fernandes, H.; Sousa, J.; Varandas, C.A.F.

2011-01-01

Remote participation is a key success factor for worldwide organizations and video-conference is an important aspect when laboratory collaborators are geographically dispersed. Several tools for video-conference are available worldwide. However, there is a need for a default integrated set of tools which provide all the needed features for remote participation between cooperating laboratories. Moreover, laboratories currently use different video-conference tools to communicate leading to a non-compatible method among them. OpenMeetings is open source software which provides video-conferences through web-browsing. It is operating system independent, requires no computer installation providing easy integration with already existing tools and customization of requirements. This paper intends to give an OpenMeetings overview as a video-conference application between worldwide laboratories and to demonstrate its integration with the European Fusion Development Agreement (EFDA) Federation authentication and authorization features. EFDA Federation is a multi-organization security infrastructure, whose purpose is to provide sharing and provision of a wide set of resources so that authenticated users may access them in a transparent and secure mode. This infrastructure is based on a distributed security technology called PAPI (Point of Access to Providers of Information). OpenMeetings can be a valuable EFDA Federation resource and a good approach as a method to provide a worldwide laboratory video-conferencing application, based on standard browsers.

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.

Pyradi: an open-source toolkit for infrared calculation and data processing

CSIR Research Space (South Africa)

Willers, CJ

2012-09-01

Full Text Available of such a toolkit facilitates and increases productivity during subsequent tool development: “develop once and use many times”. The concept of an extendible toolkit lends itself naturally to the open-source philosophy, where the toolkit user-base develops...

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.

Developing a low-cost open-source CTD for research and outreach

Science.gov (United States)

Thaler, A. D.; Sturdivant, K.

2013-12-01

Developing a low-cost open-source CTD for research and outreach Andrew David Thaler and Kersey Sturdivant Conductivity, temperature, and depth (CTD). With these three measurements, marine scientists can unlock ocean patterns hidden beneath the waves. The ocean is not uniform, it its filled with swirling eddies, temperature boundaries, layers of high and low salinity, changing densities, and many other physical characteristics. To reveal these patterns, oceanographers use a tool called the CTD. A CTD is found on almost every major research vessel. Rare is the scientific expedition-whether it be coastal work in shallow estuaries or journeys to the deepest ocean trenches-that doesn't begin with the humble CTD cast. The CTD is not cheap. Commercial CTD's start at more the 5,000 and can climb as high as 25,000 or more. We believe that the prohibitive cost of a CTD is an unacceptable barrier to open science. The price tag excludes individuals and groups who lack research grants or significant private funds from conducting oceanographic research. We want to make this tool-the workhorse of oceanographic research-available to anyone with an interest in the oceans. The OpenCTD is a low-cost, open-source CTD suitable for both educators and scientists. The platform is built using readily available parts and is powered by an Arduino-based microcontroller. Our goal is to create a device that is accurate enough to be used for scientific research and can be constructed for less than $200. Source codes, circuit diagrams, and building plans will be freely available. The final instrument will be effective to 200 meters depth. Why 200 meters? For many coastal regions, 200 meters of water depth covers the majority of the ocean that is accessible by small boat. The OpenCTD is targeted to people working in this niche, where entire research projects can be conducted for less than the cost of a commercial CTD. However, the Open CTD is scalable, and anyone with the inclination can adapt our

OpenDOAR Policy tools and applications

CERN Document Server

CERN. Geneva; Van de Sompel, Herbert

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.

OpenDOAR Policy tools and applications

CERN Multimedia

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

Open Source Telecommunication Companies

OpenAIRE

Peter Liu

2007-01-01

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 pro...

User Friendly Open GIS Tool for Large Scale Data Assimilation - a Case Study of Hydrological Modelling

Science.gov (United States)

Gupta, P. K.

2012-08-01

Open source software (OSS) coding has tremendous advantages over proprietary software. These are primarily fuelled by high level programming languages (JAVA, C++, Python etc...) and open source geospatial libraries (GDAL/OGR, GEOS, GeoTools etc.). Quantum GIS (QGIS) is a popular open source GIS package, which is licensed under GNU GPL and is written in C++. It allows users to perform specialised tasks by creating plugins in C++ and Python. This research article emphasises on exploiting this capability of QGIS to build and implement plugins across multiple platforms using the easy to learn - Python programming language. In the present study, a tool has been developed to assimilate large spatio-temporal datasets such as national level gridded rainfall, temperature, topographic (digital elevation model, slope, aspect), landuse/landcover and multi-layer soil data for input into hydrological models. At present this tool has been developed for Indian sub-continent. An attempt is also made to use popular scientific and numerical libraries to create custom applications for digital inclusion. In the hydrological modelling calibration and validation are important steps which are repetitively carried out for the same study region. As such the developed tool will be user friendly and used efficiently for these repetitive processes by reducing the time required for data management and handling. Moreover, it was found that the developed tool can easily assimilate large dataset in an organised manner.

When to make proprietary software open source

NARCIS (Netherlands)

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

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,

Open Genetic Code: on open source in the life sciences

OpenAIRE

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 ...

Curious exceptions? : open source software and "open" technology

NARCIS (Netherlands)

Nuvolari, A.; Rullani, F.; St. Amant, Kirk; Still, Brian

2007-01-01

The aim of thts chapter is to explore the differences and commonalities between open source software and other cases of open technology. The concept of open technology is used here to indicate various models of innovation based on the participation of a wide range of different actors who freely

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.

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…

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 of... = common grazing ground (Sesotho)  Shared space for creative productivity  Emphasise African nature of scope and needs 4 Meraka Open Source Centre  Open Source Centre is part of the Meraka  Institute.  Currently, there are two offices:  CSIR headquarters  Soweto  Set up to amplify the beneficial impact of...

Open-source Software for Exoplanet Atmospheric Modeling

Science.gov (United States)

Cubillos, Patricio; Blecic, Jasmina; Harrington, Joseph

2018-01-01

I will present a suite of self-standing open-source tools to model and retrieve exoplanet spectra implemented for Python. These include: (1) a Bayesian-statistical package to run Levenberg-Marquardt optimization and Markov-chain Monte Carlo posterior sampling, (2) a package to compress line-transition data from HITRAN or Exomol without loss of information, (3) a package to compute partition functions for HITRAN molecules, (4) a package to compute collision-induced absorption, and (5) a package to produce radiative-transfer spectra of transit and eclipse exoplanet observations and atmospheric retrievals.

Spaces of Open-source Politics

DEFF Research Database (Denmark)

Husted, Emil; Plesner, Ursula

2017-01-01

. Inspired by the literature on organizational space, the analysis explores how different organizational spaces configure the party’s process of policy development, thereby adding to our understanding of the relationship between organizational space and political organization. We analyze three different....... Curiously, it seems that physical spaces open up the political process, while digital spaces close it down by fixing meaning. Accordingly, we argue that open-source politics should not be equated with online politics but may be highly dependent on physical spaces. Furthermore, digital spaces may provide......The recent proliferation of Web 2.0 applications and their role in contemporary political life have inspired the coining of the term ‘open-source politics’. This article analyzes how open-source politics is organized in the case of a radical political party in Denmark called The Alternative...

Open source laboratory sample rotator mixer and shaker

Directory of Open Access Journals (Sweden)

Karankumar C. Dhankani

2017-04-01

Full Text Available An open-source 3-D printable laboratory sample rotator mixer is developed here in two variants that allow users to opt for the level of functionality, cost saving and associated complexity needed in their laboratories. First, a laboratory sample rotator is designed and demonstrated that can be used for tumbling as well as gentle mixing of samples in a variety of tube sizes by mixing them horizontally, vertically, or any position in between. Changing the mixing angle is fast and convenient and requires no tools. This device is battery powered and can be easily transported to operate in various locations in a lab including desktops, benches, clean hoods, chemical hoods, cold rooms, glove boxes, incubators or biological hoods. Second, an on-board Arduino-based microcontroller is incorporated that adds the functionality of a laboratory sample shaker. These devices can be customized both mechanically and functionally as the user can simply select the operation mode on the switch or alter the code to perform custom experiments. The open source laboratory sample rotator mixer can be built by non-specialists for under US$30 and adding shaking functionality can be done for under $20 more. Thus, these open source devices are technically superior to the proprietary commercial equipment available on the market while saving over 90% of the costs.

Open Source Opens Opportunities for Army's Simulation System

National Research Council Canada - National Science Library

Parsons, Douglas J; Wittman, Jr, Robert L

2005-01-01

.... Postured as an open-architecture, open-source application, the OneSAF program will put this software into the hands of a vast number of developers throughout the Department of Defense with the intent...

Defining an Open Source Strategy for NASA

Science.gov (United States)

Mattmann, C. A.; Crichton, D. J.; Lindsay, F.; Berrick, S. W.; Marshall, J. J.; Downs, R. R.

2011-12-01

Over the course of the past year, we have worked to help frame a strategy for NASA and open source software. This includes defining information processes to understand open source licensing, attribution, commerciality, redistribution, communities, architectures, and interactions within the agency. Specifically we held a training session at the NASA Earth Science Data Systems Working Group meeting in Open Source software as it relates to the NASA Earth Science data systems enterprise, including EOSDIS, the Distributed Active Archive Centers (DAACs), ACCESS proposals, and the MEASURES communities, and efforts to understand how open source software can be both consumed and produced within that ecosystem. In addition, we presented at the 1st NASA Open Source Summit (OSS) and helped to define an agency-level strategy, a set of recommendations and paths forward for how to identify healthy open source communities, how to deal with issues such as contributions originating from other agencies, and how to search out talent with the right skills to develop software for NASA in the modern age. This talk will review our current recommendations for open source at NASA, and will cover the set of thirteen recommendations output from the NASA Open Source Summit and discuss some of their implications for the agency.

Enabling Open Hardware through FOSS tools

CERN Multimedia

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.

Open Source Software: critical review of scientific literature and other sources

OpenAIRE

Querol del Amo, Marc

2007-01-01

This thesis presents the results of a survey of Open Source Licensing literature. It aims to assist the reader in choosing the best license for his/her business. For this reason, the content of this thesis can be divided into: (i) an open source licensing overview, (ii) the explication of the main features of the most popular open source licenses, (iii) the consequences of using one or another and (iv) the critical or controversial issues related to Open Source Licensing. Furthermore, at the ...

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....

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.

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…

OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays

Directory of Open Access Journals (Sweden)

Sham P C

2008-12-01

Full Text Available Abstract Background Large scale genome-wide association studies have become popular since the introduction of high throughput genotyping platforms. Efficient management of the vast array of data generated poses many challenges. Description We have developed an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip® Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix Power Tools. The genotype and corresponding pedigree data are stored in a relational database for efficient downstream data manipulation and analysis, such as calculation of allele and genotype frequencies, sample identity checking, and export of genotype data in various file formats for analysis using commonly-available software. A novel method for genotyping error estimation is implemented using linkage disequilibrium information from the HapMap project. All functionalities are accessible via a web-based user interface. Conclusion OpenADAM provides an open source database system for management of Affymetrix genome-wide association SNP data.

A Survey of Industrial Involvement in Open Source

OpenAIRE

Røsdal, Andreas

2006-01-01

This thesis presents the results of an explorative survey of industrial involvement in open source. The survey is performed in collaboration with participants from the European ITEA project, COSI (Co-development using inner & Open source in Software Intensive products). The survey was performed to explore aspects of industrial involvement in open source, as industrial management of open source project, industrial use of open source components, related development, and communication processes,...

a Free and Open Source Tool to Assess the Accuracy of Land Cover Maps: Implementation and Application to Lombardy Region (italy)

Science.gov (United States)

Bratic, G.; Brovelli, M. A.; Molinari, M. E.

2018-04-01

The availability of thematic maps has significantly increased over the last few years. Validation of these maps is a key factor in assessing their suitability for different applications. The evaluation of the accuracy of classified data is carried out through a comparison with a reference dataset and the generation of a confusion matrix from which many quality indexes can be derived. In this work, an ad hoc free and open source Python tool was implemented to automatically compute all the matrix confusion-derived accuracy indexes proposed by literature. The tool was integrated into GRASS GIS environment and successfully applied to evaluate the quality of three high-resolution global datasets (GlobeLand30, Global Urban Footprint, Global Human Settlement Layer Built-Up Grid) in the Lombardy Region area (Italy). In addition to the most commonly used accuracy measures, e.g. overall accuracy and Kappa, the tool allowed to compute and investigate less known indexes such as the Ground Truth and the Classification Success Index. The promising tool will be further extended with spatial autocorrelation analysis functions and made available to researcher and user community.

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

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

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

Science.gov (United States)

Fiene, Bruce F.

1994-01-01

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

An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

Science.gov (United States)

Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

2016-01-01

The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%.

The Growth of open source: A look at how companies are utilizing open source software in their business models

OpenAIRE

Feare, David

2009-01-01

This paper examines how open source software is being incorporated into the business models of companies in the software industry. The goal is to answer the question of whether the open source model can help sustain economic growth. While some companies are able to maintain a "pure" open source approach with their business model, the reality is that most companies are relying on proprietary add-on value in order to generate revenue because open source itself is simply not big business. Ultima...

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. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

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

OpenTURNS, an open source uncertainty engineering software

International Nuclear Information System (INIS)

Popelin, A.L.; Dufoy, A.

2013-01-01

The needs to assess robust performances for complex systems have lead to the emergence of a new industrial simulation challenge: to take into account uncertainties when dealing with complex numerical simulation frameworks. EDF has taken part in the development of an Open Source software platform dedicated to uncertainty propagation by probabilistic methods, named OpenTURNS for Open source Treatment of Uncertainty, Risk and Statistics. OpenTURNS includes a large variety of qualified algorithms in order to manage uncertainties in industrial studies, from the uncertainty quantification step (with possibilities to model stochastic dependence thanks to the copula theory and stochastic processes), to the uncertainty propagation step (with some innovative simulation algorithms as the ziggurat method for normal variables) and the sensitivity analysis one (with some sensitivity index based on the evaluation of means conditioned to the realization of a particular event). It also enables to build some response surfaces that can include the stochastic modeling (with the chaos polynomial method for example). Generic wrappers to link OpenTURNS to the modeling software are proposed. At last, OpenTURNS is largely documented to provide rules to help use and contribution

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

Science.gov (United States)

Paton, C; Karopka, T

2017-08-01

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

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

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

Science.gov (United States)

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

2014-12-01

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

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.

Adoption of Free Open Source Geographic Information System Solution for Health Sector in Zanzibar Tanzania

OpenAIRE

BAKAR, Abubakar D.; KIMARO, Honest C.; SULTAN, Abu Bakar MD; HAMIAR, S.

2014-01-01

The study aims at developing in-depth understanding on how Open Source Geographic Information System technology is used to provide solutions for data visualization in the health sector of Zanzibar, Tanzania. The study focuses on implementing the health visualization solutions for the purpose of bridging the gap during the transition period from proprietary software to the Free Open-Source Software using Key Indicator Data System. The developed tool facilitates data integration between the two...

Forked and Integrated Variants In An Open-Source Firmware Project

DEFF Research Database (Denmark)

Stanciulescu, Stefan; Schulze, Sandro; Wasowski, Andrzej

2015-01-01

and interactive source management platforms such as Github. We study advantages and disadvantages of forking using the case of Marlin, an open source firmware for 3D printers. We find that many problems and advantages of cloning do translate to forking. Interestingly, the Marlin community uses both forking......Code cloning has been reported both on small (code fragments) and large (entire projects) scale. Cloning-in-the-large, or forking, is gaining ground as a reuse mechanism thanks to availability of better tools for maintaining forked project variants, hereunder distributed version control systems...

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. PMID:25229451

DABAM: an open-source database of X-ray mirrors metrology

Energy Technology Data Exchange (ETDEWEB)

Sanchez del Rio, Manuel, E-mail: srio@esrf.eu [ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble (France); Bianchi, Davide [AC2T Research GmbH, Viktro-Kaplan-Strasse 2-C, 2700 Wiener Neustadt (Austria); Cocco, Daniele [SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Glass, Mark [ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble (France); Idir, Mourad [NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Metz, Jim [InSync Inc., 2511C Broadbent Parkway, Albuquerque, NM 87107 (United States); Raimondi, Lorenzo; Rebuffi, Luca [Elettra-Sincrotrone Trieste SCpA, Basovizza (TS) (Italy); Reininger, Ruben; Shi, Xianbo [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Siewert, Frank [BESSY II, Helmholtz Zentrum Berlin, Institute for Nanometre Optics and Technology, Albert-Einstein-Strasse 15, 12489 Berlin (Germany); Spielmann-Jaeggi, Sibylle [Swiss Light Source at Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Takacs, Peter [Instrumentation Division, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Tomasset, Muriel [Synchrotron Soleil (France); Tonnessen, Tom [InSync Inc., 2511C Broadbent Parkway, Albuquerque, NM 87107 (United States); Vivo, Amparo [ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble (France); Yashchuk, Valeriy [Advanced Light Source, Lawrence Berkeley National Laboratory, MS 15-R0317, 1 Cyclotron Road, Berkeley, CA 94720-8199 (United States)

2016-04-20

DABAM, an open-source database of X-ray mirrors metrology to be used with ray-tracing and wave-propagation codes for simulating the effect of the surface errors on the performance of a synchrotron radiation beamline. An open-source database containing metrology data for X-ray mirrors is presented. It makes available metrology data (mirror heights and slopes profiles) that can be used with simulation tools for calculating the effects of optical surface errors in the performances of an optical instrument, such as a synchrotron beamline. A typical case is the degradation of the intensity profile at the focal position in a beamline due to mirror surface errors. This database for metrology (DABAM) aims to provide to the users of simulation tools the data of real mirrors. The data included in the database are described in this paper, with details of how the mirror parameters are stored. An accompanying software is provided to allow simple access and processing of these data, calculate the most usual statistical parameters, and also include the option of creating input files for most used simulation codes. Some optics simulations are presented and discussed to illustrate the real use of the profiles from the database.

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/. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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...

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…

The 2016 Bioinformatics Open Source Conference (BOSC).

Science.gov (United States)

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

2016-01-01

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

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.

Open Tools for Integrated Modelling to Understand SDG development - The OPTIMUS program

Science.gov (United States)

Howells, Mark; Zepeda, Eduardo; Rogner, H. Holger; Sanchez, Marco; Roehrl, Alexander; Cicowiez, Matrin; Mentis, Dimitris; Korkevelos, Alexandros; Taliotis, Constantinos; Broad, Oliver; Alfstad, Thomas

2016-04-01

The recently adopted Sustainable Development Goals (SDGs) - a set of 17 measurable and time-bound goals with 169 associated targets for 2030 - are highly inclusive challenges before the world community ranging from eliminating poverty to human rights, inequality, a secure world and protection of the environment. Each individual goal or target by themselves present enormous tasks, taken together they are overwhelming. There strong and weak interlinkages, hence trade-offs and complementarities among goals and targets. Some targets may affect several goals while other goals and targets may conflict or be mutually exclusive (Ref). Meeting each of these requires the judicious exploitation of resource, with energy playing an important role. Such complexity demands to be addressed in an integrated way using systems analysis tools to support informed policy formulation, planning, allocation of scarce resources, monitoring progress, effectiveness and review at different scales. There is no one size fits all methodology that conceivably could include all goal and targets simultaneously. But there are methodologies encapsulating critical subsets of the goal and targets with strong interlinkages with a 'soft' reflection on the weak interlinkages. Universal food security or sustainable energy for all inherently support goals and targets on human rights and equality but possibly at the cost of biodiversity or desertification. Integrated analysis and planning tools are not yet commonplace at national universities - or indeed in many policy making organs. What is needed is a fundamental realignment of institutions and integrations of their planning processes and decision making. We introduce a series of open source tools to support the SDG planning and implementation process. The Global User-friendly CLEW Open Source (GLUCOSE) tool optimizes resource interactions and constraints; The Global Electrification Tool kit (GETit) provides the first global spatially explicit

Why develop open-source software? The role of non-pecuniary benefits, monetary rewards, and open-source licence type

OpenAIRE

Robert M. Sauer

2007-01-01

A review of the basic theory of optimal open-source software contributions points to three key factors affecting the decision to contribute to the open-source development process: nonpecuniary benefits, future expected monetary returns, and open-source licence type. This paper argues that existing large-scale software developer surveys are inadequate for measuring the relative importance of these three factors. Previous econometric studies that collect their own unique datasets also fall shor...

Developing an Open Source Option for NASA Software

Science.gov (United States)

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

2003-01-01

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

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.

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. © The Author(s) 2015.

USER FRIENDLY OPEN GIS TOOL FOR LARGE SCALE DATA ASSIMILATION – A CASE STUDY OF HYDROLOGICAL MODELLING

Directory of Open Access Journals (Sweden)

P. K. Gupta

2012-08-01

Full Text Available Open source software (OSS coding has tremendous advantages over proprietary software. These are primarily fuelled by high level programming languages (JAVA, C++, Python etc... and open source geospatial libraries (GDAL/OGR, GEOS, GeoTools etc.. Quantum GIS (QGIS is a popular open source GIS package, which is licensed under GNU GPL and is written in C++. It allows users to perform specialised tasks by creating plugins in C++ and Python. This research article emphasises on exploiting this capability of QGIS to build and implement plugins across multiple platforms using the easy to learn – Python programming language. In the present study, a tool has been developed to assimilate large spatio-temporal datasets such as national level gridded rainfall, temperature, topographic (digital elevation model, slope, aspect, landuse/landcover and multi-layer soil data for input into hydrological models. At present this tool has been developed for Indian sub-continent. An attempt is also made to use popular scientific and numerical libraries to create custom applications for digital inclusion. In the hydrological modelling calibration and validation are important steps which are repetitively carried out for the same study region. As such the developed tool will be user friendly and used efficiently for these repetitive processes by reducing the time required for data management and handling. Moreover, it was found that the developed tool can easily assimilate large dataset in an organised manner.

Towards open-source, low-cost haptics for surgery simulation.

Science.gov (United States)

Suwelack, Stefan; Sander, Christian; Schill, Julian; Serf, Manuel; Danz, Marcel; Asfour, Tamim; Burger, Wolfgang; Dillmann, Rüdiger; Speidel, Stefanie

2014-01-01

In minimally invasive surgery (MIS), virtual reality (VR) training systems have become a promising education tool. However, the adoption of these systems in research and clinical settings is still limited by the high costs of dedicated haptics hardware for MIS. In this paper, we present ongoing research towards an open-source, low-cost haptic interface for MIS simulation. We demonstrate the basic mechanical design of the device, the sensor setup as well as its software integration.

A Platform for Innovation and Standards Evaluation: a Case Study from the OpenMRS Open-Source Radiology Information System.

Science.gov (United States)

Gichoya, Judy W; Kohli, Marc; Ivange, Larry; Schmidt, Teri S; Purkayastha, Saptarshi

2018-05-10

Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology. Since 2011, the authors, along with a community of open-source contributors, have worked on developing an open-source radiology information system (RIS) across two communities-OpenMRS and LibreHealth. The main purpose of the RIS is to implement core radiology workflows, on which others can build and test new radiology standards. This work has resulted in three major releases of the system, with current architectural changes driven by changing technology, development of new standards in health and imaging informatics, and changing user needs. At their core, both these communities are focused on building general-purpose EHR systems, but based on user contributions from the fringes, we have been able to create an innovative system that has been used by hospitals and clinics in four different countries. We provide an overview of the history of the LibreHealth RIS, the architecture of the system, overview of standards integration, describe challenges of developing an open-source product, and future directions. Our goal is to attract more participation and involvement to further develop the LibreHealth RIS into an Enterprise Imaging System that can be used in other clinical imaging including pathology and dermatology.

Making a Business out of Open Source

CERN Multimedia

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...

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.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Science.gov (United States)

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

2016-02-01

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

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

International Nuclear Information System (INIS)

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/

New Open-Source Version of FLORIS Released | News | NREL

Science.gov (United States)

New Open-Source Version of FLORIS Released New Open-Source Version of FLORIS Released January 26 , 2018 National Renewable Energy Laboratory (NREL) researchers recently released an updated open-source simplified and documented. Because of the living, open-source nature of the newly updated utility, NREL

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.

Open source information acquisition, analysis and integration in the IAEA Department of Safeguards

International Nuclear Information System (INIS)

Barletta, M.; Zarimpas, N.; Zarucki, R.

2010-10-01

Acquisition and analysis of open source information plays an increasingly important role in the IAEA strengthened safeguards system. The Agency's focal point for open source information collection and analysis is the Division of Safeguards Information Management (SGIM) within the IAEA Department of Safeguards. In parallel with the approval of the Model Additional Protocol in 1997, a new centre of information acquisition and analysis expertise was created within SGIM. By acquiring software, developing databases, retraining existing staff and hiring new staff with diverse analytical skills, SGIM is pro actively contributing to the future implementation of information-driven safeguards in collaboration with other Divisions within the Department of Safeguards. Open source information support is now fully integrated with core safeguards processes and activities, and has become an effective tool in the work of the Department of Safeguards. This provides and overview of progress realized through the acquisition and use of open source information in several thematic areas: evaluation of additional protocol declarations; support to the State Evaluation process; in-depth investigation of safeguards issues, including assisting inspections and complementary access; research on illicit nuclear procurement networks and trafficking; and monitoring nuclear developments. Demands for open source information have steadily grown and are likely to continue to grow in the future. Coupled with the enormous growth and accessibility in the volume and sources of information, new challenges are presented, both technical and analytical. This paper discusses actions taken and future plans for multi-source and multi-disciplinary analytic integration to strengthen confidence in safeguards conclusions - especially regarding the absence of undeclared nuclear materials and activities. (Author)

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.

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

Science.gov (United States)

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

2015-12-01

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

Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources.

Science.gov (United States)

Tsay, Ming-Yueh; Wu, Tai-Luan; Tseng, Ling-Li

2017-01-01

This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System). The 2001-2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations. Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems. The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system.

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

Science.gov (United States)

Villano, Matt

2006-01-01

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

An open-source toolbox for multiphase flow in porous media

Science.gov (United States)

Horgue, P.; Soulaine, C.; Franc, J.; Guibert, R.; Debenest, G.

2015-02-01

Multiphase flow in porous media provides a wide range of applications: from the environmental understanding (aquifer, site-pollution) to industrial process improvements (oil production, waste management). Modeling of such flows involves specific volume-averaged equations and therefore specific computational fluid dynamics (CFD) tools. In this work, we develop a toolbox for modeling multiphase flow in porous media with OpenFOAM®, an open-source platform for CFD. The underlying idea of this approach is to provide an easily adaptable tool that can be used in further studies to test new mathematical models or numerical methods. The package provides the most common effective properties models of the literature (relative permeability, capillary pressure) and specific boundary conditions related to porous media flows. To validate this package, solvers based on the IMplicit Pressure Explicit Saturation (IMPES) method are developed in the toolbox. The numerical validation is performed by comparison with analytical solutions on academic cases. Then, a satisfactory parallel efficiency of the solver is shown on a more complex configuration.

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.

Science.gov (United States)

Prakash, Meher K; Lang, Brian; Heinrich, Henriette; Valli, Piero V; Bauerfeind, Peter; Sonnenberg, Amnon; Beerenwinkel, Niko; Misselwitz, Benjamin

2017-06-05

Colorectal cancer (CRC) is a leading cause of cancer-related mortality. CRC incidence and mortality can be reduced by several screening strategies, including colonoscopy, but randomized CRC prevention trials face significant obstacles such as the need for large study populations with long follow-up. Therefore, CRC screening strategies will likely be designed and optimized based on computer simulations. Several computational microsimulation tools have been reported for estimating efficiency and cost-effectiveness of CRC prevention. However, none of these tools is publicly available. There is a need for an open source framework to answer practical questions including testing of new screening interventions and adapting findings to local conditions. We developed and implemented a new microsimulation model, Colon Modeling Open Source Tool (CMOST), for modeling the natural history of CRC, simulating the effects of CRC screening interventions, and calculating the resulting costs. CMOST facilitates automated parameter calibration against epidemiological adenoma prevalence and CRC incidence data. Predictions of CMOST were highly similar compared to a large endoscopic CRC prevention study as well as predictions of existing microsimulation models. We applied CMOST to calculate the optimal timing of a screening colonoscopy. CRC incidence and mortality are reduced most efficiently by a colonoscopy between the ages of 56 and 59; while discounted life years gained (LYG) is maximal at 49-50 years. With a dwell time of 13 years, the most cost-effective screening is at 59 years, at $17,211 discounted USD per LYG. While cost-efficiency varied according to dwell time it did not influence the optimal time point of screening interventions within the tested range. Predictions of CMOST are highly similar compared to a randomized CRC prevention trial as well as those of other microsimulation tools. This open source tool will enable health-economics analyses in for various countries

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.

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.

Science.gov (United States)

Kohlhoff, Kai J; Sosnick, Marc H; Hsu, William T; Pande, Vijay S; Altman, Russ B

2011-08-15

Data clustering techniques are an essential component of a good data analysis toolbox. Many current bioinformatics applications are inherently compute-intense and work with very large datasets. Sequential algorithms are inadequate for providing the necessary performance. For this reason, we have created Clustering Algorithms for Massively Parallel Architectures, Including GPU Nodes (CAMPAIGN), a central resource for data clustering algorithms and tools that are implemented specifically for execution on massively parallel processing architectures. CAMPAIGN is a library of data clustering algorithms and tools, written in 'C for CUDA' for Nvidia GPUs. The library provides up to two orders of magnitude speed-up over respective CPU-based clustering algorithms and is intended as an open-source resource. New modules from the community will be accepted into the library and the layout of it is such that it can easily be extended to promising future platforms such as OpenCL. Releases of the CAMPAIGN library are freely available for download under the LGPL from https://simtk.org/home/campaign. Source code can also be obtained through anonymous subversion access as described on https://simtk.org/scm/?group_id=453. kjk33@cantab.net.

ACToR Chemical Structure processing using Open Source ChemInformatics Libraries (FutureToxII)

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 ove...

ERPLAB: An Open-Source Toolbox for the Analysis of Event-Related Potentials

Directory of Open Access Journals (Sweden)

Javier eLopez-Calderon

2014-04-01

Full Text Available ERPLAB Toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB’s EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB’s tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user’s guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations.

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

Requirements Specification for Open Source Software Selection

OpenAIRE

YANG, YING

2008-01-01

Open source software has been widely used. The software world is enjoying the advantages of collaboration and cooperation in software development and use with the advent of open source movement. However, little research is concerned about the practical guidelines of OSS selection. It is hard for an organization to make a decision whether they should use the OSS or not, and to select an appropriate one from a number of OSS candidates. This thesis studies how to select an open source software f...

Technical Note: PLASTIMATCH MABS, an open source tool for automatic image segmentation

International Nuclear Information System (INIS)

Zaffino, Paolo; Spadea, Maria Francesca; Raudaschl, Patrik; Fritscher, Karl; Sharp, Gregory C.

2016-01-01

Purpose: Multiatlas based segmentation is largely used in many clinical and research applications. Due to its good performances, it has recently been included in some commercial platforms for radiotherapy planning and surgery guidance. Anyway, to date, a software with no restrictions about the anatomical district and image modality is still missing. In this paper we introduce PLASTIMATCH MABS, an open source software that can be used with any image modality for automatic segmentation. Methods: PLASTIMATCH MABS workflow consists of two main parts: (1) an offline phase, where optimal registration and voting parameters are tuned and (2) an online phase, where a new patient is labeled from scratch by using the same parameters as identified in the former phase. Several registration strategies, as well as different voting criteria can be selected. A flexible atlas selection scheme is also available. To prove the effectiveness of the proposed software across anatomical districts and image modalities, it was tested on two very different scenarios: head and neck (H&N) CT segmentation for radiotherapy application, and magnetic resonance image brain labeling for neuroscience investigation. Results: For the neurological study, minimum dice was equal to 0.76 (investigated structures: left and right caudate, putamen, thalamus, and hippocampus). For head and neck case, minimum dice was 0.42 for the most challenging structures (optic nerves and submandibular glands) and 0.62 for the other ones (mandible, brainstem, and parotid glands). Time required to obtain the labels was compatible with a real clinical workflow (35 and 120 min). Conclusions: The proposed software fills a gap in the multiatlas based segmentation field, since all currently available tools (both for commercial and for research purposes) are restricted to a well specified application. Furthermore, it can be adopted as a platform for exploring MABS parameters and as a reference implementation for comparing against

Technical Note: PLASTIMATCH MABS, an open source tool for automatic image segmentation

Energy Technology Data Exchange (ETDEWEB)

Zaffino, Paolo; Spadea, Maria Francesca [Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro 88100 (Italy); Raudaschl, Patrik; Fritscher, Karl [Institute for Biomedical Image Analysis, Private University of Health Sciences, Medical Informatics and Technology, Hall in Tirol 6060 (Austria); Sharp, Gregory C. [Department for Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114 (United States)

2016-09-15

Purpose: Multiatlas based segmentation is largely used in many clinical and research applications. Due to its good performances, it has recently been included in some commercial platforms for radiotherapy planning and surgery guidance. Anyway, to date, a software with no restrictions about the anatomical district and image modality is still missing. In this paper we introduce PLASTIMATCH MABS, an open source software that can be used with any image modality for automatic segmentation. Methods: PLASTIMATCH MABS workflow consists of two main parts: (1) an offline phase, where optimal registration and voting parameters are tuned and (2) an online phase, where a new patient is labeled from scratch by using the same parameters as identified in the former phase. Several registration strategies, as well as different voting criteria can be selected. A flexible atlas selection scheme is also available. To prove the effectiveness of the proposed software across anatomical districts and image modalities, it was tested on two very different scenarios: head and neck (H&N) CT segmentation for radiotherapy application, and magnetic resonance image brain labeling for neuroscience investigation. Results: For the neurological study, minimum dice was equal to 0.76 (investigated structures: left and right caudate, putamen, thalamus, and hippocampus). For head and neck case, minimum dice was 0.42 for the most challenging structures (optic nerves and submandibular glands) and 0.62 for the other ones (mandible, brainstem, and parotid glands). Time required to obtain the labels was compatible with a real clinical workflow (35 and 120 min). Conclusions: The proposed software fills a gap in the multiatlas based segmentation field, since all currently available tools (both for commercial and for research purposes) are restricted to a well specified application. Furthermore, it can be adopted as a platform for exploring MABS parameters and as a reference implementation for comparing against

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...

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

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.

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

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

OpenComet: An automated tool for comet assay image analysis

Directory of Open Access Journals (Sweden)

Benjamin M. Gyori

2014-01-01

Full Text Available Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

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.

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

Science.gov (United States)

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

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

Open source information acquisition, analysis and integration in the IAEA Department of Safeguards

Energy Technology Data Exchange (ETDEWEB)

Barletta, M.; Zarimpas, N.; Zarucki, R., E-mail: M.Barletta@iaea.or [IAEA, Wagramerstrasse 5, P.O. Box 100, 1400 Vienna (Austria)

2010-10-15

Acquisition and analysis of open source information plays an increasingly important role in the IAEA strengthened safeguards system. The Agency's focal point for open source information collection and analysis is the Division of Safeguards Information Management (SGIM) within the IAEA Department of Safeguards. In parallel with the approval of the Model Additional Protocol in 1997, a new centre of information acquisition and analysis expertise was created within SGIM. By acquiring software, developing databases, retraining existing staff and hiring new staff with diverse analytical skills, SGIM is pro actively contributing to the future implementation of information-driven safeguards in collaboration with other Divisions within the Department of Safeguards. Open source information support is now fully integrated with core safeguards processes and activities, and has become an effective tool in the work of the Department of Safeguards. This provides and overview of progress realized through the acquisition and use of open source information in several thematic areas: evaluation of additional protocol declarations; support to the State Evaluation process; in-depth investigation of safeguards issues, including assisting inspections and complementary access; research on illicit nuclear procurement networks and trafficking; and monitoring nuclear developments. Demands for open source information have steadily grown and are likely to continue to grow in the future. Coupled with the enormous growth and accessibility in the volume and sources of information, new challenges are presented, both technical and analytical. This paper discusses actions taken and future plans for multi-source and multi-disciplinary analytic integration to strengthen confidence in safeguards conclusions - especially regarding the absence of undeclared nuclear materials and activities. (Author)

Development of WEB Applications of The Component – Open Source

Directory of Open Access Journals (Sweden)

Arturo Sergio Medina Castillo

2013-06-01

Full Text Available Nowadays software development not starting from scratch, however already has a set of tools provided by frameworks, which enables faster application development, relevant and indispensable factor for supporting continuous improvement processes seeking higher levels of competitiveness in this global society.In all respects the development of Web applications, whether open source or proprietary, is developing rapidly, by providing service levels of communication, interoperability, access to internal and external customers that allows management support different business processes.

Freely Licensed and Open Source Pipelines for Art Based Film and Media Production

Directory of Open Access Journals (Sweden)

Anthony Whitehead

2009-08-01

Full Text Available Given the number of free/libre and open source licensed tools, and the number of "no cost" applications at the fingertips of the artist/animator/film developer today, the ability to "create what you will" is now an option for everyone. The advent of affordable media development tools has opened up the world of media production to those who were previously locked out of the Hollywood studio system. Proprietary software including Adobe Creative Suite, Autodesk?s Maya, Nuke, After Effects, Final Draft, and a litany of other necessary tools creates a financial wall so high that ?will? cannot overcome it alone. In this article, we examine a standard pipeline from a birds-eye-view for anyone with a will to create an Indie film. Without breaking the bank, the entire pipeline is achievable using F/LOSS tools and content that is available under a creative commons license. This allows high quality media development for all. In many cases, these same tools are being used by the Hollywood elite.

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process.

Science.gov (United States)

Araujo, Pablo Granda; Gras, Anna; Ginovart, Marta

2016-01-01

Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4 (+), NO3 (-), NO2 (-), N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

A THEORETICAL MODEL OF SUPPORTING OPEN SOURCE FRONT END INNOVATION THROUGH IDEA MANAGEMENT

DEFF Research Database (Denmark)

Aagaard, Annabeth

2013-01-01

to overcome these various challenges companies are looking for new models to support FEI. This theoretical paper explores in what way idea management may be applied as a tool in facilitation of front end innovation and how this facilitation may be captured in a conceptual model. First, I show through...... a literature study, how idea management and front end innovation are related and how they may support each other. Secondly, I present a theoretical model of how idea management may be applied in support of the open source front end of new product innovations. Thirdly, I present different venues of further...... exploration of active facilitation of open source front end innovation through idea management....

Learning from hackers: open-source clinical trials.

Science.gov (United States)

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

2012-05-02

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

Muticriteria decision making model for chosing between open source and non-open source software

Directory of Open Access Journals (Sweden)

Edmilson Alves de Moraes

2008-09-01

Full Text Available This article proposes the use of a multicriterio method for supporting decision on a problem where the intent is to chose for software given the options of open source and not-open source. The study shows how a method for decison making can be used to provide problem structuration and simplify the decision maker job. The method Analytic Hierarchy Process-AHP is described step-by-step and its benefits and flaws are discussed. Followin the theoretical discussion, a muliple case study is presented, where two companies are to use the decison making method. The analysis was supported by Expert Choice, a software developed based on AHP framework.

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.

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…

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

International Nuclear Information System (INIS)

Etmektzoglou, A; Mishra, P; Svatos, M

2015-01-01

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

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

Differential Expression and Functional Analysis of High-Throughput -Omics Data Using Open Source Tools.

Science.gov (United States)

Kebschull, Moritz; Fittler, Melanie Julia; Demmer, Ryan T; Papapanou, Panos N

2017-01-01

Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ, or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseases, offering a large advantage over earlier "candidate" gene or pathway analyses. A primary goal in the analysis of these high-throughput assays is the detection of those features among several thousand that differ between different groups of samples. In the context of oral biology, our group has successfully utilized -omics technology to identify key molecules and pathways in different diagnostic entities of periodontal disease.A major issue when inferring biological information from high-throughput -omics studies is the fact that the sheer volume of high-dimensional data generated by contemporary technology is not appropriately analyzed using common statistical methods employed in the biomedical sciences.In this chapter, we outline a robust and well-accepted bioinformatics workflow for the initial analysis of -omics data generated using microarrays or next-generation sequencing technology using open-source tools. Starting with quality control measures and necessary preprocessing steps for data originating from different -omics technologies, we next outline a differential expression analysis pipeline that can be used for data from both microarray and sequencing experiments, and offers the possibility to account for random or fixed effects. Finally, we present an overview of the possibilities for a functional analysis of the obtained data.

Managerial Perspective on Open Source Collaboration and Networked Innovation

OpenAIRE

Henttonen Maaret Katja; Pasi Pussinen; Timo Koivumäki

2012-01-01

This study explores the managerial perspectives towards open source software and networked innovation. We analysed six software companies who use open source software as a significant part of their product or service offering. The study found notable differences in managerial attitudes, expected benefits and key challenges related to open source software and its role in innovative activities. While all companies were using same pieces of software with open source communities, there were diffe...

Selection and Management of Open Source Software in Libraries

OpenAIRE

Vimal Kumar, V.

2007-01-01

Open source software was a revolutionary concept among computer programmers and users. To a certain extent open source solutions could provide an alternative solution to costly commercial software. Open source software is, software that users have the ability to run, copy, distribute, study, change, share and improve for any purpose. Open source library software’s does not need the initial cost of commercial software and enables libraries to have greater control over their working environmen...

ON CODE REFACTORING OF THE DIALOG SUBSYSTEM OF CDSS PLATFORM FOR THE OPEN-SOURCE MIS OPENMRS

Directory of Open Access Journals (Sweden)

A. V. Semenets

2016-08-01

The open-source MIS OpenMRS developer tools and software API are reviewed. The results of code refactoring of the dialog subsystem of the CDSS platform which is made as module for the open-source MIS OpenMRS are presented. The structure of information model of database of the CDSS dialog subsystem was updated according with MIS OpenMRS requirements. The Model-View-Controller (MVC based approach to the CDSS dialog subsystem architecture was re-implemented with Java programming language using Spring and Hibernate frameworks. The MIS OpenMRS Encounter portlet form for the CDSS dialog subsystem integration is developed as an extension. The administrative module of the CDSS platform is recreated. The data exchanging formats and methods for interaction of OpenMRS CDSS dialog subsystem module and DecisionTree GAE service are re-implemented with help of AJAX technology via jQuery library

Open Source software and social networks: Disruptive alternatives for medical imaging

International Nuclear Information System (INIS)

Ratib, Osman; Rosset, Antoine; Heuberger, Joris

2011-01-01

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

Open Source software and social networks: Disruptive alternatives for medical imaging

Energy Technology Data Exchange (ETDEWEB)

Ratib, Osman, E-mail: osman.ratib@hcuge.ch [Department of Medical Imaging and Information Sciences, University Hospital of Geneva, 24, rue Micheli-du-Crest, 1205 Geneva (Switzerland); Rosset, Antoine; Heuberger, Joris [Department of Medical Imaging and Information Sciences, University Hospital of Geneva, 24, rue Micheli-du-Crest, 1205 Geneva (Switzerland)

2011-05-15

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

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

Science.gov (United States)

Ratib, Osman; Rosset, Antoine; Heuberger, Joris

2011-05-01

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

Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources.

Directory of Open Access Journals (Sweden)

Ming-Yueh Tsay

Full Text Available This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic, two aggregate institutional repositories (OAIster and OpenDOAR, and two physics-related open sources (arXiv.org and Astrophysics Data System. The 2001-2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations. Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems. The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system.

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.

Open source system options for librarians and archivists

CERN Document Server

Tomer, Christinger

2019-01-01

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.

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

Open source software development : some historical perspectives

NARCIS (Netherlands)

Nuvolari, A.

2005-01-01

In this paper we suggest that historical studies of technology can help us to account for some, perplexing (at least for traditional economic reasoning) features of open source software development. From a historical perspective, open source software seems to be a particular case of what Robert C.

Open source software development : some historical perspectives

NARCIS (Netherlands)

Nuvolari, A.

2003-01-01

In this paper we suggest that historical studies of technology can help us to account for some, perplexing (at least for traditional economic reasoning) features of open source software development. When looked in historical perspective, open source software seems to be a particular case of what

Scalable Open Source Smart Grid Simulator (SGSim)

DEFF Research Database (Denmark)

Ebeid, Emad Samuel Malki; Jacobsen, Rune Hylsberg; Stefanni, Francesco

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...

ADAPTING OPEN-SOURCE SOFTWARE FOR ENTERPRISE

Directory of Open Access Journals (Sweden)

Bogdan MICU GHILIC

2013-06-01

Full Text Available Low developed companies do not use ERP solutions for resource management, they don't have CRM systems for tracking customers, online presence is low and consequently they are selling low volumes. Their work does not generate enough capital to buy specialized software and the local community is too small to create open-source software for them.When adapting an open-source enterprise solution, from a certain level of integration, it is necessary to align to the Romanian legislation. For this you need more than a simple translation. For example, in accounting, the Romanian chart of accounts should be used, the local fiscal calendar, the rules of the Romanian legislation and the specific identifiers for Romanian companies. The solution: Open source applications can be localized. A small community cannot create complex system starting from nothing, but they can adapt existing ones already created and used all over the world. Given the individual characteristics of the Romanian market, open source ERP, CM and e-commerce will be integrated by specialized consultancy agency in Romania just as is done in France (Compiere, Spain (Openbravo, Belgium (OpenERP or the United States (Apache oFBiz. This will not generate license costs for the companies, only the expenses for hardware and implementation consultancy. If we can create a common infrastructure, hardware cost will be waived for cloud SaaS offering, in opposition with the on-premise option.

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

Science.gov (United States)

Clark, Alex M; Sarker, Malabika; Ekins, Sean

2014-01-01

We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

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.

An Open Source-based Approach to the Development of Research Reactor Simulator

International Nuclear Information System (INIS)

Joo, Sung Moon; Suh, Yong Suk; Park, Cheol Park

2016-01-01

In reactor design, operator training, safety analysis, or research using a reactor, it is essential to simulate time dependent reactor behaviors such as neutron population, fluid flow, and heat transfer. Furthermore, in order to use the simulator to train and educate operators, a mockup of the reactor user interface is required. There are commercial software tools available for reactor simulator development. However, it is costly to use those commercial software tools. Especially for research reactors, it is difficult to justify the high cost as regulations on research reactor simulators are not as strict as those for commercial Nuclear Power Plants(NPPs). An open source-based simulator for a research reactor is configured as a distributed control system based on EPICS framework. To demonstrate the use of the simulation framework proposed in this work, we consider a toy example. This example approximates a 1-second impulse reactivity insertion in a reactor, which represents the instantaneous removal and reinsertion of a control rod. The change in reactivity results in a slightly delayed change in power and corresponding increases in temperatures throughout the system. We proposed an approach for developing research reactor simulator using open source software tools, and showed preliminary results. The results demonstrate that the approach presented in this work can provide economical and viable way of developing research reactor simulators

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.

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

OpenAIRE

Lindman, Juho; Rajala, Risto

2012-01-01

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-orien...

Dilemmas within Commercial Involvement in Open Source Software

DEFF Research Database (Denmark)

Ciesielska, Malgorzata; Westenholz, Ann

2016-01-01

to free-riding. There are six levels of commercial involvement in open source communities, and each of them is characterized by a different dilemma. Originality/value – The paper sheds light on the various level of involvement of business in open source movement and emphasize that the popularized “open......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...

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.

The case for open-source software in drug discovery.

Science.gov (United States)

DeLano, Warren L

2005-02-01

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

The Economics of Technology Sharing: Open Source and Beyond

OpenAIRE

Josh Lerner; Jean Tirole

2004-01-01

This paper reviews our understanding of the growing open source movement. We highlight how many aspects of open source software appear initially puzzling to an economist. As we have acknowledged, our ability to answer confidently many of the issues raised here questions is likely to increase as the open source movement itself grows and evolves. At the same time, it is heartening to us how much of open source activities can be understood within existing economic frameworks, despite the presenc...

Open-Source Telephony Infrastructure

CERN Document Server

CERN. Geneva

2018-01-01

TONE (Telephony Open-source Network Evolution) is CERN’s future-proof telephony network. Over the past few years, TONE has evolved from its initial design to a solid reality that accommodates some of CERN’s most critical communication services.   TONE’s architecture was designed to: -          Use VoIP (Voice over IP) standard protocols. -          Avoid vendor lock-in by using open-source components. -          Reduce operational costs. -          Be built on top on the IT department’s Agile Infrastructure, combining Virtual Machines and redundant physical servers.   In this presentation we will review the project’s past and future milestones, main use cases and detailed network architecture.

Open-Source Wax RepRap 3-D Printer for Rapid Prototyping Paper-Based Microfluidics.

Science.gov (United States)

Pearce, J M; Anzalone, N C; Heldt, C L

2016-08-01

The open-source release of self-replicating rapid prototypers (RepRaps) has created a rich opportunity for low-cost distributed digital fabrication of complex 3-D objects such as scientific equipment. For example, 3-D printable reactionware devices offer the opportunity to combine open hardware microfluidic handling with lab-on-a-chip reactionware to radically reduce costs and increase the number and complexity of microfluidic applications. To further drive down the cost while improving the performance of lab-on-a-chip paper-based microfluidic prototyping, this study reports on the development of a RepRap upgrade capable of converting a Prusa Mendel RepRap into a wax 3-D printer for paper-based microfluidic applications. An open-source hardware approach is used to demonstrate a 3-D printable upgrade for the 3-D printer, which combines a heated syringe pump with the RepRap/Arduino 3-D control. The bill of materials, designs, basic assembly, and use instructions are provided, along with a completely free and open-source software tool chain. The open-source hardware device described here accelerates the potential of the nascent field of electrochemical detection combined with paper-based microfluidics by dropping the marginal cost of prototyping to nearly zero while accelerating the turnover between paper-based microfluidic designs. © 2016 Society for Laboratory Automation and Screening.

Open Science: Open source licenses in scientific research

OpenAIRE

Guadamuz, Andres

2006-01-01

The article examines the validity of OSS (open source software) licenses for scientific, as opposed to creative works. It draws on examples of OSS licenses to consider their suitability for the scientific community and scientific research.

PLUS: open-source toolkit for ultrasound-guided intervention systems.

Science.gov (United States)

Lasso, Andras; Heffter, Tamas; Rankin, Adam; Pinter, Csaba; Ungi, Tamas; Fichtinger, Gabor

2014-10-01

A variety of advanced image analysis methods have been under the development for ultrasound-guided interventions. Unfortunately, the transition from an image analysis algorithm to clinical feasibility trials as part of an intervention system requires integration of many components, such as imaging and tracking devices, data processing algorithms, and visualization software. The objective of our paper is to provide a freely available open-source software platform-PLUS: Public software Library for Ultrasound-to facilitate rapid prototyping of ultrasound-guided intervention systems for translational clinical research. PLUS provides a variety of methods for interventional tool pose and ultrasound image acquisition from a wide range of tracking and imaging devices, spatial and temporal calibration, volume reconstruction, simulated image generation, and recording and live streaming of the acquired data. This paper introduces PLUS, explains its functionality and architecture, and presents typical uses and performance in ultrasound-guided intervention systems. PLUS fulfills the essential requirements for the development of ultrasound-guided intervention systems and it aspires to become a widely used translational research prototyping platform. PLUS is freely available as open source software under BSD license and can be downloaded from http://www.plustoolkit.org.

Open Source, Open Innovation and Intellectual Property Rights – A Lightning Talk

OpenAIRE

Kilamo , Terhi; Hammouda , Imed; Kairamo , Ville; Räsänen , Petri; Saarinen , Jukka ,

2012-01-01

Part 2: Lightning Talks; International audience; Open innovation projects are fast paced aiming at producing a quick proof of concept of an innovative software product. This need for speedy results makes the use of open source components as a basis for the work appealing. Open source brings with it an inherent risk of license conflicts that may become an issue when aiming to develope an innovative demo into an actual product. In this study, the first results of investigating the knowledge the...

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

Science.gov (United States)

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

2017-08-01

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

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

Directory of Open Access Journals (Sweden)

Pablo Araujo Granda

2016-01-01

Full Text Available Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2 to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc. MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

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

Science.gov (United States)

Ramirez, P.; Goodale, C. E.; Bui, B.; Chang, G.; Kim, R. M.; Law, E.; Malhotra, S.; Rodriguez, L.; Sadaqathullah, S.; Mattmann, C. A.; Crichton, D. J.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is responsible for the development of an information system to support lunar exploration, decision analysis, and release of lunar data to the public. The data available through the lunar portal is predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). This project has created a gold source of data, models, and tools for lunar explorers to exercise and incorporate into their activities. At Jet Propulsion Laboratory (JPL), we focused on engineering and building the infrastructure to support cataloging, archiving, accessing, and delivery of lunar data. We decided to use a RESTful service-oriented architecture to enable us to abstract from the underlying technology choices and focus on interfaces to be used internally and externally. This decision allowed us to leverage several open source software components and integrate them by either writing a thin REST service layer or relying on the API they provided; the approach chosen was dependent on the targeted consumer of a given interface. We will discuss our varying experience using open source products; namely Apache OODT, Oracle Berkley DB XML, Apache Solr, and Oracle OpenSSO (now named OpenAM). Apache OODT, developed at NASA's Jet Propulsion Laboratory and recently migrated over to Apache, provided the means for ingestion and cataloguing of products within the infrastructure. Its usage was based upon team experience with the project and past benefit received on other projects internal and external to JPL. Berkeley DB XML, distributed by Oracle for both commercial and open source use, was the storage technology chosen for our metadata. This decision was in part based on our use Federal Geographic Data Committee (FGDC) Metadata, which is expressed in XML, and the desire to keep it in its native form and exploit other technologies built on

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.

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...

BioContainers: an open-source and community-driven framework for software standardization

Science.gov (United States)

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

BioContainers: an open-source and community-driven framework for software standardization.

Science.gov (United States)

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

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…

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

NARCIS (Netherlands)

Amrit, Chintan Amrit; van Hillegersberg, 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

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.

Analysis of open source GIS software

OpenAIRE

Božnis, Andrius

2006-01-01

GIS is one of the most perspective information technology sciences sphere. GIS conjuncts the digital image analysis and data base systems. This makes GIS wide applicable and very high skills demanding system. There is a lot of commercial GIS software which is well advertised and which functionality is pretty well known, while open source software is forgotten. In this diploma work is made analysis of available open source GIS software on the Internet, in the scope of different projects interr...

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

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

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…

Open Source Software and Open Content: Interview met Jan Hylén

NARCIS (Netherlands)

Lambert Berenbroek

2005-01-01

Jan Hylén also attending the Surf Education Days 2005, held a presentation about Open Source Software and Open Content (such as the MIT Open Courseware project and the Open Access initiative). Jan Hylén is working at the Centre for Educational Research and Innovation (CERI) of the Organization of

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…

Managerial Perspective on Open Source Collaboration and Networked Innovation

Directory of Open Access Journals (Sweden)

Henttonen Maaret Katja

2012-09-01

Full Text Available This study explores the managerial perspectives towards open source software and networked innovation. We analysed six software companies who use open source software as a significant part of their product or service offering. The study found notable differences in managerial attitudes, expected benefits and key challenges related to open source software and its role in innovative activities. While all companies were using same pieces of software with open source communities, there were different levels of engagement in the development of the software and information flows between companies and communities. A deeper level of involvement enables the exchange of more than just the code: like ideas, influences, opinions and even innovations or parts of them. The differences in managerial views on open source and networked innovation may be explained by industry domains, value chain position and leadership style

OpenSesame: An Open-source, Graphical Experiment Builder for the Social Sciences

NARCIS (Netherlands)

Mathot, S.; Schreij, D.B.B.; Theeuwes, J.

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,

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.

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Science.gov (United States)

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Collection and Analysis of Open Source News for Information Awareness and Early Warning in Nuclear Safeguards

International Nuclear Information System (INIS)

Cojazzi, Giacomo G.M.; Van Der Goot, Erik; Verile, Marco; Wolfart, Erik; Rutan Fowler, Marcy; Feldman, Yana; Hammond, William; Schweighardt, John; Ferguson, Mattew

2013-01-01

Acquisition and analysis of open source information plays an increasingly important role in the IAEA’s move towards safeguards implementation based on all safeguards relevant information known about a State. The growing volume of open source information requires the development of technology and tools capable of effectively collecting relevant information, filtering out “noise”, organizing valuable information in a clear and accessible manner, and assessing its relevance. In this context, the IAEA’s Division of Information Management (SGIM) and the EC’s Joint Research Centre (JRC) are currently implementing a joint project to advance the effectiveness and efficiency of the IAEA’s workflow for open source information collection and analysis. The objective is to provide tools to support SGIM in the production of the SGIM Open Source Highlights, which is a daily news brief consisting of the most pertinent news stories relevant to safeguards and non-proliferation. The process involves the review and selection of hundreds of articles from a wide array of specifically selected sources. The joint activity exploits the JRC’s Europe Media Monitor (EMM) and NewsDesk applications: EMM automatically collects and analyses news articles from a pre-defined list of web sites, and NewsDesk allows an analyst to manually select the most relevant articles from the EMM stream for further processing. The paper discusses the IAEA’s workflow for the production of SGIM Open Source Highlights and describes the capabilities of EMM and NewsDesk. It then provides an overview of the joint activities since the project started in 2011, which were focused i) on setting up a separate EMM installation dedicated to the nuclear safeguards and security domain (Nuclear Security Media Monitor, NSMM) and ii) on evaluating the NSMM/NewsDesk for meeting the IAEA’s needs. Finally, it presents the current use NSMM/NewsDesk at the IAEA and proposes options for further integration with the

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...

Un uso sostenibile delle risorse idriche con dati telerilevati e software Open Source

Directory of Open Access Journals (Sweden)

Pasquale Nino

2009-03-01

Full Text Available Sustainable agricultural water use by means of open source decision support systems and Earth Observation data.The PLEIADeS project (funded by European VI Framework Program addresses the improvement of water use and management in agriculture through innovative Information Technologies and the most recent Earth Observation (EO methodologies. Within this framework a tool, based on Open Source software, which aims at helping water managers to optimize the water consumption, has been realized. One of the key features of the system is the delivering of a near real-time irrigation schedule to farmers produced through the integration of EO-derived product and fi eld data inside a GIS environment that provides a reliable crop requirement estimation at farm level.

Un uso sostenibile delle risorse idriche con dati telerilevati e software Open Source

Directory of Open Access Journals (Sweden)

Pasquale Nino

2009-03-01

Full Text Available Sustainable agricultural water use by means of open source decision support systems and Earth Observation data. The PLEIADeS project (funded by European VI Framework Program addresses the improvement of water use and management in agriculture through innovative Information Technologies and the most recent Earth Observation (EO methodologies. Within this framework a tool, based on Open Source software, which aims at helping water managers to optimize the water consumption, has been realized. One of the key features of the system is the delivering of a near real-time irrigation schedule to farmers produced through the integration of EO-derived product and fi eld data inside a GIS environment that provides a reliable crop requirement estimation at farm level.

Combining Open-Source Packages for Planetary Exploration

Science.gov (United States)

Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

2015-04-01

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

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.

Implementing Open Data: The Open Data Commons Project

Directory of Open Access Journals (Sweden)

Jordan Hatcher

2008-02-01

Full Text Available Free and libre/open source software (F/LOSS movements have spawned similar solutions in many other contexts, each at differing stages of development. As F/LOSS enters the routine and familiarity of middle age, the open content movement--open source for non-software copyright and best embodied by the work of Creative Commons--has just graduated university and is getting a feel for the world. Even younger is the open data movement, whose legal tools have just started to come online.

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

GNU Data Language (GDL) - a free and open-source implementation of IDL

Science.gov (United States)

Arabas, Sylwester; Schellens, Marc; Coulais, Alain; Gales, Joel; Messmer, Peter

2010-05-01

GNU Data Language (GDL) is developed with the aim of providing an open-source drop-in replacement for the ITTVIS's Interactive Data Language (IDL). It is free software developed by an international team of volunteers led by Marc Schellens - the project's founder (a list of contributors is available on the project's website). The development is hosted on SourceForge where GDL continuously ranks in the 99th percentile of most active projects. GDL with its library routines is designed as a tool for numerical data analysis and visualisation. As its proprietary counterparts (IDL and PV-WAVE), GDL is used particularly in geosciences and astronomy. GDL is dynamically-typed, vectorized and has object-oriented programming capabilities. The library routines handle numerical calculations, data visualisation, signal/image processing, interaction with host OS and data input/output. GDL supports several data formats such as netCDF, HDF4, HDF5, GRIB, PNG, TIFF, DICOM, etc. Graphical output is handled by X11, PostScript, SVG or z-buffer terminals, the last one allowing output to be saved in a variety of raster graphics formats. GDL is an incremental compiler with integrated debugging facilities. It is written in C++ using the ANTLR language-recognition framework. Most of the library routines are implemented as interfaces to open-source packages such as GNU Scientific Library, PLPlot, FFTW, ImageMagick, and others. GDL features a Python bridge (Python code can be called from GDL; GDL can be compiled as a Python module). Extensions to GDL can be written in C++, GDL, and Python. A number of open software libraries written in IDL, such as the NASA Astronomy Library, MPFIT, CMSVLIB and TeXtoIDL are fully or partially functional under GDL. Packaged versions of GDL are available for several Linux distributions and Mac OS X. The source code compiles on some other UNIX systems, including BSD and OpenSolaris. The presentation will cover the current status of the project, the key

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

The Spaces of Open-Source Politics

DEFF Research Database (Denmark)

Husted, Emil; Plesner, Ursula

The recent proliferation of Web 2.0 technologies and their role in contemporary political life has inspired the coining of the term ‘open-source politics’. This article analyzes how open-source politics is organized in the case of a young radical political party called The Alternative. Inspired...... processes, but may provide both closure and disconnection between the party’s universal body and its particular body. In conclusion, we propose that such a disconnection might be a precondition for success when institutionalizing radical politics, as it allows parties like The Alternative to maintain...

Open Source and Proprietary Project Management Tools for SMEs.

OpenAIRE

Veronika Abramova; Francisco Pires; Jorge Bernardino

2017-01-01

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 t...

FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Simon Mitternacht

2016-02-01

Full Text Available 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.

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.

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

Developing Open Source System Expertise in Europe

DEFF Research Database (Denmark)

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

2011-01-01

programme (IP). The aim of this IP is to exchange knowledge of and experience in local methods and techniques in the field of open source software knowledge in ICT by engaging a group of international students and lecturers in a joint, explorative investigation of contemporary methods of open...... 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...... source software systems. In addition the program focuses on the students learning interpersonal skills, such as personal and professional skills, multidisciplinary teamwork, communication, communication in a foreign language and leadership. The target group consists of European engineering students who...

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...... with examples of its use. Previous research results where OpenBEM was employed will be mentioned....

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.

Tracing catchment fine sediment sources using the new SIFT (SedIment Fingerprinting Tool) open source software.

Science.gov (United States)

Pulley, S; Collins, A L

2018-09-01

The mitigation of diffuse sediment pollution requires reliable provenance information so that measures can be targeted. Sediment source fingerprinting represents one approach for supporting these needs, but recent methodological developments have resulted in an increasing complexity of data processing methods rendering the approach less accessible to non-specialists. A comprehensive new software programme (SIFT; SedIment Fingerprinting Tool) has therefore been developed which guides the user through critical data analysis decisions and automates all calculations. Multiple source group configurations and composite fingerprints are identified and tested using multiple methods of uncertainty analysis. This aims to explore the sediment provenance information provided by the tracers more comprehensively than a single model, and allows for model configurations with high uncertainties to be rejected. This paper provides an overview of its application to an agricultural catchment in the UK to determine if the approach used can provide a reduction in uncertainty and increase in precision. Five source group classifications were used; three formed using a k-means cluster analysis containing 2, 3 and 4 clusters, and two a-priori groups based upon catchment geology. Three different composite fingerprints were used for each classification and bi-plots, range tests, tracer variability ratios and virtual mixtures tested the reliability of each model configuration. Some model configurations performed poorly when apportioning the composition of virtual mixtures, and different model configurations could produce different sediment provenance results despite using composite fingerprints able to discriminate robustly between the source groups. Despite this uncertainty, dominant sediment sources were identified, and those in close proximity to each sediment sampling location were found to be of greatest importance. This new software, by integrating recent methodological developments in

Why Open Source Hardware matters and why you should care

OpenAIRE

Gürkaynak, Frank K.

2017-01-01

Open source hardware is currently where open source software was about 30 years ago. The idea is well received by enthusiasts, there is interest and the open source hardware has gained visible momentum recently, with several well-known universities including UC Berkeley, Cambridge and ETH Zürich actively working on large projects involving open source hardware, attracting the attention of companies big and small. But it is still not quite there yet. In this talk, based on my experience on the...

Open source workflow : a viable direction for BPM?

NARCIS (Netherlands)

Wohed, P.; Russell, N.C.; Hofstede, ter A.H.M.; Andersson, B.; Aalst, van der W.M.P.; Bellahsène, Z.; Léonard, M.

2008-01-01

With the growing interest in open source software in general and business process management and workflow systems in particular, it is worthwhile investigating the state of open source workflow management. The plethora of these offerings (recent surveys such as [4,6], each contain more than 30 such

Can open-source R&D reinvigorate drug research?

Science.gov (United States)

Munos, Bernard

2006-09-01

The low number of novel therapeutics approved by the US FDA in recent years continues to cause great concern about productivity and declining innovation. Can open-source drug research and development, using principles pioneered by the highly successful open-source software movement, help revive the industry?

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

Directory of Open Access Journals (Sweden)

Ali Niknafs

2012-03-01

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

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Directory of Open Access Journals (Sweden)

Konrad J Karczewski

Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Developing open-source codes for electromagnetic geophysics using industry support

Science.gov (United States)

Key, K.

2017-12-01

Funding for open-source software development in academia often takes the form of grants and fellowships awarded by government bodies and foundations where there is no conflict-of-interest between the funding entity and the free dissemination of the open-source software products. Conversely, funding for open-source projects in the geophysics industry presents challenges to conventional business models where proprietary licensing offers value that is not present in open-source software. Such proprietary constraints make it easier to convince companies to fund academic software development under exclusive software distribution agreements. A major challenge for obtaining commercial funding for open-source projects is to offer a value proposition that overcomes the criticism that such funding is a give-away to the competition. This work draws upon a decade of experience developing open-source electromagnetic geophysics software for the oil, gas and minerals exploration industry, and examines various approaches that have been effective for sustaining industry sponsorship.

A Systematic Approach for Evaluating BPM Systems: Case Studies on Open Source and Proprietary Tools

OpenAIRE

Delgado , Andrea; Calegari , Daniel; Milanese , Pablo; Falcon , Renatta; García , Esteban

2015-01-01

Part 3: Examples and Case Studies; International audience; Business Process Management Systems (BPMS) provide support for modeling, developing, deploying, executing and evaluating business processes in an organization. Selecting a BPMS is not a trivial task, not only due to the many existing alternatives, both in the open source and proprietary realms, but also because it requires a thorough evaluation of its capabilities, contextualizing them in the organizational environment in which they w...

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

Science.gov (United States)

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

2011-01-01

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

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)....

Nurturing reliable and robust open-source scientific software

Science.gov (United States)

Uieda, L.; Wessel, P.

2017-12-01

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

Open source 3D-printed 1000 μL micropump

Directory of Open Access Journals (Sweden)

Jorge Bravo-Martinez

2018-04-01

Full Text Available Scientific innovation goes hand in hand with technological innovation, so scientific work depends to a great extent on the hardware available in the laboratory. The investment in developing countries is still far below that of OECD countries, which was about 2.4% of the gross domestic product (GDP in 2015. In stark contrast, Brazil made the highest investment of Latin American countries at just 1.2%. Today, the “open-source revolution” appears more than ever to be a powerful ally for the promotion of development and the narrowing of the economic gap between developed and developing countries. In this context, this article presents the design of a 1000 μl 3D printed micropump. It is a practical and simple design inspired by pipette pumps. The present design was printed with a 3D printer and assembled very easily with common tools. Upon comparison of the micropump’s performance, it exhibits a systematic error between 1.4 and 3.8% of the volume and a random error between 0.38 and 9.5% of the volumen. Keywords: Open source, 3D printed micropump, 3D printing, DIY labware

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.

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review.

Science.gov (United States)

Syzdykova, Assel; Malta, André; Zolfo, Maria; Diro, Ermias; Oliveira, José Luis

2017-11-13

Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code

Tracking PACS usage with open source tools.

Science.gov (United States)

French, Todd L; Langer, Steve G

2011-08-01

A typical choice faced by Picture Archiving and Communication System (PACS) administrators is deciding how many PACS workstations are needed and where they should be sited. Oftentimes, the social consequences of having too few are severe enough to encourage oversupply and underutilization. This is costly, at best in terms of hardware and electricity, and at worst (depending on the PACS licensing and support model) in capital costs and maintenance fees. The PACS administrator needs tools to asses accurately the use to which her fleet is being subjected, and thus make informed choices before buying more workstations. Lacking a vended solution for this challenge, we developed our own.

Embracing Open Source for NASA's Earth Science Data Systems

Science.gov (United States)

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

2017-01-01

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

psiTurk: An open-source framework for conducting replicable behavioral experiments online.

Science.gov (United States)

Gureckis, Todd M; Martin, Jay; McDonnell, John; Rich, Alexander S; Markant, Doug; Coenen, Anna; Halpern, David; Hamrick, Jessica B; Chan, Patricia

2016-09-01

Online data collection has begun to revolutionize the behavioral sciences. However, conducting carefully controlled behavioral experiments online introduces a number of new of technical and scientific challenges. The project described in this paper, psiTurk, is an open-source platform which helps researchers develop experiment designs which can be conducted over the Internet. The tool primarily interfaces with Amazon's Mechanical Turk, a popular crowd-sourcing labor market. This paper describes the basic architecture of the system and introduces new users to the overall goals. psiTurk aims to reduce the technical hurdles for researchers developing online experiments while improving the transparency and collaborative nature of the behavioral sciences.

OpenSR: An Open-Source Stimulus-Response Testing Framework

Directory of Open Access Journals (Sweden)

Carolyn C. Matheus

2015-01-01

Full Text Available Stimulus–response (S–R tests provide a unique way to acquire information about human perception by capturing automatic responses to stimuli and attentional processes. This paper presents OpenSR, a user-centered S–R testing framework providing a graphical user interface that can be used by researchers to customize, administer, and manage one type of S–R test, the implicit association test. OpenSR provides an extensible open-source Web-based framework that is platform independent and can be implemented on most computers using any operating system. In addition, it provides capabilities for automatically generating and assigning participant identifications, assigning participants to different condition groups, tracking responses, and facilitating collecting and exporting of data. The Web technologies and languages used in creating the OpenSR framework are discussed, namely, HTML5, CSS3, JavaScript, jQuery, Twitter Bootstrap, Python, and Django. OpenSR is available for free download.

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.

Perspectives on Open Source Software

National Research Council Canada - National Science Library

Hissam, Scott

2001-01-01

Open source software (OSS) is emerging as the software community's next "silver bullet" and appears to be playing a significant role in the acquisition and development plans of the Department of Defense (DoD) and industry...

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.

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…

Adoption of open source digital library software packages: a survey

OpenAIRE

Jose, Sanjo

2007-01-01

Open source digital library packages are gaining popularity nowadays. To build a digital library under economical conditions open source software is preferable. This paper tries to identify the extent of adoption of open source digital library software packages in various organizations through an online survey. It lays down the findings from the survey.

Open-Source RTOS Space Qualification: An RTEMS Case Study

Science.gov (United States)

Zemerick, Scott

2017-01-01

NASA space-qualification of reusable off-the-shelf real-time operating systems (RTOSs) remains elusive due to several factors notably (1) The diverse nature of RTOSs utilized across NASA, (2) No single NASA space-qualification criteria, lack of verification and validation (V&V) analysis, or test beds, and (3) different RTOS heritages, specifically open-source RTOSs and closed vendor-provided RTOSs. As a leader in simulation test beds, the NASA IV&V Program is poised to help jump-start and lead the space-qualification effort of the open source Real-Time Executive for Multiprocessor Systems (RTEMS) RTOS. RTEMS, as a case-study, can be utilized as an example of how to qualify all RTOSs, particularly the reusable non-commercial (open-source) ones that are gaining usage and popularity across NASA. Qualification will improve the overall safety and mission assurance of RTOSs for NASA-agency wide usage. NASA's involvement in space-qualification of an open-source RTOS such as RTEMS will drive the RTOS industry toward a more qualified and mature open-source RTOS product.

Technology collaboration by means of an open source government

Science.gov (United States)

Berardi, Steven M.

2009-05-01

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

How to use Open Source Software for Manage a Library System

OpenAIRE

Sumithchandra, Pandula

2009-01-01

Open source is an approach to the design, development, and distribution of software, offering practical accessibility to a software's source code. Some consider open source as one of various possible design approaches, while others consider it a critical strategic element of their operations. Before open source became widely adopted, developers and producers used a variety of phrases to describe the concept; the term open source gained popularity with the rise of the Internet, which provided ...