WorldWideScience

Sample records for rapid open-source method

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

    Science.gov (United States)

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

    2011-08-01

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

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

    DEFF Research Database (Denmark)

    Lørup Buch, Johannes; Ramløv, H

    2016-01-01

    The aim of this study is to provide the reader with a simple setup that can detect antifreeze proteins (AFP) by inhibition of ice recrystallisation in very small sample sizes. This includes an open source cryostage, a method for preparing and loading samples as well as a software analysis method...

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

    Science.gov (United States)

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

    2014-01-01

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

  4. 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.

  5. 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

  6. Parallel Resolved Open Source CFD-DEM: Method, Validation and Application

    Directory of Open Access Journals (Sweden)

    A. Hager

    2014-03-01

    Full Text Available In the following paper the authors present a fully parallelized Open Source method for calculating the interaction of immersed bodies and surrounding fluid. A combination of computational fluid dynamics (CFD and a discrete element method (DEM accounts for the physics of both the fluid and the particles. The objects considered are relatively big compared to the cells of the fluid mesh, i.e. they cover several cells each. Thus this fictitious domain method (FDM is called resolved. The implementation is realized within the Open Source framework CFDEMcOupling (www.cfdem.com, which provides an interface between OpenFOAM® based CFD-solvers and the DEM software LIGGGHTS (www.liggghts.com. While both LIGGGHTS and OpenFOAM® were already parallelized, only a recent improvement of the algorithm permits the fully parallel computation of resolved problems. Alongside with a detailed description of the method, its implementation and recent improvements, a number of application and validation examples is presented in the scope of this paper.

  7. An open-source method to analyze optokinetic reflex responses in larval zebrafish.

    Science.gov (United States)

    Scheetz, Seth D; Shao, Enhua; Zhou, Yangzhong; Cario, Clinton L; Bai, Qing; Burton, Edward A

    2018-01-01

    Optokinetic reflex (OKR) responses provide a convenient means to evaluate oculomotor, integrative and afferent visual function in larval zebrafish models, which are commonly used to elucidate molecular mechanisms underlying development, disease and repair of the vertebrate nervous system. We developed an open-source MATLAB-based solution for automated quantitative analysis of OKR responses in larval zebrafish. The package includes applications to: (i) generate sinusoidally-transformed animated grating patterns suitable for projection onto a cylindrical screen to elicit the OKR; (ii) determine and record the angular orientations of the eyes in each frame of a video recording showing the OKR response; and (iii) analyze angular orientation data from the tracking program to yield a set of parameters that quantify essential elements of the OKR. The method can be employed without modification using the operating manual provided. In addition, annotated source code is included, allowing users to modify or adapt the software for other applications. We validated the algorithms and measured OKR responses in normal larval zebrafish, showing good agreement with published quantitative data, where available. We provide the first open-source method to elicit and analyze the OKR in larval zebrafish. The wide range of parameters that are automatically quantified by our algorithms significantly expands the scope of quantitative analysis previously reported. Our method for quantifying OKR responses will be useful for numerous applications in neuroscience using the genetically- and chemically-tractable zebrafish model. Published by Elsevier B.V.

  8. GSL: An Open Source Framework for the Rapid Development of Data Archive Access Services

    Science.gov (United States)

    McWhirter, J.; Boler, F. M.; Bock, Y.; Squibb, M. B.; Ratzesberger, L.

    2011-12-01

    The Geodetic Seamless Archive Center (GSAC) project is a NASA ROSES ACCESS funded effort with the goal to define and implement a web service API for uniform querying across multiple geodetic data repositories. The project information technology partners include two International GNSS Service (IGS) Data Centers, CDDIS and SOPAC, and a third global NSF and NASA-funded Data Center, UNAVCO. A science partner, the University of Nevada, Reno Geodetic Laboratory is utilizing the services and contributing new quality assessment products. Each of the participant data centers has its own internal database schema and various web-based access mechanisms to suit the needs of their individual user communities. The software engineering challenge that we faced was to unify these access mechanisms into a common web service API. To facilitate the development of the GSAC interfaces within these disparate repositories we have developed a Java-based open source middleware framework called the GSAC Service Layer (GSL). It was recognized early on in the project that much of the required functionality within each repository could be provided by a common software layer, thus achieving a substantial reduction in the development effort required by each partner institution. The GSL provides a range of common services for repository configuration, initialization, database management, web interface generation, and data model and metadata creation. Each repository implementation then simply focuses on the core task of responding to query requests and delivering to the GSL layer the internal results. The GSL layer is then responsible for encoding the results in the desired format. A fundamental challenge in developing a framework such as the GSL is balancing the trade-off between the agnosticism needed within the GSL so that it is applicable to a wide range of problem domains and the specific needs required for a particular repository implementations. The GSL addresses this challenge through an

  9. Rapid instrument prototyping with open source hardware and software: Application to water quality in hypersaline estuaries.

    Science.gov (United States)

    Loose, B.; O'Shea, R.

    2016-02-01

    We describe the design and deployment of a water quality sonde that utilizes mobile phone networks for near-real time data telemetry. The REOL or Realtime Estuary Ocean Logger has the unique and valuable capability of logging data internally and simultaneously relaying the information to a webserver using a cellular modem. The internal circuitry consists of a GSM cellular modem, a microcontroller, and an SD card for data storage - these components are low cost, and backed up with circuit diagrams and programming libraries that are published under open source license. This configuration is versatile and is capable of reading instrument output from a broad spectrum of devices, including serial, TTL, analog voltage (0 - 5V), and analog current (typically 4-20 mA). We find the greatest challenges lie in development of smart software that is capable of handling the conditions brought on by this harsh environment. We have programmed the sonde to first determine whether it is submerged by water, and record the temperature on the electronics before deciding whether to telemeter measurements over the cellular network. The Google App EngineTM provides an interactive visualization platform. We have tested the REOL with a variety of water quality sensors. In the configuration described here, we use a thermistor, depth gauge and torroidal conductivity sensor to measure water temperature, water level and conductivity up to 200 mS/cm. The latter is necessary for studies in hypersaline estuaries, where porewater salinity can exceed 100 g/kg. We present data from two estuaries in West Africa and from a longer-term deployment in the Narragansett Bay, Rhode Island.

  10. Dimensional Error in Rapid Prototyping with Open Source Software and Low-cost 3D-printer.

    Science.gov (United States)

    Rendón-Medina, Marco A; Andrade-Delgado, Laura; Telich-Tarriba, Jose E; Fuente-Del-Campo, Antonio; Altamirano-Arcos, Carlos A

    2018-01-01

    Rapid prototyping models (RPMs) had been extensively used in craniofacial and maxillofacial surgery, especially in areas such as orthognathic surgery, posttraumatic or oncological reconstructions, and implantology. Economic limitations are higher in developing countries such as Mexico, where resources dedicated to health care are limited, therefore limiting the use of RPM to few selected centers. This article aims to determine the dimensional error of a low-cost fused deposition modeling 3D printer (Tronxy P802MA, Shenzhen, Tronxy Technology Co), with Open source software. An ordinary dry human mandible was scanned with a computed tomography device. The data were processed with open software to build a rapid prototype with a fused deposition machine. Linear measurements were performed to find the mean absolute and relative difference. The mean absolute and relative difference was 0.65 mm and 1.96%, respectively ( P = 0.96). Low-cost FDM machines and Open Source Software are excellent options to manufacture RPM, with the benefit of low cost and a similar relative error than other more expensive technologies.

  11. 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......-symmetric and half-space problems. It also contains a number of improvements such a dealing with thin objects and close surfaces, meshing for 2D and axisymmetrical problems, analytical solutions for verification, and a number of additional functions. This paper gives an overview of the capabilities of the program...... with examples of its use. Previous research results where OpenBEM was employed will be mentioned....

  12. An open source based high content screening method for cell biology laboratories investigating cell spreading and adhesion.

    Directory of Open Access Journals (Sweden)

    Andre Schmandke

    Full Text Available Adhesion dependent mechanisms are increasingly recognized to be important for a wide range of biological processes, diseases and therapeutics. This has led to a rising demand of pharmaceutical modulators. However, most currently available adhesion assays are time consuming and/or lack sensitivity and reproducibility or depend on specialized and expensive equipment often only available at screening facilities. Thus, rapid and economical high-content screening approaches are urgently needed.We established a fully open source high-content screening method for identifying modulators of adhesion. We successfully used this method to detect small molecules that are able to influence cell adhesion and cell spreading of Swiss-3T3 fibroblasts in general and/or specifically counteract Nogo-A-Δ20-induced inhibition of adhesion and cell spreading. The tricyclic anti-depressant clomipramine hydrochloride was shown to not only inhibit Nogo-A-Δ20-induced cell spreading inhibition in 3T3 fibroblasts but also to promote growth and counteract neurite outgrowth inhibition in highly purified primary neurons isolated from rat cerebellum.We have developed and validated a high content screening approach that can be used in any ordinarily equipped cell biology laboratory employing exclusively freely available open-source software in order to find novel modulators of adhesion and cell spreading. The versatility and adjustability of the whole screening method will enable not only centers specialized in high-throughput screens but most importantly also labs not routinely employing screens in their daily work routine to investigate the effects of a wide range of different compounds or siRNAs on adhesion and adhesion-modulating molecules.

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

    Science.gov (United States)

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

    2014-12-01

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

  14. A transferable approach towards rapid inventory data capturing for seismic vulnerability assessment using open-source geospatial technologies

    Science.gov (United States)

    Wieland, M.; Pittore, M.; Parolai, S.; Zschau, J.

    2012-04-01

    Geospatial technologies are increasingly being used in pre-disaster vulnerability assessment and post-disaster impact assessment for different types of hazards. Especially the use of remote sensing data has been strongly promoted in recent years due to its capabilities of providing up-to-date information over large areas at a comparatively low cost with increasingly high spatial, temporal and spectral resolution. Despite its clear potentials, a purely remote sensing based approach has its limitations in that it is only capable of providing information about the birds-eye view of the objects of interest. The use of omnidirectional imaging in addition can provide the necessary street-view that furthermore allows for a rapid visual screening of a buildings façade. In this context, we propose an integrated approach to rapid inventory data capturing for the assessment of structural vulnerability of buildings in case of an earthquake. Globally available low-cost data sources are preferred and the tools are developed on an open-source basis to allow for a high degree of transferability and usability. On a neighbourhood scale medium spatial but high temporal and spectral resolution satellite images are analysed to outline areas of homogeneous urban structure. Following a proportional allocation scheme, for each urban structure type representative sample areas are selected for a more detailed analysis of the building stock with high resolution image data. On a building-by-building scale a ground-based, rapid visual survey is performed using an omnidirectional imaging system driven around with a car inside the identified sample areas. Processing of the acquired images allows for an extraction of vulnerability-related features of single buildings (e.g. building height, detection of soft-storeys). An analysis of high resolution satellite images provides with further inventory features (e.g. footprint area, shape irregularity). Since we are dealing with information coming from

  15. An Open Source Approach for Modern Teaching Methods: The Interactive TGUI System

    Directory of Open Access Journals (Sweden)

    Gerlinde Dinges

    2011-03-01

    Full Text Available In order to facilitate teaching complex topics in an interactive way, the authors developed a computer-assisted teaching system, a graphical user interface named TGUI (Teaching Graphical User Interface. TGUI was introduced at the beginning of 2009 in the Austrian Journal of Statistics (Dinges and Templ 2009 as being an effective instrument to train and teach staff on mathematical and statistical topics. While the fundamental principles were retained, the current TGUI system has been undergone a complete redesign. The ultimate goal behind the reimplementation was to share the advantages of TGUI and provide teachers and people who need to hold training courses with a strong tool that can enrich their lectures with interactive features. The idea was to go a step beyond the current modular blended-learning systems (see, e.g., Da Rin 2003 or the related teaching techniques of classroom-voting (see, e.g., Cline 2006. In this paper the authors have attempted to exemplify basic idea and concept of TGUI by means of statistics seminars held at Statistics Austria. The powerful open source software R (R Development Core Team 2010a is the backend for TGUI, which can therefore be used to process even complex statistical contents. However, with specifically created contents the interactive TGUI system can be used to support a wide range of courses and topics. The open source R packages TGUICore and TGUITeaching are freely available from the Comprehensive R Archive Network at http://CRAN.R-project.org/.

  16. Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa

    OpenAIRE

    Dillon, David G; Pirie, Fraser; Rice, Stephen; Pomilla, Cristina; Sandhu, Manjinder S.; Motala, Ayesha A; Young, Elizabeth H.

    2014-01-01

    Objectives Existing electronic data capture options are often financially unfeasible in resource-poor settings or difficult to support technically in the field. To help facilitate large-scale multicenter studies in sub-Saharan Africa, the African Partnership for Chronic Disease Research (APCDR) has developed an open-source electronic questionnaire (EQ). Study Design and Setting To assess its relative validity, we compared the EQ against traditional pen-and-paper methods using 200 randomized i...

  17. Open-Source Colorimeter

    Science.gov (United States)

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

    2013-01-01

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

  18. 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.

  19. 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...

  20. 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…

  1. Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.

    Science.gov (United States)

    Dillon, David G; Pirie, Fraser; Rice, Stephen; Pomilla, Cristina; Sandhu, Manjinder S; Motala, Ayesha A; Young, Elizabeth H

    2014-12-01

    Existing electronic data capture options are often financially unfeasible in resource-poor settings or difficult to support technically in the field. To help facilitate large-scale multicenter studies in sub-Saharan Africa, the African Partnership for Chronic Disease Research (APCDR) has developed an open-source electronic questionnaire (EQ). To assess its relative validity, we compared the EQ against traditional pen-and-paper methods using 200 randomized interviews conducted in an ongoing type 2 diabetes case-control study in South Africa. During its 3-month validation, the EQ had a lower frequency of errors (EQ, 0.17 errors per 100 questions; paper, 0.73 errors per 100 questions; P-value ≤0.001), and a lower monetary cost per correctly entered question, compared with the pen-and-paper method. We found no marked difference in the average duration of the interview between methods (EQ, 5.4 minutes; paper, 5.6 minutes). This validation study suggests that the EQ may offer increased accuracy, similar interview duration, and increased cost-effectiveness compared with paper-based data collection methods. The APCDR EQ software is freely available (https://github.com/apcdr/questionnaire). Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  2. 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...

  3. 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.

  4. 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...

  5. Open Source in Education

    Science.gov (United States)

    Lakhan, Shaheen E.; Jhunjhunwala, Kavita

    2008-01-01

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

  6. Evaluating Open Source Portals

    Science.gov (United States)

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

    2008-01-01

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

  7. Open Source Physics

    CERN Document Server

    Wee, Loo Kang

    2013-01-01

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

  8. 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.

  9. Rapid and efficient localization of depth electrodes and cortical labeling using free and open source medical software in epilepsy surgery candidates

    Directory of Open Access Journals (Sweden)

    Juan Pablo Princich

    2013-12-01

    Full Text Available Depth intracranial electrodes (IEs placement is one of the most used procedures to identify the epileptogenic zone (EZ in surgical treatment of drug resistant epilepsy patients, about 20-30% of this population. IEs localization is therefore a critical issue defining the EZ and its relation with eloquent functional areas. That information is then used to target the resective surgery and has great potential to affect outcome.We designed a methodological procedure intended to avoid the need for highly specialized medical resources and reduce time to identify the anatomical location of IEs, during the first instances of intracranial EEG recordings. This workflow is based on established open source software; 3D Slicer and Freesurfer that uses MRI and Post-implant CT fusion for the localization of IEs and its relation with automatic labeled surrounding cortex. To test this hypothesis we assessed the time elapsed between the surgical implantation process and the final anatomical localization of IEs by means of our proposed method compared against traditional visual analysis of raw post-implant imaging in two groups of patients.All IEs were identified in the first 24 Hs (6-24 Hs of implantation using our method in 4 patients of the first group. For the control group; all IEs were identified by experts with an overall time range of 36 h to 3 days using traditional visual analysis. It included (7 patients, 3 patients implanted with IEs and the same 4 patients from the first group. Time to localization was restrained in this group by the specialized personnel and the image quality available.To validate our method; we trained two inexperienced operators to assess the position of IEs contacts on four patients (5 intracranial electrodes using the proposed method. We quantified the discrepancies between operators and we also assessed the efficiency of our method to define the EZ comparing the findings against the results of traditional analysis.

  10. 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

  11. Investigation, Analysis and Implementation of Open Source Mobile Communication Software

    OpenAIRE

    Paudel, Suresh

    2016-01-01

    Over the past few years, open source software has transformed the mobile communication networks. The development of VoIP technologies has enabled the migration of telco protocols and services to the IP network with help of open source software. This allows for deployment of mobile networks in rural areas with lower cost. The usage of open source GSM is very useful for developing countries which do not yet have full mobile coverage. Open source GSM allows very rapid and economical deployment o...

  12. Software Open Source, Software Gratis?

    OpenAIRE

    Rakhmawati, Nur Aini

    2006-01-01

    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 so...

  13. 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.

  14. Open source clustering software.

    Science.gov (United States)

    de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

    2004-06-12

    We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

  15. Defining Open Source

    Directory of Open Access Journals (Sweden)

    Russ Nelson

    2007-09-01

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

  16. eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows.

    Science.gov (United States)

    Kiefer, Patrick; Schmitt, Uwe; Vorholt, Julia A

    2013-04-01

    The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS. The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users. Supplementary data are available at Bioinformatics online.

  17. 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.

  18. Intrinsic Motivation in Open Source Software Development

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  19. CodeRAnts: A recommendation method based on collaborative searching and ant colonies, applied to reusing of open source code

    Directory of Open Access Journals (Sweden)

    Isaac Caicedo-Castro

    2014-01-01

    Full Text Available This paper presents CodeRAnts, a new recommendation method based on a collaborative searching technique and inspired on the ant colony metaphor. This method aims to fill the gap in the current state of the matter regarding recommender systems for software reuse, for which prior works present two problems. The first is that, recommender systems based on these works cannot learn from the collaboration of programmers and second, outcomes of assessments carried out on these systems present low precision measures and recall and in some of these systems, these metrics have not been evaluated. The work presented in this paper contributes a recommendation method, which solves these problems.

  20. 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...

  1. Open Source Vulnerability Database Project

    OpenAIRE

    Jake Kouns

    2008-01-01

    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 co...

  2. 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.

  3. Crime analysis using open source information

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  4. Catch-up validation study of an in vitro skin irritation test method based on an open source reconstructed epidermis (phase II).

    Science.gov (United States)

    Groeber, F; Schober, L; Schmid, F F; Traube, A; Kolbus-Hernandez, S; Daton, K; Hoffmann, S; Petersohn, D; Schäfer-Korting, M; Walles, H; Mewes, K R

    2016-10-01

    To replace the Draize skin irritation assay (OECD guideline 404) several test methods based on reconstructed human epidermis (RHE) have been developed and were adopted in the OECD test guideline 439. However, all validated test methods in the guideline are linked to RHE provided by only three companies. Thus, the availability of these test models is dependent on the commercial interest of the producer. To overcome this limitation and thus to increase the accessibility of in vitro skin irritation testing, an open source reconstructed epidermis (OS-REp) was introduced. To demonstrate the capacity of the OS-REp in regulatory risk assessment, a catch-up validation study was performed. The participating laboratories used in-house generated OS-REp to assess the set of 20 reference substances according to the performance standards amending the OECD test guideline 439. Testing was performed under blinded conditions. The within-laboratory reproducibility of 87% and the inter-laboratory reproducibility of 85% prove a high reliability of irritancy testing using the OS-REp protocol. In addition, the prediction capacity was with an accuracy of 80% comparable to previous published RHE based test protocols. Taken together the results indicate that the OS-REp test method can be used as a standalone alternative skin irritation test replacing the OECD test guideline 404. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Open Source Software and the Intellectual Commons.

    Science.gov (United States)

    Dorman, David

    2002-01-01

    Discusses the Open Source Software method of software development and its relationship to control over information content. Topics include digital library resources; reference services; preservation; the legal and economic status of information; technical standards; access to digital data; control of information use; and copyright and patent laws.…

  6. Communal Resources in Open Source Software Development

    Science.gov (United States)

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

    2008-01-01

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

  7. 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.

  8. Catch-up validation study of an in vitro skin irritation test method based on an open source reconstructed epidermis (phase I).

    Science.gov (United States)

    Mewes, K R; Fischer, A; Zöller, N N; Laubach, V; Bernd, A; Jacobs, A; van Rompay, A; Liebsch, M; Pirow, R; Petersohn, D

    2016-10-01

    We have developed a new in vitro skin irritation test based on an open source reconstructed epidermis (OS-REp) with openly accessible protocols for tissue production and test performance. Due to structural, mechanistic and procedural similarity, a blinded catch-up validation study for skin irritation according to OECD Performance Standards (PS) was conducted in three laboratories to promote regulatory acceptance, with OS-REp models produced at a single production site only. While overall sensitivity and predictive capacity met the PS requirements, overall specificity was only 57%. A thorough analysis of the test results led to the assumption that some of the false-positive classifications could have been evoked by volatile skin-irritating chemicals tested in the same culture plate as the non-irritants falsely predicted as irritants. With GC/MS and biological approaches the cross-contamination effect was confirmed and the experimental set-up adapted accordingly. Retesting of the affected chemicals with the improved experimental set-up and otherwise identical protocol resulted in correct classifications as non-irritants. Taking these re-test results into account, 93% overall sensitivity, 70% specificity and 82% accuracy was achieved, which is in accordance with the OECD PS. A sufficient reliability of the method was indicated by a within-laboratory-reproducibility of 85-95% and a between-laboratory-reproducibility of 90%. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Open Source and Open Standards

    NARCIS (Netherlands)

    Koper, Rob

    2006-01-01

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

  14. Open source in Experimental Psychology

    OpenAIRE

    Dalmaijer, Edwin

    2015-01-01

    Talk on using open-source software in experimental psychology. Presented on 3 March 2015, at the Attention, Brain and Cognitive Development group (http://www.psy.ox.ac.uk/research/attention-brain-and-cognitive-development-group) at the University of Oxford's Department of Experimental Psychology.

  15. Open Source Wifi Hotspot Implementation

    Directory of Open Access Journals (Sweden)

    Tyler Sondag

    2007-06-01

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

  16. 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.

  17. An 'open source' networked identity

    DEFF Research Database (Denmark)

    Larsen, Malene Charlotte

    2013-01-01

    This paper examines the concept of identity in relation to youth practices on social network sites (SNS). The paper illustrates how writing “I love you” or other emotional statements on each other’s profiles on SNS is not only a common way for Danish teenagers to communicate and practice friendship...... communicative actions – are not only performing their own identity, but are becoming co-constructors of each other's identities, which the author characterizes as an 'open source' networked identity....

  18. Increased security through open source

    OpenAIRE

    Hoepman, J.H.; Jacobs, B.P.F.

    2007-01-01

    In this paper we discuss the impact of open source on both the security and transparency of a software system. We focus on the more technical aspects of this issue, combining and extending arguments developed over the years. We stress that our discussion of the problem only applies to software for general purpose computing systems. For embedded systems, where the software usually cannot easily be patched or upgraded, different considerations may apply.

  19. Data from thermal testing of the Open Source Cryostage

    DEFF Research Database (Denmark)

    Buch, Johannes Lørup; Ramløv, Hans

    2016-01-01

    The data presented here is related to the research article "An open source cryostage and software analysis method for detection of antifreeze activity" (Buch and Ramløv, 2016) [1]. The design of the Open Source Cryostage (OSC) is tested in terms of thermal limits, thermal efficiency and electrical...

  20. Measuring Modularity in Open Source Code Bases

    Directory of Open Access Journals (Sweden)

    Roberto Milev

    2009-03-01

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

  1. 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

  2. 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.

  3. Practical open source software for libraries

    CERN Document Server

    Engard, Nicole

    2010-01-01

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

  4. Future of Open Source systems

    Directory of Open Access Journals (Sweden)

    Karel Charvát

    2010-02-01

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

  5. 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

  6. 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,

  7. The HYPE Open Source Community

    Science.gov (United States)

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

    2013-12-01

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

  8. 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…

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. JSMAA: open source software for SMAA computations

    Science.gov (United States)

    Tervonen, Tommi

    2014-01-01

    Most software for multi-criteria decision analysis (MCDA) implement a small set of compatible methods as a closed monolithic program. With such software tools, the decision models have to be input by hand. In some applications, however, the model can be generated using external information sources, and thus it would be beneficial if the MCDA software could integrate in the comprehensive information infrastructure. This article motivates for the need of model generation in the methodological context of stochastic multicriteria acceptability analysis (SMAA), and describes the JSMAA software that implements SMAA-2, SMAA-O and SMAA-TRI methods. JSMAA is an open source and divided in separate graphical user interface and library components, enabling its use in systems with a model generation subsystem.

  16. Intrinsic Motivation versus Signaling in Open Source Software Development

    DEFF Research Database (Denmark)

    Bitzer, J; Schrettl, W; Schröder, P

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

  17. POKEHEAD: An Open Source Interactive Headphone Based HCI Platform

    DEFF Research Database (Denmark)

    Højlund, Marie; Trento, Stefano; Goudarzi, Visda

    2012-01-01

    This paper introduces a novel interactive, human-computer interface and remote social communication system based on an augmented, hi-fidelity audio headphone platform. Specifically, this system- named Pokehead, currently utilizes the DUL embedded open-source accelerometer platform to gather 3-axis......, open source implementation. Our rapid prototype proved to be robust enough to work in performance for demonstration purposes and serves as a working proof of concept. In this paper we provide a technical description of our prototype, illustrate the context and motivation behind the project, and offer...

  18. 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...

  19. 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...

  20. 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.

  1. 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…

  2. Intrusion Detection using Open Source Tools

    Directory of Open Access Journals (Sweden)

    Jack TIMOFTE

    2008-01-01

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

  3. Legal Challenges to Open Source Licences

    Directory of Open Access Journals (Sweden)

    Andrés Guadamuz González

    2005-06-01

    Full Text Available This paper will concentrate on presenting a legal analysis of two of the main challenges to open source software: SCO’s litigation and software patents. The paper discusses the validity of such challenges, their possible impact to the future of open source software, and the possible legal defences used against them.

  4. Een boekje open over Open Source ERP

    NARCIS (Netherlands)

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

    2009-01-01

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

  5. 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...

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

    Directory of Open Access Journals (Sweden)

    Le Guilloux Vincent

    2009-06-01

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

  7. Keystone Organization for Ontario's Open Source Ecosystem

    Directory of Open Access Journals (Sweden)

    Rowland Few

    2007-08-01

    Full Text Available Many companies, individuals and organizations in Ontario produce and use open source assets and processes to provide unique value to their customers, clients, and themselves. To better enable these companies, individuals and organizations to (i co-evolve capabilities and roles, (ii align themselves with companies holding leadership roles, and (iii invest in shared visions, the Talent First Network (TFN has become the keystone organization of Ontario's open source ecosystem. This article introduces the TFN and identifies the steps it is taking to better support the Ontario Open Source Ecosystem.

  8. On Open- source Multi-robot simulators

    CSIR Research Space (South Africa)

    Namoshe, M

    2008-07-01

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

  9. Scribus – Open Source Desktop Publishing

    OpenAIRE

    Christoph Kaindel

    2010-01-01

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

  10. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

    This chapter presents research on deep learning in a digital learning environment and raises the question if digital instructional designs can catalyze deeper learning than traditional classroom teaching. As a theoretical point of departure the notion of ‘situated learning’ is utilized...... and contrasted to the notion of functionalistic learning in a digital context. The mechanism that enables deep learning in this context is ‘The Open Source Learning Stream’. ‘The Open Source Learning Stream’ is the notion of sharing ‘learning instances’ in a digital space (discussion board, Facebook group......, 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...

  11. Open source 3D printers: an appropriate technology for building low cost optics labs for the developing communities

    Science.gov (United States)

    Gwamuri, J.; Pearce, Joshua M.

    2017-08-01

    The recent introduction of RepRap (self-replicating rapid prototyper) 3-D printers and the resultant open source technological improvements have resulted in affordable 3-D printing, enabling low-cost distributed manufacturing for individuals. This development and others such as the rise of open source-appropriate technology (OSAT) and solar powered 3-D printing are moving 3-D printing from an industry based technology to one that could be used in the developing world for sustainable development. In this paper, we explore some specific technological improvements and how distributed manufacturing with open-source 3-D printing can be used to provide open-source 3-D printable optics components for developing world communities through the ability to print less expensive and customized products. This paper presents an open-source low cost optical equipment library which enables relatively easily adapted customizable designs with the potential of changing the way optics is taught in resource constraint communities. The study shows that this method of scientific hardware development has a potential to enables a much broader audience to participate in optical experimentation both as research and teaching platforms. Conclusions on the technical viability of 3-D printing to assist in development and recommendations on how developing communities can fully exploit this technology to improve the learning of optics through hands-on methods have been outlined.

  12. 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.

  13. An open source image processing method to quantitatively assess tissue growth after non-invasive magnetic resonance imaging in bone marrow stromal cell seeded 3D plymeric scaffolds

    NARCIS (Netherlands)

    Leferink, Anne Marijke; Fratila, R.M.; Koenrades, Maaike Anne; van Blitterswijk, Clemens; Velders, Aldrik; Moroni, Lorenzo

    2014-01-01

    Monitoring extracellular matrix (ECM) components is one of the key methods used to determine tissue quality in three-dimensional (3D) scaffolds for regenerative medicine and clinical purposes. This is even more important when multipotent human bone marrow stromal cells (hMSCs) are used, as it could

  14. 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

    respondents worldwide. 15 interviews (face-to-face or by telephone) with experts in different countries provided additional insights into Open Source usage and certification. The findings led to the development of a certification framework of three main categories with in total eleven sub-categories, i.e., "Certified Open Source Geospatial Data Associate / Professional", "Certified Open Source Geospatial Analyst Remote Sensing & GIS", "Certified Open Source Geospatial Cartographer", "Certified Open Source Geospatial Expert", "Certified Open Source Geospatial Associate Developer / Professional Developer", "Certified Open Source Geospatial Architect". Each certification is described by pre-conditions, scope and objectives, course content, recommended software packages, target group, expected benefits, and the methods of examination. Examinations can be flanked by proofs of professional career paths and achievements which need a peer qualification evaluation. After a couple of years a recertification is required. The concept seeks the accreditation by the OSGeo Foundation (and other bodies) and international support by a group of geospatial scientific institutions to achieve wide and international acceptance for this Open Source geospatial certification model. A business case for Open Source certification and a corresponding SWOT model is examined to support the goals of the Geo-For-All initiative of the ICA-OSGeo pact.

  15. A FRAMEWORK FOR AN OPEN SOURCE GEOSPATIAL CERTIFICATION MODEL

    Directory of Open Access Journals (Sweden)

    T. U. R. Khan

    2016-06-01

    evaluated with 105 respondents worldwide. 15 interviews (face-to-face or by telephone with experts in different countries provided additional insights into Open Source usage and certification. The findings led to the development of a certification framework of three main categories with in total eleven sub-categories, i.e., “Certified Open Source Geospatial Data Associate / Professional”, “Certified Open Source Geospatial Analyst Remote Sensing & GIS”, “Certified Open Source Geospatial Cartographer”, “Certified Open Source Geospatial Expert”, “Certified Open Source Geospatial Associate Developer / Professional Developer”, “Certified Open Source Geospatial Architect”. Each certification is described by pre-conditions, scope and objectives, course content, recommended software packages, target group, expected benefits, and the methods of examination. Examinations can be flanked by proofs of professional career paths and achievements which need a peer qualification evaluation. After a couple of years a recertification is required. The concept seeks the accreditation by the OSGeo Foundation (and other bodies and international support by a group of geospatial scientific institutions to achieve wide and international acceptance for this Open Source geospatial certification model. A business case for Open Source certification and a corresponding SWOT model is examined to support the goals of the Geo-For-All initiative of the ICA-OSGeo pact.

  16. Dilemmas within Commercial Involvement in Open Source Software

    DEFF Research Database (Denmark)

    Ciesielska, Malgorzata; Westenholz, Ann

    2016-01-01

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

  17. Data from thermal testing of the Open Source Cryostage

    DEFF Research Database (Denmark)

    Buch, Johannes Lørup; Ramløv, Hans

    2016-01-01

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

  18. Open Source Software : the Intersection of IP and Security in Open Source

    OpenAIRE

    Kelton, Greg

    2011-01-01

    The use of open source software continues to grow on a daily basis. Today, enterprise applications contain 40% to 70% open source code and this fact has legal, development, IT security, risk management and compliance organizations focusing their attention on its use, as never before. They increasingly understand that the open source content within an application must be detected. Once uncovered, decisions regarding compliance with intellectual property licensing obligations must be made and k...

  19. 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...

  20. 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…

  1. 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.

  2. Managing multicentre clinical trials with open source.

    Science.gov (United States)

    Raptis, Dimitri Aristotle; Mettler, Tobias; Fischer, Michael Alexander; Patak, Michael; Lesurtel, Mickael; Eshmuminov, Dilmurodjon; de Rougemont, Olivier; Graf, Rolf; Clavien, Pierre-Alain; Breitenstein, Stefan

    2014-03-01

    Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

  3. 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.

  4. 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.

  5. 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.

  6. Open Source Approach to Project Management Tools

    Directory of Open Access Journals (Sweden)

    Romeo MARGEA

    2011-01-01

    Full Text Available Managing large projects involving different groups of people and complex tasks can be challenging. The solution is to use Project management software, which allows a more efficient management of projects. However, famous project management systems can be costly and may require expensive custom servers. Even if free software is not as complex as Microsoft Project, is noteworthy to think that not all projects need all the features, amenities and power of such systems. There are free and open source software alternatives that meet the needs of most projects, and that allow Web access based on different platforms and locations. A starting stage in adopting an OSS in-house is finding and identifying existing open source solution. In this paper we present an overview of Open Source Project Management Software (OSPMS based on articles, reviews, books and developers’ web sites, about those that seem to be the most popular software in this category.

  7. The 2017 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; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

    2017-01-01

    The Bioinformatics Open Source Conference (BOSC) is a 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. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

  8. Spaces of Open-source Politics

    DEFF Research Database (Denmark)

    Husted, Emil; Plesner, Ursula

    2017-01-01

    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....... 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...... spaces constructed by The Alternative as techniques for practicing open-source politics and observe that physical and digital spaces create an oscillation between openness and closure. In turn, this oscillation produces a dialectical relationship between practices of imagination and affirmation...

  9. The 2017 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; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

    2017-01-01

    The Bioinformatics Open Source Conference (BOSC) is a 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. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

  10. Balmorel open source energy system model

    DEFF Research Database (Denmark)

    Wiese, Frauke; Bramstoft, Rasmus; Koduvere, Hardi

    2018-01-01

    As the world progresses towards a cleaner energy future with more variable renewable energy sources, energy system models are required to deal with new challenges. This article describes design, development and applications of the open source energy system model Balmorel, which is a result...... of Balmorel as well as to inspire to new model developments and encourage new users to join the community. Some of the key strengths of the model are the flexible handling of the time and space dimensions and the combination of operation and investment optimisation. Its open source character enables diverse...

  11. DEIMOS – an Open Source Image Database

    Directory of Open Access Journals (Sweden)

    M. Blazek

    2011-12-01

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

  12. 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.

  13. Clod-o-meter: A New Method for the Calculation of Shrinkage/Swelling Curves for Soil Clods by Integrating an Open Source Software Solution and Digital Imagery Analysis

    Science.gov (United States)

    Abou Najm, M. R.; Stewart, R. D.; Rupp, D. E.; Selker, J. S.

    2010-12-01

    Characterizing the shrinkage and swelling dynamics of swelling soils is fundamental to the understanding of soil cracking and moisture movement within the vadose zone. The shrinkage and swelling curves relate the change in the soil’s specific volume (volume of soil/mass of solids) to the change in the soil’s moisture content. Current methods determine clod volume by dipping saran-coated clods in water or by relying on expensive equipment and proprietary software (such as using laser scanners to measure the sample in three dimensions). We propose an alternative method for determining the volume of a soil clod, which is both low-cost and utilizes completely free and open-source software. To measure the volume, the clod is placed on a stand and imaged from multiple angles using a digital camera. The images are then combined using the free Microsoft program, Photosynth, to create a 3-dimensional point cloud (a three-dimensional set of vertices, representing the outer surface of the object). This point cloud is then edited using the open source program Meshlab to remove outliers and create a Poisson surface mesh. Finally, an Octave code is used to calculate the relative volume of the 3-dimensional surface. To obtain the actual volume of the clod, the relative volume needs to be calibrated using an object within the same 3D image with known dimensions and volume. For this analysis we used the soil clod holder (a cylinder painted with bright, random patterns) as the calibration object to be able to calculate the real volume of the clod from the relative volume obtained by Octave. The clods were kept at room temperature under small temperature and humidity fluctuations to ensure slow and uniform shrinkage. This procedure was repeated at multiple moisture contents (clod weight was recorded immediately prior to each image session). To verify the final volume calculation from the image processing, the clod was dipped in saran resin and placed into a water-filled graduated

  14. SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data

    Directory of Open Access Journals (Sweden)

    Kumar Saurabh Singh

    2015-06-01

    Full Text Available One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS. Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.

  15. SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.

    Science.gov (United States)

    Singh, Kumar Saurabh; Thual, Dominique; Spurio, Roberto; Cannata, Nicola

    2015-06-03

    One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.

  16. System level modelling with open source tools

    DEFF Research Database (Denmark)

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

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

  17. Developer Network : Open Source Personal Digital Assistant ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    They will convene a technical workshop of users, developers and open source proponents to come up with a prototype application - electronic forms for use on a handheld computer and uploading data back to the computer - that can be used to satisfy immediate requirements and form the basis for further development.

  18. Developer Network : Open Source Personal Digital Assistant ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    This grant will allow a network of health application users to review and appraise existing commercial and free software applications. They will convene a technical workshop of users, developers and open source proponents to come up with a prototype application - electronic forms for use on a handheld computer and ...

  19. Scribus – Open Source Desktop Publishing

    Directory of Open Access Journals (Sweden)

    Christoph Kaindel

    2010-12-01

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

  20. Open source OCR framework using mobile devices

    Science.gov (United States)

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

    2008-02-01

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

  1. Open source software migration: Best practices

    CSIR Research Space (South Africa)

    Molefe, Onkgopotse M

    2010-09-01

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

  2. 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.

  3. DKIE: Open Source Information Extraction for Danish

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  4. 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.

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

    Science.gov (United States)

    Jurica, Peter; van Leeuwen, Cees

    2008-01-01

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

  6. 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.

  7. 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.

  8. 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

  9. AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment

    Directory of Open Access Journals (Sweden)

    Stålring Jonna C

    2011-07-01

    Full Text Available Abstract Background Machine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR modeling. QSAR data sets often encompass tens of thousands of compounds and the size of proprietary, as well as public data sets, is rapidly growing. Hence, there is a demand for computationally efficient machine learning algorithms, easily available to researchers without extensive machine learning knowledge. In granting the scientific principles of transparency and reproducibility, Open Source solutions are increasingly acknowledged by regulatory authorities. Thus, an Open Source state-of-the-art high performance machine learning platform, interfacing multiple, customized machine learning algorithms for both graphical programming and scripting, to be used for large scale development of QSAR models of regulatory quality, is of great value to the QSAR community. Results This paper describes the implementation of the Open Source machine learning package AZOrange. AZOrange is specially developed to support batch generation of QSAR models in providing the full work flow of QSAR modeling, from descriptor calculation to automated model building, validation and selection. The automated work flow relies upon the customization of the machine learning algorithms and a generalized, automated model hyper-parameter selection process. Several high performance machine learning algorithms are interfaced for efficient data set specific selection of the statistical method, promoting model accuracy. Using the high performance machine learning algorithms of AZOrange does not require programming knowledge as flexible applications can be created, not only at a scripting level, but also in a graphical programming environment. Conclusions AZOrange is a step towards meeting the needs for an Open Source high performance machine learning platform, supporting the

  10. AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment.

    Science.gov (United States)

    Stålring, Jonna C; Carlsson, Lars A; Almeida, Pedro; Boyer, Scott

    2011-07-28

    Machine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR) modeling. QSAR data sets often encompass tens of thousands of compounds and the size of proprietary, as well as public data sets, is rapidly growing. Hence, there is a demand for computationally efficient machine learning algorithms, easily available to researchers without extensive machine learning knowledge. In granting the scientific principles of transparency and reproducibility, Open Source solutions are increasingly acknowledged by regulatory authorities. Thus, an Open Source state-of-the-art high performance machine learning platform, interfacing multiple, customized machine learning algorithms for both graphical programming and scripting, to be used for large scale development of QSAR models of regulatory quality, is of great value to the QSAR community. This paper describes the implementation of the Open Source machine learning package AZOrange. AZOrange is specially developed to support batch generation of QSAR models in providing the full work flow of QSAR modeling, from descriptor calculation to automated model building, validation and selection. The automated work flow relies upon the customization of the machine learning algorithms and a generalized, automated model hyper-parameter selection process. Several high performance machine learning algorithms are interfaced for efficient data set specific selection of the statistical method, promoting model accuracy. Using the high performance machine learning algorithms of AZOrange does not require programming knowledge as flexible applications can be created, not only at a scripting level, but also in a graphical programming environment. AZOrange is a step towards meeting the needs for an Open Source high performance machine learning platform, supporting the efficient development of highly accurate QSAR models

  11. Performances evaluation of different open source

    Directory of Open Access Journals (Sweden)

    Arun Patel

    2016-06-01

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

  12. 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.

  13. 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.

  14. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

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

  15. Scalable Open Source Smart Grid Simulator (SGSim)

    DEFF Research Database (Denmark)

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

    2017-01-01

    The future smart power grid will consist of an unlimited number of smart devices that communicate with control units to maintain the grid’s sustainability, efficiency, and balancing. In order to build and verify such controllers over a large grid, a scalable simulation environment is needed....... 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...... and appliances. By using SGSim, different smart grid control strategies and protocols can be tested, validated and evaluated in a scalable environment....

  16. Efficient Open Source Lidar for Desktop Users

    Science.gov (United States)

    Flanagan, Jacob P.

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

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

    Directory of Open Access Journals (Sweden)

    Røttingen John-Arne

    2011-09-01

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

  18. Quality Classifiers for Open Source Software Repositories

    OpenAIRE

    Tsatsaronis, George; Halkidi, Maria; Giakoumakis, Emmanouel A.

    2009-01-01

    Open Source Software (OSS) often relies on large repositories, like SourceForge, for initial incubation. The OSS repositories offer a large variety of meta-data providing interesting information about projects and their success. In this paper we propose a data mining approach for training classifiers on the OSS meta-data provided by such data repositories. The classifiers learn to predict the successful continuation of an OSS project. The `successfulness' of projects is defined in terms of th...

  19. Meteorological Error Budget Using Open Source Data

    Science.gov (United States)

    2016-09-01

    Approved for public release; distribuiton unlimited. 4 The sites selected were in both the northern and southern hemispheres , and included...ARL-TR-7831 ● SEP 2016 US Army Research Laboratory Meteorological Error Budget Using Open- Source Data by J Cogan, J Smith, P...needed. Do not return it to the originator. ARL-TR-7831 ● SEP 2016 US Army Research Laboratory Meteorological Error Budget Using

  20. 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.

  1. 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

  2. Open Source Software Development Projects: Determinants of Project Popularity

    OpenAIRE

    Sen, Ravi

    2006-01-01

    This paper is an initial exploration of the determinants of open source project success as measured by project popularity. We simultaneously model the impact of project-specific characteristics on project popularity, and the impact of intended users and choice of operating system on the choice of end-user license. These models are jointly estimated using Full Information Maximum Likelihood Method. The results show that the software-user license, age of the project, project status, certain typ...

  3. The free/open source software movement: Resistance or change?

    OpenAIRE

    Georgopoulou, Panayiota

    2009-01-01

    At a time when private companies are inventing methods of “locking information” and when neo-liberal governments are imposing strict sanctions on those who violate intellectual property rights, the Free/Open Source Software (FOSS) movement has been countering neo-liberalism and general privatization: it defies ownership regulations in a key area of growth in contemporary capitalistic societies, namely, the construction and use of information. At the end of the ‘90s, FOSS seemed to be a disrup...

  4. Cassandra: An open source Monte Carlo package for molecular simulation.

    Science.gov (United States)

    Shah, Jindal K; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy; Keene, Brian P; Khan, Sandip; Paluch, Andrew S; Rai, Neeraj; Romanielo, Lucienne L; Rosch, Thomas W; Yoo, Brian; Maginn, Edward J

    2017-07-15

    Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Clawpack: Building an open source ecosystem for solving hyperbolic PDEs

    Science.gov (United States)

    Iverson, Richard M.; Mandli, K.T.; Ahmadia, Aron J.; Berger, M.J.; Calhoun, Donna; George, David L.; Hadjimichael, Y.; Ketcheson, David I.; Lemoine, Grady L.; LeVeque, Randall J.

    2016-01-01

    Clawpack is a software package designed to solve nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. The package includes a number of variants aimed at different applications and user communities. Clawpack has been actively developed as an open source project for over 20 years. The latest major release, Clawpack 5, introduces a number of new features and changes to the code base and a new development model based on GitHub and Git submodules. This article provides a summary of the most significant changes, the rationale behind some of these changes, and a description of our current development model. Clawpack: building an open source ecosystem for solving hyperbolic PDEs.

  6. 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

  7. An open-source thermodynamic software library

    DEFF Research Database (Denmark)

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

    This is a technical report which accompanies the article ”An open-source thermodynamic software library” which describes an efficient Matlab and C implementation for evaluation of thermodynamic properties. In this technical report we present the model equations, that are also presented in the paper......, together with a full set of first and second order derivatives with respect to temperature and pressure, and in cases where applicable, also with respect to mole numbers. The library is based on parameters and correlations from the DIPPR database and the Peng-Robinson and the Soave-Redlich-Kwong equations...

  8. Open Source Live Distributions for Computer Forensics

    Science.gov (United States)

    Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

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

  9. Open Source Real Time Operating Systems Overview

    Energy Technology Data Exchange (ETDEWEB)

    Straumann, Till

    2001-12-11

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

  10. Open-source, community-driven microfluidics with Metafluidics.

    Science.gov (United States)

    Kong, David S; Thorsen, Todd A; Babb, Jonathan; Wick, Scott T; Gam, Jeremy J; Weiss, Ron; Carr, Peter A

    2017-06-07

    Microfluidic devices have the potential to automate and miniaturize biological experiments, but open-source sharing of device designs has lagged behind sharing of other resources such as software. Synthetic biologists have used microfluidics for DNA assembly, cell-free expression, and cell culture, but a combination of expense, device complexity, and reliance on custom set-ups hampers their widespread adoption. We present Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device. We use Metafluidics to share designs and fabrication instructions for both a microfluidic ring-mixer device and a 32-channel tabletop microfluidic controller. This device and controller are applied to build genetic circuits using standard DNA assembly methods including ligation, Gateway, Gibson, and Golden Gate. Metafluidics is intended to enable a broad community of engineers, DIY enthusiasts, and other nontraditional participants with limited fabrication skills to contribute to microfluidic research.

  11. Repositorios digitales y software open source

    Directory of Open Access Journals (Sweden)

    Doria, María Vanesa

    2015-06-01

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

  12. 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 contra......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......, Twitter hashtags etc.). The ‘learning instances’ are described as mediated signs of learning expressed through text in the stream that is further developed by peers and by the teacher. The expressions of ‘learning instances’ are analyzed and categorized according to whether it expresses prestructural......, 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...

  13. Open source software to control Bioflo bioreactors.

    Science.gov (United States)

    Burdge, David A; Libourel, Igor G L

    2014-01-01

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

  14. 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.

  15. International free and open source software law review

    National Research Council Canada - National Science Library

    2009-01-01

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

  16. Sharing Open Source License and Copyright Data with SPDX

    OpenAIRE

    Michlmayr, Martin

    2010-01-01

    Organizations across the globe are creating and distributing products that include open source software. To ensure compliance with the open source licenses, each company needs to evaluate exactly what open source licenses and copyrights are included - resulting in duplicated effort and redundancy. This talk will provide an overview of a new Software Package Data Exchange (SPDX) specification. This specification will provide a common format to share information about the open source licenses a...

  17. 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...

  18. Open Source Software The Challenge Ahead

    CERN Multimedia

    CERN. Geneva

    2007-01-01

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

  19. Building Energy Management Open Source Software

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-08-25

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

  20. The architecture of open source applications

    CERN Document Server

    Wilson, Greg

    2012-01-01

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

  1. Evolution of an Open Source Strategy

    Directory of Open Access Journals (Sweden)

    Ronald Baecker

    2007-10-01

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

  2. An Affordable Open-Source Turbidimeter

    Science.gov (United States)

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

    2014-01-01

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

  3. An Affordable Open-Source Turbidimeter

    Directory of Open Access Journals (Sweden)

    Christopher D. Kelley

    2014-04-01

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

  4. An open source business model for malaria.

    Directory of Open Access Journals (Sweden)

    Christine Årdal

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

  5. An open source business model for malaria.

    Science.gov (United States)

    Årdal, Christine; Røttingen, John-Arne

    2015-01-01

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

  6. 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

  7. 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.

  8. Building Eclectic Personal Learning Landscapes with Open Source Tools

    NARCIS (Netherlands)

    Kalz, Marco

    2008-01-01

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

  9. 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…

  10. 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…

  11. A survey of open source tools for business intelligence

    DEFF Research Database (Denmark)

    Thomsen, Christian; Pedersen, Torben Bach

    2005-01-01

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

  12. Rapid methods for detection of bacteria

    DEFF Research Database (Denmark)

    Corfitzen, Charlotte B.; Andersen, B.Ø.; Miller, M.

    2006-01-01

    Traditional methods for detection of bacteria in drinking water e.g. Heterotrophic Plate Counts (HPC) or Most Probable Number (MNP) take 48-72 hours to give the result. New rapid methods for detection of bacteria are needed to protect the consumers against contaminations. Two rapid methods...

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

    OpenAIRE

    Yang, Seungwon; Kavanaugh, Andrea L.

    2011-01-01

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

  14. Clawpack: building an open source ecosystem for solving hyperbolic PDEs

    Directory of Open Access Journals (Sweden)

    Kyle T. Mandli

    2016-08-01

    Full Text Available Clawpack is a software package designed to solve nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. The package includes a number of variants aimed at different applications and user communities. Clawpack has been actively developed as an open source project for over 20 years. The latest major release, Clawpack 5, introduces a number of new features and changes to the code base and a new development model based on GitHub and Git submodules. This article provides a summary of the most significant changes, the rationale behind some of these changes, and a description of our current development model.

  15. Clawpack: building an open source ecosystem for solving hyperbolic PDEs

    KAUST Repository

    Mandli, Kyle T.

    2016-08-08

    Clawpack is a software package designed to solve nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. The package includes a number of variants aimed at different applications and user communities. Clawpack has been actively developed as an open source project for over 20 years. The latest major release, Clawpack 5, introduces a number of new features and changes to the code base and a new development model based on GitHub and Git submodules. This article provides a summary of the most significant changes, the rationale behind some of these changes, and a description of our current development model.

  16. Suicide bombing of the Mineralnye Vody Train: case study in using open-source information for open-source health intelligence.

    Science.gov (United States)

    Lee, Catherine Y; Davis, Timothy E; Noji, Eric K

    2007-01-01

    Open-source information consists of a range of publicly available material, including various periodicals, news reports, journal publications, photographs, and maps. Although intelligence agencies regularly use open-source information in developing strategically important intelligence, the disaster community has yet to evaluate its use for planning or research purposes. This study examines how open-source information, in the form of Internet news reports and public access disaster databases, can be used to develop a rapid, 72-hour case report. Open-source information was extrapolated from several news reports on a terrorist bombing that occurred in Russia on 05 December 2003, using a self-devised "data" collection sheet, and background information collected on the nature of similar disasters using three public access databases. The bulk of health-related information was collected in the first 13 hours after the event, including casualty demographics, immediate dead, total dead, admitted, and treated-and-released. The complex and prolonged rescue of casualties was identified, as well as the presence of unexploded ordnance. This incident also was identified as the first publicly reported suicide terrorist bombing of a commuter train. Open-source information has the potential to be a helpful tool in reconstructing a chain of events and response. However, its use must be validated further and used appropriately. Standards for collection and analysis also must be developed.

  17. Innovative rapid construction/reconstruction methods.

    Science.gov (United States)

    2005-07-01

    Innovative construction and reconstruction methods provide the opportunity to significantly reduce the time of roadway projects while maintaining the necessary quality of workmanship. The need for these rapid methods stems from the increase in ...

  18. Open Source Powder based Rapid Prototyping Machine for Ceramics

    NARCIS (Netherlands)

    Budding, A.; Vaneker, Thomas H.J.; Winnubst, Aloysius J.A.

    2013-01-01

    3DP (Three Dimensional Printing) technology is one of the SFF (Solid Freeform Fabrication) technologies which have recently come into the spotlight due to its adaptability to various applications. However, commercial 3DP machines are limited as to the use of building material, without voiding the

  19. XNAT Central: Open sourcing imaging research data.

    Science.gov (United States)

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

    2016-01-01

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

  20. Open source integrated modeling environment Delta Shell

    Science.gov (United States)

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

    2012-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Ray, Jaideep; Brownstein, John S. [Boston Children%3CU%2B2019%3Es Hospital, Boston, MA

    2013-02-01

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

  2. TREMOR12: An Open-Source Mobile App for Tremor Quantification

    Science.gov (United States)

    Kubben, Pieter L.; Kuijf, Mark L.; Ackermans, Linda P.C.M.; Leentjes, Albert F.G.; Temel, Yasin

    2016-01-01

    Background Evaluating the effect of treatment of tremor is mostly performed with clinical rating scales. Mobile applications facilitate a more rapid, objective, and quantitative evaluation of treatment effect. Existing mobile apps do not offer raw data access, which limits algorithm development. Objective To develop a novel open-source mobile app for tremor quantification. Methods TREMOR12 is an open-source mobile app that samples acceleration, rotation, rotation speed, and gravity, each in 3 axes and time-stamped in a frequency up to 100 Hz. The raw measurement data can be exported as a comma-separated value file for further analysis in the TREMOR12P data processing module. The app was evaluated with 3 patients suffering from essential tremor, who were between 55 and 71 years of age. Results This proof-of-concept study shows that the TREMOR12 app is able to detect and register tremor characteristics such as acceleration, rotation, rotation speed, and gravity in a simple and nonburdensome way. The app is compatible with current regulatory oversight by the European Union (MEDDEV regulations) and the Food and Drug Administration (FDA) guidance on mobile medical applications. Conclusion TREMOR12 offers low-cost tremor quantification for research purposes and algorithm development, and may help to improve treatment evaluation. PMID:27395052

  3. RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

    Science.gov (United States)

    Kaushik, Gaurav; Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

    2017-01-01

    As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.

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

    Science.gov (United States)

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

    2015-01-01

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

  5. An Open Source Extensible Smart Energy Framework

    Energy Technology Data Exchange (ETDEWEB)

    Rankin, Linda [V-Squared, Portland, OR (United States)

    2017-03-23

    Aggregated distributed energy resources are the subject of much interest in the energy industry and are expected to play an important role in meeting our future energy needs by changing how we use, distribute and generate electricity. This energy future includes an increased amount of energy from renewable resources, load management techniques to improve resiliency and reliability, and distributed energy storage and generation capabilities that can be managed to meet the needs of the grid as well as individual customers. These energy assets are commonly referred to as Distributed Energy Resources (DER). DERs rely on a means to communicate information between an energy provider and multitudes of devices. Today DER control systems are typically vendor-specific, using custom hardware and software solutions. As a result, customers are locked into communication transport protocols, applications, tools, and data formats. Today’s systems are often difficult to extend to meet new application requirements, resulting in stranded assets when business requirements or energy management models evolve. By partnering with industry advisors and researchers, an implementation DER research platform was developed called the Smart Energy Framework (SEF). The hypothesis of this research was that an open source Internet of Things (IoT) framework could play a role in creating a commodity-based eco-system for DER assets that would reduce costs and provide interoperable products. SEF is based on the AllJoynTM IoT open source framework. The demonstration system incorporated DER assets, specifically batteries and smart water heaters. To verify the behavior of the distributed system, models of water heaters and batteries were also developed. An IoT interface for communicating between the assets and a control server was defined. This interface supports a series of “events” and telemetry reporting, similar to those defined by current smart grid communication standards. The results of this

  6. Assessing the Open Source Development Processes Using OMM

    Directory of Open Access Journals (Sweden)

    Etiel Petrinja

    2012-01-01

    Full Text Available The assessment of development practices in Free Libre Open Source Software (FLOSS projects can contribute to the improvement of the development process by identifying poor practices and providing a list of necessary practices. Available assessment methods (e.g., Capability Maturity Model Integration (CMMI do not address sufficiently FLOSS-specific aspects (e.g., geographically distributed development, importance of the contributions, reputation of the project, etc.. We present a FLOSS-focused, CMMI-like assessment/improvement model: the QualiPSo Open Source Maturity Model (OMM. OMM focuses on the development process. This makes it different from existing assessment models that are focused on the assessment of the product. We have assessed six FLOSS projects using OMM. Three projects were started and led by a software company, and three are developed by three different FLOSS communities. We identified poorly addressed development activities as the number of commit/bug reports, the external contributions, and the risk management. The results showed that FLOSS projects led by companies adopt standard project management approaches as product planning, design definition, and testing, that are less often addressed by community led FLOSS projects. The OMM is valuable for both the FLOSS community, by identifying critical development activities necessary to be improved, and for potential users that can better decide which product to adopt.

  7. Accuracy Assessment of Open Source Digital Elevation Models

    Directory of Open Access Journals (Sweden)

    Aqeel Abboud Abdul Hassan

    2018-02-01

    Full Text Available Digital Elevation Model is a three-dimensional representation of the earth's surface, which is essential for Geoscience and hydrological implementations. DEM can be created utilizing Photogrammetry techniques, radar interferometry, laser scanning and land surveying. There are some world agencies provide open source digital elevation models which are freely available for all users, such as the National Aeronautics and Space Administration (NASA, Japan Aerospace Exploration Agency’s (JAXA and others. ALOS, SRTM and ASTER are satellite based DEMs which are open source products. The technologies that are used for obtaining raw data and the methods used for its processing and on the other hand the characteristics of natural land and land cover type, these and other factors are the cause of implied errors produced in the digital elevation model which can't be avoided. In this paper, ground control points observed by the differential global positioning system DGPS were used to compare the validation and performance of different satellite based digital elevation models. For validation, standard statistical tests were applied such as Mean Error (ME and Root Mean Square Error (RMSE which showed ALOS DEM had ME and RMSE are -1.262m and 1.988m, while SRTM DEM had ME of -0.782m with RMSE of 2.276m and ASTER DEM had 4.437m and 6.241m, respectively. These outcomes can be very helpful for analysts utilizing such models in different areas of work.

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

    Science.gov (United States)

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

    2017-03-01

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

  9. Eucalyptus: an open-source cloud computing infrastructure

    Science.gov (United States)

    Nurmi, Daniel; Wolski, Rich; Grzegorczyk, Chris; Obertelli, Graziano; Soman, Sunil; Youseff, Lamia; Zagorodnov, Dmitrii

    2009-07-01

    Utility computing, elastic computing, and cloud computing are all terms that refer to the concept of dynamically provisioning processing time and storage space from a ubiquitous "cloud" of computational resources. Such systems allow users to acquire and release the resources on demand and provide ready access to data from processing elements, while relegating the physical location and exact parameters of the resources. Over the past few years, such systems have become increasingly popular, but nearly all current cloud computing offerings are either proprietary or depend upon software infrastructure that is invisible to the research community. In this work, we present Eucalyptus, an open-source software implementation of cloud computing that utilizes compute resources that are typically available to researchers, such as clusters and workstation farms. In order to foster community research exploration of cloud computing systems, the design of Eucalyptus emphasizes modularity, allowing researchers to experiment with their own security, scalability, scheduling, and interface implementations. In this paper, we outline the design of Eucalyptus, describe our own implementations of the modular system components, and provide results from experiments that measure performance and scalability of a Eucalyptus installation currently deployed for public use. The main contribution of our work is the presentation of the first research-oriented open-source cloud computing system focused on enabling methodical investigations into the programming, administration, and deployment of systems exploring this novel distributed computing model.

  10. 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.

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

    Science.gov (United States)

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

    2016-02-15

    The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available. © The Author 2015. Published by Oxford University Press.

  12. Analýza trhu open source business intelligence

    OpenAIRE

    Formánek, Václav

    2010-01-01

    Thesis analysis the situation in business inteligence market and focuses on open source applications. Thesis includes insight into the past, present and future trends in this field. Functionality of open source applications is compared among them and also compared with functionality of traditional vendors. This section describes positives and negatives of open source model. Final part includes results of survey launched in Czech republic. Consecutive analysis is focused on particular findings...

  13. Open Source vs. Closed Source Software: Towards Measuring Security

    OpenAIRE

    Schryen, Guido; Kadura, Rouven

    2009-01-01

    The increasing availability and deployment of open source software in personal and commercial environments makes open source software highly appealing for hackers, and others who are interested in exploiting software vulnerabilities. This deployment has resulted in a debate “full of religion” on the security of open source software compared to that of closed source software. However, beyond such arguments, only little quantitative analysis on this research issue has taken place. We discuss th...

  14. 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...... 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)....

  15. 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.

  16. An open-source toolbox for automated phenotyping of mice in behavioral tasks

    Directory of Open Access Journals (Sweden)

    Tapan P Patel

    2014-10-01

    Full Text Available Classifying behavior patterns in mouse models of neurological, psychiatric and neurodevelopmental disorders is critical for understanding disease causality and treatment. However, complete characterization of behavior is time-intensive, prone to subjective scoring, and often requires specialized equipment. Although several reports describe automated home-cage monitoring and individual task scoring methods, we report the first open source, comprehensive toolbox for automating the scoring of several common behavior tasks used by the neuroscience community. We show this new toolbox is robust and achieves equal or better consistency when compared to manual scoring methods. We use this toolbox to study the alterations in behavior that occur following blast-induced traumatic brain injury (bTBI, and study if these behavior patterns are altered following genetic deletion of the transcription factor Ets-like kinase 1 (Elk-1. Due to the role of Elk-1 in neuronal survival and proposed role in synaptic plasticity, we hypothesized that Elk-1 deletion would improve some neurobehavioral deficits, while impairing others, following blast exposure. In Elk-1 knockout animals, deficits in open field, spatial object recognition and elevated zero maze performance after blast exposure disappeared, while new significant deficits appeared in spatial and associative memory. These are the first data suggesting a molecular mediator of anxiety deficits following blast-induced traumatic brain injury, and represent the utility of the broad screening tool we developed. More broadly, we envision this open-source toolbox will provide a more consistent and rapid analysis of behavior across many neurological diseases, promoting the rapid discovery of novel pathways mediating disease progression and treatment.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Jonathan Younker

    2013-06-01

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

  19. An Offline-Online Android Application for Hazard Event Mapping Using WebGIS Open Source Technologies

    Science.gov (United States)

    Olyazadeh, Roya; Jaboyedoff, Michel; Sudmeier-Rieux, Karen; Derron, Marc-Henri; Devkota, Sanjaya

    2016-04-01

    Nowadays, Free and Open Source Software (FOSS) plays an important role in better understanding and managing disaster risk reduction around the world. National and local government, NGOs and other stakeholders are increasingly seeking and producing data on hazards. Most of the hazard event inventories and land use mapping are based on remote sensing data, with little ground truthing, creating difficulties depending on the terrain and accessibility. Open Source WebGIS tools offer an opportunity for quicker and easier ground truthing of critical areas in order to analyse hazard patterns and triggering factors. This study presents a secure mobile-map application for hazard event mapping using Open Source WebGIS technologies such as Postgres database, Postgis, Leaflet, Cordova and Phonegap. The objectives of this prototype are: 1. An Offline-Online android mobile application with advanced Geospatial visualisation; 2. Easy Collection and storage of events information applied services; 3. Centralized data storage with accessibility by all the service (smartphone, standard web browser); 4. Improving data management by using active participation in hazard event mapping and storage. This application has been implemented as a low-cost, rapid and participatory method for recording impacts from hazard events and includes geolocation (GPS data and Internet), visualizing maps with overlay of satellite images, viewing uploaded images and events as cluster points, drawing and adding event information. The data can be recorded in offline (Android device) or online version (all browsers) and consequently uploaded through the server whenever internet is available. All the events and records can be visualized by an administrator and made public after approval. Different user levels can be defined to access the data for communicating the information. This application was tested for landslides in post-earthquake Nepal but can be used for any other type of hazards such as flood, avalanche

  20. A new method for rapid Canine retraction

    Directory of Open Access Journals (Sweden)

    "Khavari A

    2001-06-01

    Full Text Available Distraction osteogenesis method (Do in bone lengthening and rapid midpalatal expansion have shown the great ability of osteognic tissues for rapid bone formation under distraction force and special protocol with optimum rate of one millimeter per day. Periodontal membrane of teeth (PDM is the extension of periostium in the alveolar socked. Orthodontic force distracts PDM fibers in the tension side and then bone formation will begin.Objects: Rapid retraction of canine tooth into extraction space of first premolar by DO protocol in order to show the ability of the PDM in rapid bone formation. The other objective was reducing total orthodontic treatment time of extraction cases.Patients and Methods: Tweleve maxillary canines in six patients were retracted rapidly in three weeks by a custom-made tooth-born appliance. Radiographic records were taken to evaluate the effects of heavy applied force on canine and anchorage teeth.Results: Average retraction was 7.05 mm in three weeks (2.35 mm/week. Canines rotated distal- in by mean 3.5 degrees.Anchorage loss was from 0 to 0.8 mm with average of 0.3 mm.Root resorption of canines was negligible, and was not significant clinically. Periodontium was normal after rapid retraction. No hazard for pulp vitality was observed.Discussion: PDM responded well to heavy distraction force by Do protocol. Rapid canine retraction seems to be a safe method and can considerabely reduce orthodontic time.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gopalakrishnan, Pradeep; Tafti, Danesh

    2013-02-01

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment...

  3. A scoping review of rapid review methods.

    Science.gov (United States)

    Tricco, Andrea C; Antony, Jesmin; Zarin, Wasifa; Strifler, Lisa; Ghassemi, Marco; Ivory, John; Perrier, Laure; Hutton, Brian; Moher, David; Straus, Sharon E

    2015-09-16

    Rapid reviews are a form of knowledge synthesis in which components of the systematic review process are simplified or omitted to produce information in a timely manner. Although numerous centers are conducting rapid reviews internationally, few studies have examined the methodological characteristics of rapid reviews. We aimed to examine articles, books, and reports that evaluated, compared, used or described rapid reviews or methods through a scoping review. MEDLINE, EMBASE, the Cochrane Library, internet websites of rapid review producers, and reference lists were searched to identify articles for inclusion. Two reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted. We included 100 articles plus one companion report that were published between 1997 and 2013. The studies were categorized as 84 application papers, seven development papers, six impact papers, and four comparison papers (one was included in two categories). The rapid reviews were conducted between 1 and 12 months, predominantly in Europe (58 %) and North America (20 %). The included studies failed to report 6 % to 73 % of the specific systematic review steps examined. Fifty unique rapid review methods were identified; 16 methods occurred more than once. Streamlined methods that were used in the 82 rapid reviews included limiting the literature search to published literature (24 %) or one database (2 %), limiting inclusion criteria by date (68 %) or language (49 %), having one person screen and another verify or screen excluded studies (6 %), having one person abstract data and another verify (23 %), not conducting risk of bias/quality appraisal (7 %) or having only one reviewer conduct the quality appraisal (7 %), and presenting results as a narrative summary (78 %). Four case studies were identified that compared the results of rapid reviews to systematic reviews. Three studies found that the conclusions between

  4. 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

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

    DEFF Research Database (Denmark)

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

    This article’s objective is to set up some foundational theory and practices for Open Source Development (OSD) of tangible products, a novel and emerging approach derived from the well-known open source software movement. As a contribution to the first steps of research in this discipline a clear...

  6. Integrating an Automatic Judge into an Open Source LMS

    Science.gov (United States)

    Georgouli, Katerina; Guerreiro, Pedro

    2011-01-01

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

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

    Science.gov (United States)

    Conner, Trey; Gresham, Morgan; McCracken, Jill

    2011-01-01

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

  8. 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.

  9. 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.

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

    Science.gov (United States)

    Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

    2011-01-01

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

  11. The open-source movement: an introduction for forestry professionals

    Science.gov (United States)

    Patrick Proctor; Paul C. Van Deusen; Linda S. Heath; Jeffrey H. Gove

    2005-01-01

    In recent years, the open-source movement has yielded a generous and powerful suite of software and utilities that rivals those developed by many commercial software companies. Open-source programs are available for many scientific needs: operating systems, databases, statistical analysis, Geographic Information System applications, and object-oriented programming....

  12. Open Source Library Management Systems: A Multidimensional Evaluation

    Science.gov (United States)

    Balnaves, Edmund

    2008-01-01

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

  13. Open Source as Appropriate Technology for Global Education

    Science.gov (United States)

    Carmichael, Patrick; Honour, Leslie

    2002-01-01

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

  14. 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.

  15. Governance of Open Source Software Foundations: Who Holds the Power?

    Directory of Open Access Journals (Sweden)

    Ludovico Prattico

    2012-12-01

    Full Text Available The research reported in this article attempts to discover who holds the power in open source software foundations through the analysis of governance documents. Artificial neural network analysis is used to analyse the content of the bylaws of six open source foundations (Apache, Eclipse, GNOME, Plone, Python, and SPI for the purpose of identifying power structures. Results of the research suggest that: i the actions of an open source software foundation are centered around one of three groups: Members, Chairman/President/Executive Director, and Board of Directors; ii in only one of the six foundations is the Board of Directors responsible for both the community and the product; and iii artificial neural network analysis of the content of bylaws provides unbiased insights of the power structure of open source software foundations. These results may prove useful to those who contribute to open source foundations and use their products and services.

  16. 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.

  17. 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.

  18. Ambit-Tautomer: An Open Source Tool for Tautomer Generation.

    Science.gov (United States)

    Kochev, Nikolay T; Paskaleva, Vesselina H; Jeliazkova, Nina

    2013-06-01

    We present a new open source tool for automatic generation of all tautomeric forms of a given organic compound. Ambit-Tautomer is a part of the open source software package Ambit2. It implements three tautomer generation algorithms: combinatorial method, improved combinatorial method and incremental depth-first search algorithm. All algorithms utilize a set of fully customizable rules for tautomeric transformations. The predefined knowledge base covers 1-3, 1-5 and 1-7 proton tautomeric shifts. Some typical supported tautomerism rules are keto-enol, imin-amin, nitroso-oxime, azo-hydrazone, thioketo-thioenol, thionitroso-thiooxime, amidine-imidine, diazoamino-diazoamino, thioamide-iminothiol and nitrosamine-diazohydroxide. Ambit-Tautomer uses a simple energy based system for tautomer ranking implemented by a set of empirically derived rules. A fine-grained output control is achieved by a set of post-generation filters. We performed an exhaustive comparison of the Ambit-Tautomer Incremental algorithm against several other software packages which offer tautomer generation: ChemAxon Marvin, Molecular Networks MN.TAUTOMER, ACDLabs, CACTVS and the CDK implementation of the algorithm, based on the mobile H atoms listed in the InChI. According to the presented test results, Ambit-Tautomer's performance is either comparable to or better than the competing algorithms. Ambit-Tautomer module is available for download as a Java library, a command line application, a demo web page or OpenTox API compatible Web service. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Risto Rajala

    2012-01-01

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

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

    Science.gov (United States)

    Bassingthwaighte, James B.

    2013-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  2. 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.

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

    Science.gov (United States)

    Deibel, Eric

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Ulhøi, John Parm

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    B T Wittbrodt

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

  6. Nektar++: An open-source spectral/ hp element framework

    Science.gov (United States)

    Cantwell, C. D.; Moxey, D.; Comerford, A.; Bolis, A.; Rocco, G.; Mengaldo, G.; De Grazia, D.; Yakovlev, S.; Lombard, J.-E.; Ekelschot, D.; Jordi, B.; Xu, H.; Mohamied, Y.; Eskilsson, C.; Nelson, B.; Vos, P.; Biotto, C.; Kirby, R. M.; Sherwin, S. J.

    2015-07-01

    Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/ hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/ hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains.

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

    Science.gov (United States)

    Hansen, Michael Schacht; Sørensen, Thomas Sangild

    2013-06-01

    This work presents a new open source framework for medical image reconstruction called the "Gadgetron." The framework implements a flexible system for creating streaming data processing pipelines where data pass through a series of modules or "Gadgets" from raw data to reconstructed images. The data processing pipeline is configured dynamically at run-time based on an extensible markup language configuration description. The framework promotes reuse and sharing of reconstruction modules and new Gadgets can be added to the Gadgetron framework through a plugin-like architecture without recompiling the basic framework infrastructure. Gadgets are typically implemented in C/C++, but the framework includes wrapper Gadgets that allow the user to implement new modules in the Python scripting language for rapid prototyping. In addition to the streaming framework infrastructure, the Gadgetron comes with a set of dedicated toolboxes in shared libraries for medical image reconstruction. This includes generic toolboxes for data-parallel (e.g., GPU-based) execution of compute-intensive components. The basic framework architecture is independent of medical imaging modality, but this article focuses on its application to Cartesian and non-Cartesian parallel magnetic resonance imaging. Copyright © 2012 Wiley Periodicals, Inc.

  8. 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

  9. The Utility of Open Source Software in Military Systems

    National Research Council Canada - National Science Library

    Esperon, Agustin I; Munoz, Jose P; Tanneau, Jean M

    2005-01-01

    The MILOS (Military Systems based on Open-source Software) project was a European research program in the Eurofinder framework, attached to the CEPA 6 and co-financed by the Ministry of Defence of France and Spain...

  10. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

    Doak, J.; Howell, J.A.

    1995-08-01

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

  12. Open Source Geospatial Tools: Applications in Earth Observation

    National Research Council Canada - National Science Library

    McInerney, Daniel; Kempeneers, Pieter

    2015-01-01

    This book focuses on the use of open source software for geospatial analysis. It demonstrates the effectiveness of the command line interface for handling both vector, raster and 3D geospatial data...

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

    Data.gov (United States)

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

  14. Open-source software gets boost at UN

    CERN Multimedia

    Schenker, J L

    2003-01-01

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

  15. The Utility of Open Source Software in Military Systems

    National Research Council Canada - National Science Library

    Esperon, Agustin I; Munoz, Jose P; Tanneau, Jean M

    2005-01-01

    .... The companies involved were THALES and GMV. The MILOS project aimed to demonstrate benefits of Open Source Software in large software based military systems, by casting off constraints inherent to traditional proprietary COTS and by taking...

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

    Science.gov (United States)

    Edwards, Jacob

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

  17. Starchive: The Open Access, Open Source Stellar Database

    Science.gov (United States)

    Tanner, A. M.; Muna, D.; Addison, B.; Zohrabi, F.; Geneser, C.; Niffenegger, R.

    2017-11-01

    It has become clear that we must understand the host stars as well as their exoplanets. The Starchive is an open source, open access stellar database and intuitive front-end to help astronomers find planets and determine habitability.

  18. Open Source BI Platforms: A Functional and Architectural Comparison

    Science.gov (United States)

    Golfarelli, Matteo

    While in the past the BI market was strictly dominated by closed source and commercial tools, the last few years were characterized by the birth of open source solutions: first as single BI tools, and later as complete BI platforms. An Open Source BI platform provides a full spectrum of BI capabilities within a unified system that reduces the overhead for the development and management of each application, and lets the user feel like he/she was using a single BI solution. This paper proposes a comparative evaluation of three different Open Source BI platforms (namely JasperSoft, Pentaho and SpagoBI) aimed at understanding their current features, their future potentialities and their limits when adopted in real projects as well as a basis for research prototyping. Overall we try to understand if the open source phenomenon will be able to become a valid alternative to commercial platforms within the BI context.

  19. Open source Modeling and optimization tools for Planning

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-10

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

  20. Close connections between open science and open-source software

    OpenAIRE

    YouHua Chen; XueKe Lu; YouFang Chen

    2014-01-01

    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 ...

  1. Application of Open Source GIS in District Health Information Systems

    OpenAIRE

    Andresen, Trond; Vik, Lars Gunnar

    2005-01-01

    This thesis considers issues surrounding use and development of open source geographical information systems (GIS) as a part of the district health information systems in developing countries. The base for this thesis is field work done by the two authors in three different states in India in cooperation with the Health Information System Program India. The thesis looks into the general concepts of open source and geographical information systems in the Indian context, and present a GIS appli...

  2. Openness, Open Source, and the Veil of Ignorance

    OpenAIRE

    Scotchmer, Suzanne

    2010-01-01

    The open source movement evolved in the one industrial context where openness is not required by intellectual property law.1 Nevertheless, openness itself cannot be the driving force behind the open source movement. This is because openness can be achieved in many ways other than the GPL, for example, with proprietary licenses, or licenses that are even more permissive than the GPL, such as the BSD license. Early commentators explained this new development model by focussing on the m...

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

    Directory of Open Access Journals (Sweden)

    Mohamed R. Elabnody

    2015-08-01

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

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

    OpenAIRE

    Mohamed R. Elabnody

    2015-01-01

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

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

    Science.gov (United States)

    Shao, Yixi; Chen, Dong; Zhao, Bo

    2007-06-01

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

  6. 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.

  7. Open Source Software Compliance within the Government

    Science.gov (United States)

    2016-12-01

    concerns. DISCLAIMER: The contents of this report are not to be used for advertising , publication, or promotional purposes. Citation of trade names...copyright on their own, they act as a method to identify the copying of the larger, copyrighted material within the program. Easter Eggs are a hidden ...knowledge. Due to their unique and hidden nature, they are great markers of the original authorship and can be difficult to remove if they intentionally

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

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

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

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

    Science.gov (United States)

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

    2014-02-01

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

  10. 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.

  11. Rapid determination of capsaicinoids by colorimetric method

    OpenAIRE

    Ryu, Wang-Kyun; Kim, Hee-Woong; Kim, Geun-Dong; Rhee, Hae-Ik

    2016-01-01

    Capsaicinoids, the pungent component of chili peppers, are generally analyzed by precise analytical techniques, such as gas chromatography and high-performance liquid chromatography (HPLC), but these are not practical for the mass analyses of samples. To analyze mass samples rapidly, a colorimetric method was suggested. In this work, pigments and capsaicinoids were efficiently separated from chili pepper extract by sequential solid–liquid extraction and liquid–liquid extraction in test tubes ...

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

    Science.gov (United States)

    Wright, Jeremiah; Wagner, Andreas

    2008-06-29

    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. 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. 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.

  13. An open source, wireless capable miniature microscope system

    Science.gov (United States)

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

    2017-08-01

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

  14. 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.

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

    OpenAIRE

    Etienne Combrisson; Etienne Combrisson; Raphael Vallat; Jean-Baptiste Eichenlaub; Christian O'Reilly; Tarek Lajnef; Tarek Lajnef; Aymeric Guillot; Perrine M. Ruby; Karim Jerbi

    2017-01-01

    We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processin...

  16. Rapid Column Extraction method for SoilRapid Column Extraction method for Soil

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, Sherrod, L. III; Culligan, Brian K.

    2005-11-07

    The analysis of actinides in environmental soil and sediment samples is very important for environmental monitoring as well as for emergency preparedness. A new, rapid actinide separation method has been developed and implemented that provides total dissolution of large soil samples, high chemical recoveries and effective removal of matrix interferences. This method uses stacked TEVA Resin{reg_sign}, TRU Resin{reg_sign} and DGA-Resin{reg_sign} cartridges from Eichrom Technologies (Darien, IL, USA) that allows the rapid separation of plutonium (Pu) neptunium (Np), uranium (U), americium (Am), and curium (Cm) using a single multi-stage column combined with alpha spectrometry. The method combines a rapid fusion step for total dissolution to dissolve refractory analytes and matrix removal using cerium fluoride precipitation to remove the difficult soil matrix. By using vacuum box cartridge technology with rapid flow rates, sample preparation time is minimized.

  17. Open-source software platform for medical image segmentation applications

    Science.gov (United States)

    Namías, R.; D'Amato, J. P.; del Fresno, M.

    2017-11-01

    Segmenting 2D and 3D images is a crucial and challenging problem in medical image analysis. Although several image segmentation algorithms have been proposed for different applications, no universal method currently exists. Moreover, their use is usually limited when detection of complex and multiple adjacent objects of interest is needed. In addition, the continually increasing volumes of medical imaging scans require more efficient segmentation software design and highly usable applications. In this context, we present an extension of our previous segmentation framework which allows the combination of existing explicit deformable models in an efficient and transparent way, handling simultaneously different segmentation strategies and interacting with a graphic user interface (GUI). We present the object-oriented design and the general architecture which consist of two layers: the GUI at the top layer, and the processing core filters at the bottom layer. We apply the framework for segmenting different real-case medical image scenarios on public available datasets including bladder and prostate segmentation from 2D MRI, and heart segmentation in 3D CT. Our experiments on these concrete problems show that this framework facilitates complex and multi-object segmentation goals while providing a fast prototyping open-source segmentation tool.

  18. ExpertEyes: open-source, high-definition eyetracking.

    Science.gov (United States)

    Parada, Francisco J; Wyatte, Dean; Yu, Chen; Akavipat, Ruj; Emerick, Brandi; Busey, Thomas

    2015-03-01

    ExpertEyes is a low-cost, open-source package of hardware and software that is designed to provide portable high-definition eyetracking. The project involves several technological innovations, including portability, high-definition video recording, and multiplatform software support. It was designed for challenging recording environments, and all processing is done offline to allow for optimization of parameter estimation. The pupil and corneal reflection are estimated using a novel forward eye model that simultaneously fits both the pupil and the corneal reflection with full ellipses, addressing a common situation in which the corneal reflection sits at the edge of the pupil and therefore breaks the contour of the ellipse. The accuracy and precision of the system are comparable to or better than what is available in commercial eyetracking systems, with a typical accuracy of less than 0.4° and best accuracy below 0.3°, and with a typical precision (SD method) around 0.3° and best precision below 0.2°. Part of the success of the system comes from a high-resolution eye image. The high image quality results from uncasing common digital camcorders and recording directly to SD cards, which avoids the limitations of the analog NTSC format. The software is freely downloadable, and complete hardware plans are available, along with sources for custom parts.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Vaclav Petras

    2015-06-01

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

  1. 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!

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

  5. 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

  6. 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

  7. Open Source AV solution supporting In Situ Simulation

    DEFF Research Database (Denmark)

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

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

  8. Industrial open source solutions for product life cycle management

    Directory of Open Access Journals (Sweden)

    Jaime Campos

    2014-12-01

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

  9. Open Source Software and Schools: New Opportunities and Directions

    Directory of Open Access Journals (Sweden)

    Gary Hepburn

    2005-02-01

    Full Text Available Abstract: Integrating information and communication technology into schools has been challenging. A central component of the challenge is coping with the expense and usage restrictions of software that is installed on school computers. An alternative approach to the educational software problem is, however, emerging. This approach involves making greater use of open source software. In many cases open source software can effectively replace the proprietary or commercial software that dominates the educational computing landscape. Using this software option would result in decreased costs, increased flexibility, and increased opportunities to address social and ethical issues related to information and communication technology. In order to responsibly spend taxpayers’ money and to maximize the potential of information and communication technology in education, it is important that educators learn about open source software and challenge conceptions that give priority to proprietary software.

  10. Open Source Web Based Geospatial Processing with OMAR

    Directory of Open Access Journals (Sweden)

    Mark Lucas

    2009-01-01

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

  11. 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.

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

    DEFF Research Database (Denmark)

    Edwards, Kasper

    2001-01-01

    of epistemic communities does indeed contribute to the understanding of open source software development. But, the important learning process of open source software development is not readily explained. The paper then introduces situated learning and legitimate peripheral participation as theoretical......This paper analyses open source software (OSS) development as an epistemic community where each individual project is perceived as a single epistemic community. OSS development is a learning process where the involved parties contribute to, and learn from the community. It is discovered that theory...... perspectives. This allows the learning process to be part of the activities in the epistemic community. The combination of situated learning and epistemic communities is shown to be fruitful and capable of explaining some of the empirical observations. In particular the combination of theories can shed light...

  13. The Challenges of Open Source Software in IT Adoption

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  14. Applying open source innovation approaches in developing business innovation

    DEFF Research Database (Denmark)

    Aagaard, Annabeth; Lindgren, Peter

    2015-01-01

    More and more companies are pursuing continuous innovation through different types of open source innovation and across different partners. The growing interest in open innovation (OI) originates both from the academic community as well as amongst practitioners motivating further investigation...... and managed effectively in developing business model innovation. The aim of this paper is therefore to close this research gap and to provide new knowledge within the research field of OI and OI applications. Thus, in the present study we explore the facilitation and management of open source innovation...

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

    DEFF Research Database (Denmark)

    Vujovic, Sladjana; Ulhøi, John Parm

    2006-01-01

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

  16. A Survey of Open Source Tools for Business Intelligence

    DEFF Research Database (Denmark)

    Thomsen, Christian; Pedersen, Torben Bach

    2009-01-01

    The industrial use of open source Business Intelligence (BI) tools is becoming more common, but is still not as widespread as for other types of software. It is therefore of interest to explore which possibilities are available for open source BI and compare the tools. In this survey paper, we...... exist mature and powerful tools in all these categories. However, the functionality still falls somewhat short of that found in commercial tools. [Article copies are available for purchase from InfoSci-on-Demand.com]...

  17. Impact of Open Source software on the environmental protection

    Directory of Open Access Journals (Sweden)

    D. Viduka

    2015-03-01

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

  18. Open-Source Neural Machine Translation API Server

    Directory of Open Access Journals (Sweden)

    Tars Sander

    2017-10-01

    Full Text Available We introduce an open-source implementation of a machine translation API server. The aim of this software package is to enable anyone to run their own multi-engine translation server with neural machine translation engines, supporting an open API for client applications. Besides the hub with the implementation of the client API and the translation service providers running in the background we also describe an open-source demo web application that uses our software package and implements an online translation tool that supports collecting translation quality comparisons from users.

  19. Open source MySQL Browser for Open Innovation

    Directory of Open Access Journals (Sweden)

    Radu Bucea-Manea-Tonis

    2014-07-01

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

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

    Marturano, Antonio

    2011-01-01

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

  2. Final Report of the Open Source Software Licence Task Force

    CERN Document Server

    Fluckiger, François

    2012-01-01

    Following a proposal by the author of this report, the Heads of FP Department and IT Department, recognizing that the situation regarding Open Source Software licensing at CERN needed clarification, created the Open Source Licence Task Force (OSL Task Force) to formulate recommendations on which licence should be used for software developed at CERN. This document is the Main Volume of the final report of the OSL Task Force. It contains eight recommendations with their rationale. It is complemented by a separate Volume of Annexes and two operational notes (Instructions for Specifying the licence terms and Form to document OSL cases).

  3. Developing open source, self-contained disease surveillance software applications for use in resource-limited settings

    Directory of Open Access Journals (Sweden)

    Campbell Timothy C

    2012-09-01

    Full Text Available Abstract Background Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness. Methods As components of its Suite for Automated Global bioSurveillance (SAGES program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies. Results ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system. Conclusions OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations.

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

    Science.gov (United States)

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

    2015-03-01

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

  5. Learning from open source software projects to improve scientific review.

    Science.gov (United States)

    Ghosh, Satrajit S; Klein, Arno; Avants, Brian; Millman, K Jarrod

    2012-01-01

    Peer-reviewed publications are the primary mechanism for sharing scientific results. The current peer-review process is, however, fraught with many problems that undermine the pace, validity, and credibility of science. We highlight five salient problems: (1) reviewers are expected to have comprehensive expertise; (2) reviewers do not have sufficient access to methods and materials to evaluate a study; (3) reviewers are neither identified nor acknowledged; (4) there is no measure of the quality of a review; and (5) reviews take a lot of time, and once submitted cannot evolve. We propose that these problems can be resolved by making the following changes to the review process. Distributing reviews to many reviewers would allow each reviewer to focus on portions of the article that reflect the reviewer's specialty or area of interest and place less of a burden on any one reviewer. Providing reviewers materials and methods to perform comprehensive evaluation would facilitate transparency, greater scrutiny, and replication of results. Acknowledging reviewers makes it possible to quantitatively assess reviewer contributions, which could be used to establish the impact of the reviewer in the scientific community. Quantifying review quality could help establish the importance of individual reviews and reviewers as well as the submitted article. Finally, we recommend expediting post-publication reviews and allowing for the dialog to continue and flourish in a dynamic and interactive manner. We argue that these solutions can be implemented by adapting existing features from open-source software management and social networking technologies. We propose a model of an open, interactive review system that quantifies the significance of articles, the quality of reviews, and the reputation of reviewers.

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

    Science.gov (United States)

    Liang, S. Ng; Tan, K. O.; Lai Clement, T. H.; Ng, S. K.; Mohammed, A. H. Ali; Mailah, Musa; Azhar Yussof, Wan; Hamedon, Zamzuri; Yussof, Zulkifli

    2016-02-01

    Recent developments in open source hardware and software platforms (Android, Arduino, Linux, OpenCV etc.) have enabled rapid development of previously expensive and sophisticated system within a lower budget and flatter learning curves for developers. Using these platform, we designed and developed a Java-based 3D robotic simulation system, with graph database, which is integrated in online and offline modes with an Android-Arduino based rubbish picking remote control car. The combination of the open source hardware and software system created a flexible and expandable platform for further developments in the future, both in the software and hardware areas, in particular in combination with graph database for artificial intelligence, as well as more sophisticated hardware, such as legged or humanoid robots.

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

    Science.gov (United States)

    Hahn, Erin; Blazes, David; Lewis, Sheri

    2016-01-01

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

  8. Large Data Visualization with Open-Source Tools

    CERN Multimedia

    CERN. Geneva

    2015-01-01

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

  9. Security Vulnerabilities of the Web Based Open Source Information ...

    African Journals Online (AJOL)

    This paper exposes security vulnerabilities of the web based Open Source Information Systems (OSIS) from both system angle and human perspectives.It shows the extent of risk that can likely hinder adopting organization from attaning full intended benefits of using OSIS software. To undertake this study, a case study ...

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

    NARCIS (Netherlands)

    Koper, Rob

    2007-01-01

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

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

    DEFF Research Database (Denmark)

    Schröder, Philipp J.H.; Bitzer, Jürgen

    2006-01-01

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

  12. ARLearn - Open source mobile application platform for learning

    NARCIS (Netherlands)

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

    2013-01-01

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

  13. 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.

  14. Free and Open Source Software for librarians and libraries | Keats ...

    African Journals Online (AJOL)

    Free and Open Source Software (FOSS) is a national priority in South Africa, and is increasingly recognized as a means to achieve quality, lower costs, create agility and foster innovation. All of these are things libraries need to accomplish, so a survey of the FOSS tools available to support library functions or the role of ...

  15. Zotero : a free and open-source reference manager

    DEFF Research Database (Denmark)

    Courraud, Julie

    2014-01-01

    Zotero is a free, open-source reference management program compatible with Linux®, Mac®, and Windows® operating systems. Libraries are backed up online allowing sharing between computers and even multiple users. Zotero makes it easy to keep your reference library organised and ‘clean’. Reference...

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

    Science.gov (United States)

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

    2015-01-01

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

  17. Critical Analysis on Open Source LMSs Using FCA

    Science.gov (United States)

    Sumangali, K.; Kumar, Ch. Aswani

    2013-01-01

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

  18. Open Source Solutions for Libraries: ABCD vs Koha

    Science.gov (United States)

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

    2013-01-01

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

  19. Digital Preservation in Open-Source Digital Library Software

    Science.gov (United States)

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

    2012-01-01

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

  20. Higher Education Sub-Cultures and Open Source Adoption

    Science.gov (United States)

    van Rooij, Shahron Williams

    2011-01-01

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

  1. Electronic Health Delivery using Open Source Software and ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Electronic Health Delivery using Open Source Software and Personal Digital Assistants (Argentina and Colombia). This project aims to ... The project will be carried out by the Universidad Austral de Argentina through its centre for interdisciplinary studies and management and the economy of health (CEGES). CEGES will ...

  2. Free and Open Source Management Information Systems and ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    What is the impact of introducing an automated management information system within a microfinance institution or savings and credit cooperative on the employees, the clients and the business processes? The project will involve deployment of an open source management information system (Mifos Vanilla) in two ...

  3. The Case for Open Source Software in Digital Forensics

    Science.gov (United States)

    Zanero, Stefano; Huebner, Ewa

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

  4. Is Open Source the ERP Cure-All?

    Science.gov (United States)

    Panettieri, Joseph C.

    2008-01-01

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

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

    Science.gov (United States)

    Zollers, Michael W.

    2014-09-01

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

  6. Free and Open Source Software in North African Universities | CRDI ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Three types of tools are to be developed: software for the technological infrastructure (such as e-mail), software for administration and software for online services, especially distance education. Project partners will come from the university, government, and the private and associative sectors. Open Source in Morocco ...

  7. 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,

  8. Open-Source Urbanism: Creating, Multiplying and Managing Urban Commons

    Directory of Open Access Journals (Sweden)

    Karin Bradley

    2015-06-01

    Full Text Available Within contemporary architecture and urbanism there is marked interest in urban commons. This paper explores the creation of temporary urban commons, or, more specifically, what can be called ‘open-source urbanism’. Citing two practices – urban commons initiated by Atelier d’architecture autogérée in Paris, and Park(ing Day initiated by San Francisco-based Rebar – I argue that these practices can be understood as open-source urbanism since their initiators act as open-source programmers, constructing practice manuals to be freely copied, used, developed and shared, thus producing self-managed commons. Although this tradition of ‘commoning’ is not new, it is currently being reinvented with the use of digital technologies. Combining Elinor Ostrom’s analysis of self-managed natural resource commons with Yochai Benkler’s assertion that commons-based peer production constitutes a ‘third mode of production’ that lies beyond capitalism, socialism and their blends, I argue that open-source urbanism critiques both government and privately-led urban development by advancing a form of postcapitalist urbanism.

  9. Modular Open-Source Software for Item Factor Analysis

    Science.gov (United States)

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

    2015-01-01

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

  10. Exploring Coordination Structures in Open Source Software Development

    NARCIS (Netherlands)

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

    2007-01-01

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

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

    Science.gov (United States)

    Paton, C; Karopka, T

    2017-08-01

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

  12. Rapid determination of capsaicinoids by colorimetric method.

    Science.gov (United States)

    Ryu, Wang-Kyun; Kim, Hee-Woong; Kim, Geun-Dong; Rhee, Hae-Ik

    2017-10-01

    Capsaicinoids, the pungent component of chili peppers, are generally analyzed by precise analytical techniques, such as gas chromatography and high-performance liquid chromatography (HPLC), but these are not practical for the mass analyses of samples. To analyze mass samples rapidly, a colorimetric method was suggested. In this work, pigments and capsaicinoids were efficiently separated from chili pepper extract by sequential solid-liquid extraction and liquid-liquid extraction in test tubes followed by a colorimetric analysis on the capsaicinoids by a selective chromogenic reaction with Gibbs reagent (2,6-dichloroquinone-4-chloroimide). In the comparison of the capsaicinoid content by the colorimetric method and HPLC using acetone extracts of fresh pepper and dry red pepper as samples, R2 was 0.9973 and 0.9816, respectively, which shows a high linear correlation. In addition, a minimum of 1 μg/mL capsaicinoids can be detected and it was therefore determined that the method can efficiently analyze a great quantity of samples in a short time. Copyright © 2016. Published by Elsevier B.V.

  13. Rapid determination of capsaicinoids by colorimetric method

    Directory of Open Access Journals (Sweden)

    Wang-Kyun Ryu

    2017-10-01

    Full Text Available Capsaicinoids, the pungent component of chili peppers, are generally analyzed by precise analytical techniques, such as gas chromatography and high-performance liquid chromatography (HPLC, but these are not practical for the mass analyses of samples. To analyze mass samples rapidly, a colorimetric method was suggested. In this work, pigments and capsaicinoids were efficiently separated from chili pepper extract by sequential solid–liquid extraction and liquid–liquid extraction in test tubes followed by a colorimetric analysis on the capsaicinoids by a selective chromogenic reaction with Gibbs reagent (2,6-dichloroquinone-4-chloroimide. In the comparison of the capsaicinoid content by the colorimetric method and HPLC using acetone extracts of fresh pepper and dry red pepper as samples, R2 was 0.9973 and 0.9816, respectively, which shows a high linear correlation. In addition, a minimum of 1 μg/mL capsaicinoids can be detected and it was therefore determined that the method can efficiently analyze a great quantity of samples in a short time.

  14. wradlib - An Open Source Library for Weather Radar Data Processing

    Science.gov (United States)

    Heistermann, M.; Pfaff, Th.; Jacobi, S.

    2012-04-01

    Weather radar data is potentially useful in meteorology, hydrology, disaster prevention and mitigation. Its ability to provide information on precipitation with high spatial and temporal resolution over large areas makes it an invaluable tool for short term weather forecasting or flash flood forecasting. The indirect method of measuring the precipitation field, however, leads to a significant number of data artifacts, which usually must be removed or dealt with before the data can be used with acceptable quality. Data processing requires e.g. the transformation of measurements from polar to cartesian coordinates and from reflectivity to rainfall intensity, the composition of data from several radar sites in a common grid, clutter identification and removal, attenuation and VPR corrections, gauge adjustment and visualization. The complexity of these processing steps is a major obstacle for many potential users in science and practice. Adequate tools are available either only at significant costs with no access to the uncerlying source code, or they are incomplete, insufficiently documented and intransparent. The wradlib project has been initiated in order to lower the barrier for potential users of weather radar data in the geosciences and to provide a common platform for research on new algorithms. wradlib is an open source library for the full range of weather radar related processing algorithms, which is well documented and easy to use. The main parts of the library are currently implemented in the python programming language. Python is well known both for its ease of use as well as its ability to integrate code written in other programming languages like Fortran or C/C++. The well established Numpy and Scipy packages are used to provide decent performance for pure Python implementations of algorithms. We welcome contributions written in any computer language and will try to make them accessible from Python. We would like to present the current state of this

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

    Science.gov (United States)

    Årdal, Christine; Røttingen, John-Arne

    2012-01-01

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

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

    Science.gov (United States)

    Årdal, Christine; Røttingen, John-Arne

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-03-24

    To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14,221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data-driven precision medicine. As an open-source visualisation

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

    Science.gov (United States)

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

    2013-04-01

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

  19. 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

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

    Science.gov (United States)

    Pfaffman, Jay

    2008-01-01

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

  1. Applications of Open Source 3-D Printing on Small Farms

    Directory of Open Access Journals (Sweden)

    Joshua M. Pearce

    2013-12-01

    Full Text Available There is growing evidence that low-cost open-source 3-D printers can reduce costs by enabling distributed manufacturing of substitutes for both specialty equipment and conventional mass-manufactured products. The rate of 3-D printable designs under open licenses is growing exponentially and there arealready hundreds of designs applicable to small-scale organic farming. It has also been hypothesized that this technology could assist sustainable development in rural communities that rely on small-scale organic agriculture. To gauge the present utility of open-source 3-D printers in this organic farm context both in the developed and developing world, this paper reviews the current open-source designs available and evaluates the ability of low-cost 3-D printers to be effective at reducing the economic costs of farming.This study limits the evaluation of open-source 3-D printers to only the most-developed fused filament fabrication of the bioplastic polylactic acid (PLA. PLA is a strong biodegradable and recyclable thermoplastic appropriate for a range of representative products, which are grouped into five categories of prints: handtools, food processing, animal management, water management and hydroponics. The advantages and shortcomings of applying 3-D printing to each technology are evaluated. The results show a general izabletechnical viability and economic benefit to adopting open-source 3-D printing for any of the technologies, although the individual economic impact is highly dependent on needs and frequency of use on a specific farm. Capital costs of a 3-D printer may be saved from on-farm printing of a single advanced analytical instrument in a day or replacing hundreds of inexpensive products over a year. In order for the full potential of open-source 3-D printing to be realized to assist organic farm economic resiliency and self-sufficiency, future work is outlined in five core areas: designs of 3-D printable objects, 3-D printing

  2. Open source marketing: Camel cigarette brand marketing in the "Web 2.0" world.

    Science.gov (United States)

    Freeman, B; Chapman, S

    2009-06-01

    The international trend towards comprehensive bans on tobacco advertising has seen the tobacco industry become increasingly innovative in its approach to marketing. Further fuelling this innovation is the rapid evolution and accessibility of web-based technology. The internet, as a relatively unregulated marketing environment, provides many opportunities for tobacco companies to pursue their promotional ambitions. In this paper, "open source marketing" is considered as a vehicle that has been appropriated by the tobacco industry, through a case study of efforts to design the packaging for the Camel Signature Blends range of cigarettes. Four sources are used to explore this case study including a marketing literature search, a web-based content search via the Google search engine, interviews with advertising trade informants and an analysis of the Camel brand website. RJ Reynolds (RJR) has proven to be particularly innovative in designing cigarette packaging. RJR engaged with thousands of consumers through their Camel brand website to design four new cigarette flavours and packages. While the Camel Signature Blends packaging designs were subsequently modified for the retail market due to problems arising with their cartoon-like imagery, important lessons arise on how the internet blurs the line between marketing and market research. Open source marketing has the potential to exploit advertising ban loopholes and stretch legal definitions in order to generate positive word of mouth about tobacco products. There are also lessons in the open source marketing movement for more effective tobacco control measures including interactive social marketing campaigns and requiring plain packaging of tobacco products.

  3. Open source machine-learning algorithms for the prediction of optimal cancer drug therapies.

    Science.gov (United States)

    Huang, Cai; Mezencev, Roman; McDonald, John F; Vannberg, Fredrik

    2017-01-01

    Precision medicine is a rapidly growing area of modern medical science and open source machine-learning codes promise to be a critical component for the successful development of standardized and automated analysis of patient data. One important goal of precision cancer medicine is the accurate prediction of optimal drug therapies from the genomic profiles of individual patient tumors. We introduce here an open source software platform that employs a highly versatile support vector machine (SVM) algorithm combined with a standard recursive feature elimination (RFE) approach to predict personalized drug responses from gene expression profiles. Drug specific models were built using gene expression and drug response data from the National Cancer Institute panel of 60 human cancer cell lines (NCI-60). The models are highly accurate in predicting the drug responsiveness of a variety of cancer cell lines including those comprising the recent NCI-DREAM Challenge. We demonstrate that predictive accuracy is optimized when the learning dataset utilizes all probe-set expression values from a diversity of cancer cell types without pre-filtering for genes generally considered to be "drivers" of cancer onset/progression. Application of our models to publically available ovarian cancer (OC) patient gene expression datasets generated predictions consistent with observed responses previously reported in the literature. By making our algorithm "open source", we hope to facilitate its testing in a variety of cancer types and contexts leading to community-driven improvements and refinements in subsequent applications.

  4. PACS for Bhutan: a cost effective open source architecture for emerging countries.

    Science.gov (United States)

    Ratib, Osman; Roduit, Nicolas; Nidup, Dechen; De Geer, Gerard; Rosset, Antoine; Geissbuhler, Antoine

    2016-10-01

    This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer. • Open source imaging informatics platforms can provide cost-effective alternatives for PACS • Robust and cost-effective open architecture can provide adequate solutions for emerging countries • Imaging informatics is often lacking in hospitals equipped with digital modalities.

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

    CERN Document Server

    Chisholm, Andrew

    2016-01-01

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

  6. APPLICABILITY OF THE OPEN SOURCE PACKAGE OPENFOAM FOR NUMERICAL MODELING SEPARATED FLOW AROUND AN AIRCRAFT AT SUBSONIC AND SUPERSONIC SPEEDS

    Directory of Open Access Journals (Sweden)

    V. T. Kalugin

    2014-01-01

    Full Text Available Applicability of the open source package OpenFOAM for numerical modeling different separated flows have been considered in the cases studies of the influence of vortices and their interaction with lifting surfaces, features of the flow field of rapidly rotating aerial vehicles at presence of separation flow and study of supersonic separated flow field in flight controls.

  7. 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

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

    Directory of Open Access Journals (Sweden)

    Veronika Abramova

    2017-05-01

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

  9. Monitoring Network and Service Availability with Open-Source Software

    Directory of Open Access Journals (Sweden)

    T. Michael Silver

    2010-03-01

    Full Text Available Silver describes the implementation of a monitoring system using an open-source software package to improve the availability of services and reduce the response time when troubles occur. He provides a brief overview of the literature available on monitoring library systems, and then describes the implementation of Nagios, an open-source network monitoring system, to monitor a regional library system’s servers and wide area network. Particular attention is paid to using the plug-in architecture to monitor library services effectively. The author includes example displays and configuration files.   Editor’s note: This article is the winner of the LITA/Ex Libris Writing Award, 2009.

  10. Development open source microcontroller based temperature data logger

    Science.gov (United States)

    Abdullah, M. H.; Che Ghani, S. A.; Zaulkafilai, Z.; Tajuddin, S. N.

    2017-10-01

    This article discusses the development stages in designing, prototyping, testing and deploying a portable open source microcontroller based temperature data logger for use in rough industrial environment. The 5V powered prototype of data logger is equipped with open source Arduino microcontroller for integrating multiple thermocouple sensors with their module, secure digital (SD) card storage, liquid crystal display (LCD), real time clock and electronic enclosure made of acrylic. The program for the function of the datalogger is programmed so that 8 readings from the thermocouples can be acquired within 3 s interval and displayed on the LCD simultaneously. The recorded temperature readings at four different points on both hydrodistillation show similar profile pattern and highest yield of extracted oil was achieved on hydrodistillation 2 at 0.004%. From the obtained results, this study achieved the objective of developing an inexpensive, portable and robust eight channels temperature measuring module with capabilities to monitor and store real time data.

  11. Computer aided die design: A new open-source methodology

    Science.gov (United States)

    Carneiro, Olga Sousa; Rajkumar, Ananth; Ferrás, Luís Lima; Fernandes, Célio; Sacramento, Alberto; Nóbrega, João Miguel

    2017-05-01

    In this work we present a detailed description of how to use open source based computer codes to aid the design of complex profile extrusion dies, aiming to improve its flow distribution. The work encompasses the description of the overall open-source die design methodology, the implementation of the energy conservation equation in an existing OpenFOAM® solver, which will be then capable of simulating the steady non-isothermal flow of an incompressible generalized Newtonian fluid, and two case studies to illustrate the capabilities and practical usefulness of the developed methodology. The results obtained with these case studies, used to solve real industrial problems, demonstrate that the computational design aid is an excellent alternative, from economical and technical points of view, to the experimental trial-and-error procedure commonly used in industry.

  12. Survivability as a Tool for Evaluating Open Source Software

    Science.gov (United States)

    2015-06-01

    lacking. [Online]. Available: http://ostatic.com/blog/its-2014-and-open-source-documentation-is-still- lacking [37] W. Wagner, Lightning Bugs and Other...licenses [46] R. E. Ball , “Southeast Asia Conflict, 1964-1973,” in The Fundamentals of Aircraft Combat Survivability Analysis and Design, Second Edition, 2nd... Ball , The Fundamentals of Aircraft Survivability, Analysis and Design, J. A. Schetz, Ed. AIAA, 2003. [53] Gitorious. (2015). FlightGear. [Online

  13. The Airplane as an Open-Source Invention

    OpenAIRE

    Peter B. Meyer

    2013-01-01

    Airplanes were invented after decades of experimentation in many countries through a process we can call open-source innovation. Experimenters, inventors, and writers contributed to the airplane’s development by sharing information in publications, in clubs, by writing letters and by visiting. The hundreds of aeronautical patents before 1900 were treated like publications, not like claims to intellectual property. Inventors of modern airplanes copied earlier designs, analogously to advances i...

  14. Analyzing huge pathology images with open source software.

    Science.gov (United States)

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

    2013-06-06

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

  15. Analyzing huge pathology images with open source software

    OpenAIRE

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

    2013-01-01

    International audience; BACKGROUND: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer¿s memory. Moreover, there is no standard format. Therefore, most common open source too...

  16. The 'Grey' Intersection of Open Source information and Intelligence

    OpenAIRE

    Crowe, June (IIa); Davidson, Thomas S. (Open Source Research Group); GreyNet, Grey Literature Network Service

    2008-01-01

    The U.S. Government intelligence community (IC) is relying less on 'classified' information as a sole source and is moving toward an 'all source' product that includes open source information. Gradually, this change will result in a more comprehensive, virtual IC that will enhance or replace the smaller, classified collections of individual government bureaucracies. This has created an emerging paradigm involving technology, outsourcing, and relationships both inside and outside of the IC tha...

  17. Comparison of open source network intrusion detection systems

    OpenAIRE

    Rødfoss, Jonas Taftø

    2011-01-01

    Many companies and organizations offer IT-services (news papers, social sites, web developers and etc.) to the public, and those services needs to be protected. The amount of computer threats are increasing drastically, and many attacks are directed to those services companies offer. Larger companies have the economy to buy expensive security tools to protect their services, while smaller companies may have the same economy. Open source is an interesting field for those who ...

  18. The Determinants of Open Source Quality: An Empirical Investigation

    OpenAIRE

    Ioana Popovici

    2007-01-01

    Open source (OS) licenses differ in the conditions under which licensors and OS contributors are allowed to modify and redistribute the source code. While recent research has explored the determinants of license choice, we know little about the impact of license choice on project success. In this paper, we measure success by the speed with which programming bugs are fixed. Using data obtained from SourceForge.net, a free service that hosts OS projects, we test whether the license chosen by pr...

  19. The Open-Source Alternative in E-Government

    Directory of Open Access Journals (Sweden)

    Catalin Vrabie

    2013-08-01

    Full Text Available The last decade has changed again the face of electronic world: from Web 2.0 to open source software; from e-(electronic to m-(mobile and now to touch. For Web developers is a real challenge to make compatible interfaces to all existing Internet browsers. This proves to be even more expensive than the application itself (Softnet; 2012; SIVECO, 2012. From the point of view of the big software development companies these events are just new challenges because they afford to have many employees with different skills and by that being able to cope with market demands. But what happens with the e-government projects at the local level? Budgets are small, so hiring a company specialized in Web application development is sometimes too expensive, this responsibility usually falls in many cases on the employees of the IT department (Vrabie, 2011. If we add to this software component the hardware required for hosting the Web page inside, the budgets are already completely exceeded (or obviously they can choose some other cheap solution but whose reliability is very poor – reason for dissatisfaction among citizens. The importance of the Web platforms for interacting with citizens is very well known (Friedman, 2005; Craig; 2006; Baltac, 2011. In this context, this paper aims to examine in terms of costs, the investments in open-source applications in parallel with the use of social networks as used today. The research methodology is using for the first time an adapted version of cost-effectiveness analysis. Empirical research will be carried out on two platforms of e-Government – one of them developed inside on an open-source solution - used to support a complete interaction with the citizens. The working hypothesis starts from the fact that open source software is cheaper than those developed inside – but of course this is a question to debate at.

  20. Robust, open-source removal of systematics in Kepler data

    OpenAIRE

    Aigrain, S.; Parviainen, H.; Roberts, S.; Reece, S.; Evans, T.

    2017-01-01

    We present ARC2 (Astrophysically Robust Correction 2), an open-source Python-based systematics-correction pipeline to correct for the Kepler prime mission long cadence light curves. The ARC2 pipeline identifies and corrects any isolated discontinuities in the light curves, then removes trends common to many light curves. These trends are modelled using the publicly available co-trending basis vectors, within an (approximate) Bayesian framework with `shrinkage' priors to minimise the risk of o...

  1. Free and open-source automated 3-D microscope.

    Science.gov (United States)

    Wijnen, Bas; Petersen, Emily E; Hunt, Emily J; Pearce, Joshua M

    2016-11-01

    Open-source technology not only has facilitated the expansion of the greater research community, but by lowering costs it has encouraged innovation and customizable design. The field of automated microscopy has continued to be a challenge in accessibility due the expense and inflexible, noninterchangeable stages. This paper presents a low-cost, open-source microscope 3-D stage. A RepRap 3-D printer was converted to an optical microscope equipped with a customized, 3-D printed holder for a USB microscope. Precision measurements were determined to have an average error of 10 μm at the maximum speed and 27 μm at the minimum recorded speed. Accuracy tests yielded an error of 0.15%. The machine is a true 3-D stage and thus able to operate with USB microscopes or conventional desktop microscopes. It is larger than all commercial alternatives, and is thus capable of high-depth images over unprecedented areas and complex geometries. The repeatability is below 2-D microscope stages, but testing shows that it is adequate for the majority of scientific applications. The open-source microscope stage costs less than 3-9% of the closest proprietary commercial stages. This extreme affordability vastly improves accessibility for 3-D microscopy throughout the world. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  2. Open Source Clinical NLP – More than Any Single System

    Science.gov (United States)

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

    2014-01-01

    The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP’s mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice. PMID:25954581

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

    Science.gov (United States)

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

    2014-01-01

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

  4. Evaluating open-source cloud computing solutions for geosciences

    Science.gov (United States)

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

    2013-09-01

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

  5. Decision tree approach for classification of remotely sensed satellite data using open source support

    Science.gov (United States)

    Sharma, Richa; Ghosh, Aniruddha; Joshi, P. K.

    2013-10-01

    In this study, an attempt has been made to develop a decision tree classification (DTC) algorithm for classification of remotely sensed satellite data (Landsat TM) using open source support. The decision tree is constructed by recursively partitioning the spectral distribution of the training dataset using WEKA, open source data mining software. The classified image is compared with the image classified using classical ISODATA clustering and Maximum Likelihood Classifier (MLC) algorithms. Classification result based on DTC method provided better visual depiction than results produced by ISODATA clustering or by MLC algorithms. The overall accuracy was found to be 90% (kappa = 0.88) using the DTC, 76.67% (kappa = 0.72) using the Maximum Likelihood and 57.5% (kappa = 0.49) using ISODATA clustering method. Based on the overall accuracy and kappa statistics, DTC was found to be more preferred classification approach than others.

  6. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    Science.gov (United States)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain

  7. THOR: an open-source exo-GCM

    Science.gov (United States)

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

    2015-12-01

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

  8. 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

  9. Open Source Information Technologies Approach for Moddeling of Ankle-Foot Orthosis

    OpenAIRE

    Milusheva, Slavyana; Karastanev, Stefan; Toshev, Yuli

    2007-01-01

    Computer modeling is a perspective method for optimal design of prosthesis and orthoses. The study is oriented to develop modular ankle foot orthosis (MAFO) to assist the very frequently observed gait abnormalities relating the human ankle-foot complex using CAD modeling. The main goal is to assist the ankle- foot flexors and extensors during the gait cycle (stance and swing) using torsion spring. Utilizing 3D modeling and animating open source software (Blender 3D), it is possibl...

  10. Fiji: an open-source platform for biological-image analysis.

    Science.gov (United States)

    Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

    2012-06-28

    Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

  11. 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.

  12. Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.

    Science.gov (United States)

    Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

    2016-01-01

    This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems.

  13. Practical Experiences of Building an IPFIX Based Open Source Botnet Detector

    Directory of Open Access Journals (Sweden)

    Mark Graham

    2016-03-01

    Full Text Available The academic study of flow-based malware detection has primarily focused on NetFlow v5 and v9. In 2013 IPFIX was ratified as the flow export standard. As part of a larger project to develop protection methods for Cloud Service Providers from botnet threats, this paper considers the challenges involved in designing an open source IPFIX based botnet detection function. This paper describes how these challenges were overcome and presents an open source system built upon Xen hypervisor and Open vSwitch that is able to display botnet traffic within Cloud Service Provider-style virtualised environments. The system utilises Euler property graphs to display suspect “botnests”. The conceptual framework presented provides a vendor-neutral, real-time detection mechanism for monitoring botnet communication traffic within cloud architectures and the Internet of Things.

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

    DEFF Research Database (Denmark)

    Johansen, Peter; Richter, Stine R; Balslev-Harder, Marie

    2016-01-01

    : The pipeline correctly detected 27/27 trisomy 21, 4/4 trisomy 18, and 3/3 trisomy 13 fetuses. Neither false negatives nor false positives (chromosomes 13, 18, and 21) were observed in our validation dataset. Fetal sex was identified correctly in all but one triploid fetus (172/173). SeqFF showed a strong...... correlation (R(2)  = 0.72) to Y-chromosomal content of the male fetus samples. DISCUSSION: We have implemented NIPT into Danish health care using published open source scripts for autosomal aneuploidy detection and fetal DNA fraction estimation showing excellent false negative and false positive rates. Seq......OBJECTIVE: The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis. METHODS: Plasma-derived DNA from a total of 375...

  15. 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.

  16. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).

    Science.gov (United States)

    Kulp, Daniel W; Subramaniam, Sabareesh; Donald, Jason E; Hannigan, Brett T; Mueller, Benjamin K; Grigoryan, Gevorg; Senes, Alessandro

    2012-07-30

    We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open-source software, freely downloadable at http://msl-libraries.org. We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods. Copyright © 2012 Wiley Periodicals, Inc.

  17. Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.

    Science.gov (United States)

    Marc, David T; Khairat, Saif S

    2014-01-01

    The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

  18. MicMac GIS application: free open source

    Science.gov (United States)

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

    2016-10-01

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

  19. OSeMOSYS: The Open Source Energy Modeling System

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-10-15

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

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

    Science.gov (United States)

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

    2010-09-27

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

  1. Diagnosing turbulence for research aircraft safety using open source toolkits

    Directory of Open Access Journals (Sweden)

    T.J. Lang

    Full Text Available Open source software toolkits have been developed and applied to diagnose in-cloud turbulence in the vicinity of Earth science research aircraft, via analysis of ground-based Doppler radar data. Based on multiple retrospective analyses, these toolkits show promise for detecting significant turbulence well prior to cloud penetrations by research aircraft. A pilot study demonstrated the ability to provide mission scientists turbulence estimates in near real time during an actual field campaign, and thus these toolkits are recommended for usage in future cloud-penetrating aircraft field campaigns.

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

    OpenAIRE

    Casanovas, Pompeu

    2014-01-01

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

  3. pyLIMA : an open source microlensing software

    Science.gov (United States)

    Bachelet, Etienne

    2017-01-01

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

  4. Open Source Next Generation Visualization Software for Interplanetary Missions

    Science.gov (United States)

    Trimble, Jay; Rinker, George

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Andrei IONESCU

    2015-01-01

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

  6. Review on open source operating systems for internet of things

    Science.gov (United States)

    Wang, Zhengmin; Li, Wei; Dong, Huiliang

    2017-08-01

    Internet of Things (IoT) is an environment in which everywhere and every device became smart in a smart world. Internet of Things is growing vastly; it is an integrated system of uniquely identifiable communicating devices which exchange information in a connected network to provide extensive services. IoT devices have very limited memory, computational power, and power supply. Traditional operating systems (OS) have no way to meet the needs of IoT systems. In this paper, we thus analyze the challenges of IoT OS and survey applicable open source OSs.

  7. Infomaki: An Open Source, Lightweight Usability Testing Tool

    Directory of Open Access Journals (Sweden)

    Michael Lascarides

    2009-11-01

    Full Text Available Infomaki is an open source "lightweight" usability testing tool developed by the New York Public Library to evaluate new designs for the NYPL.org web site and uncover insights about our patrons. Designed from the ground up to be as respectful of the respondents' time as possible, it presents respondents with a single question at a time from a pool of active questions. In just over seven months of use, it has fielded over 100,000 responses from over 10,000 respondents.

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  10. IQM: an extensible and portable open source application for image and signal analysis in Java.

    Directory of Open Access Journals (Sweden)

    Philipp Kainz

    Full Text Available Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3 image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM's image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis.

  11. IQM: an extensible and portable open source application for image and signal analysis in Java.

    Science.gov (United States)

    Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

    2015-01-01

    Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM's image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis.

  12. Dynamic robustness of knowledge collaboration network of open source product development community

    Science.gov (United States)

    Zhou, Hong-Li; Zhang, Xiao-Dong

    2018-01-01

    As an emergent innovative design style, open source product development communities are characterized by a self-organizing, mass collaborative, networked structure. The robustness of the community is critical to its performance. Using the complex network modeling method, the knowledge collaboration network of the community is formulated, and the robustness of the network is systematically and dynamically studied. The characteristics of the network along the development period determine that its robustness should be studied from three time stages: the start-up, development and mature stages of the network. Five kinds of user-loss pattern are designed, to assess the network's robustness under different situations in each of these three time stages. Two indexes - the largest connected component and the network efficiency - are used to evaluate the robustness of the community. The proposed approach is applied in an existing open source car design community. The results indicate that the knowledge collaboration networks show different levels of robustness in different stages and different user loss patterns. Such analysis can be applied to provide protection strategies for the key users involved in knowledge dissemination and knowledge contribution at different stages of the network, thereby promoting the sustainable and stable development of the open source community.

  13. Open Source and Open Content: a Framework for Global Collaboration in Social-Ecological Research

    Directory of Open Access Journals (Sweden)

    Charles Schweik

    2005-06-01

    Full Text Available This paper discusses opportunities for alternative collaborative approaches for social-ecological research in general and, in this context, for modeling land-use/land-cover change. In this field, the rate of progress in academic research is steady but perhaps not as rapid or efficient as might be possible with alternative organizational frameworks. The convergence of four phenomena provides new opportunities for cross-organizational collaboration: (1 collaborative principles related to "open source" (OS software development, (2 the emerging area of "open content" (OC licensing, (3 the World Wide Web as a platform for scientific communication, and (4 the traditional concept of peer review. Although private individuals, government organizations, and even companies have shown interest in the OS paradigm as an alternative model for software development, it is less commonly recognized that this collaborative framework is a potential innovation of much greater proportions. In fact, it can guide the collective development of any intellectual content, not just software. This paper has two purposes. First, we describe OS and OC licensing, dispense with some myths about OS, and relate these structures to traditional scientific process. Second, we outline how these ideas can be applied in an area of collaborative research relevant to the study of social-ecological systems. It is important to recognize that the concept of OS is not new, but the idea of borrowing OS principles and using OC licensing for broader scientific collaboration is new. Over the last year, we have been trying to initiate such an OS/OC collaboration in the context of modeling land use and land cover. In doing so, we have identified some key issues that need to be considered, including project initiation, incentives of project participants, collaborative infrastructure, institutional design and governance, and project finance. OS/OC licensing is not a universal solution suitable for all

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

    Science.gov (United States)

    Baumann, P.; Misev, D.

    2016-12-01

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

  15. NASA's Earth Imagery Service as Open Source Software

    Science.gov (United States)

    De Cesare, C.; Alarcon, C.; Huang, T.; Roberts, J. T.; Rodriguez, J.; Cechini, M. F.; Boller, R. A.; Baynes, K.

    2016-12-01

    The NASA Global Imagery Browse Service (GIBS) is a software system that provides access to an archive of historical and near-real-time Earth imagery from NASA-supported satellite instruments. The imagery itself is open data, and is accessible via standards such as the Open Geospatial Consortium (OGC)'s Web Map Tile Service (WMTS) protocol. GIBS includes three core software projects: The Imagery Exchange (TIE), OnEarth, and the Meta Raster Format (MRF) project. These projects are developed using a variety of open source software, including: Apache HTTPD, GDAL, Mapserver, Grails, Zookeeper, Eclipse, Maven, git, and Apache Commons. TIE has recently been released for open source, and is now available on GitHub. OnEarth, MRF, and their sub-projects have been on GitHub since 2014, and the MRF project in particular receives many external contributions from the community. Our software has been successful beyond the scope of GIBS: the PO.DAAC State of the Ocean and COVERAGE visualization projects reuse components from OnEarth. The MRF source code has recently been incorporated into GDAL, which is a core library in many widely-used GIS software such as QGIS and GeoServer. This presentation will describe the challenges faced in incorporating open software and open data into GIBS, and also showcase GIBS as a platform on which scientists and the general public can build their own applications.

  16. GOSH! A roadmap for open-source science hardware

    CERN Multimedia

    Stefania Pandolfi

    2016-01-01

    The goal of the Gathering for Open Science Hardware (GOSH! 2016), held from 2 to 5 March 2016 at IdeaSquare, was to lay the foundations of the open-source hardware for science movement.   The participants in the GOSH! 2016 meeting gathered in IdeaSquare. (Image: GOSH Community) “Despite advances in technology, many scientific innovations are held back because of a lack of affordable and customisable hardware,” says François Grey, a professor at the University of Geneva and coordinator of Citizen Cyberlab – a partnership between CERN, the UN Institute for Training and Research and the University of Geneva – which co-organised the GOSH! 2016 workshop. “This scarcity of accessible science hardware is particularly obstructive for citizen science groups and humanitarian organisations that don’t have the same economic means as a well-funded institution.” Instead, open sourcing science hardware co...

  17. Status and future plans for open source QuickPIC

    Science.gov (United States)

    An, Weiming; Decyk, Viktor; Mori, Warren

    2017-10-01

    QuickPIC is a three dimensional (3D) quasi-static particle-in-cell (PIC) code developed based on the UPIC framework. It can be used for efficiently modeling plasma based accelerator (PBA) problems. With quasi-static approximation, QuickPIC can use different time scales for calculating the beam (or laser) evolution and the plasma response, and a 3D plasma wake field can be simulated using a two-dimensional (2D) PIC code where the time variable is ξ = ct - z and z is the beam propagation direction. QuickPIC can be thousand times faster than the normal PIC code when simulating the PBA. It uses an MPI/OpenMP hybrid parallel algorithm, which can be run on either a laptop or the largest supercomputer. The open source QuickPIC is an object-oriented program with high level classes written in Fortran 2003. It can be found at https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource.git

  18. Open Sourcing Social Change: Inside the Constellation Model

    Directory of Open Access Journals (Sweden)

    Tonya Surman

    2008-09-01

    Full Text Available The constellation model was developed by and for the Canadian Partnership for Children's Health and the Environment. The model offers an innovative approach to organizing collaborative efforts in the social mission sector and shares various elements of the open source model. It emphasizes self-organizing and concrete action within a network of partner organizations working on a common issue. Constellations are self-organizing action teams that operate within the broader strategic vision of a partnership. These constellations are outwardly focused, placing their attention on creating value for those in the external environment rather than on the partnership itself. While serious effort is invested into core partnership governance and management, most of the energy is devoted to the decision making, resources and collaborative effort required to create social value. The constellations drive and define the partnership. The constellation model emerged from a deep understanding of the power of networks and peer production. Leadership rotates fluidly amongst partners, with each partner having the freedom to head up a constellation and to participate in constellations that carry out activities that are of more peripheral interest. The Internet provided the platform, the partner network enabled the expertise to align itself, and the goal of reducing chemical exposure in children kept the energy flowing. Building on seven years of experience, this article provides an overview of the constellation model, discusses the results from the CPCHE, and identifies similarities and differences between the constellation and open source models.

  19. Robust, open-source removal of systematics in Kepler data

    Science.gov (United States)

    Aigrain, S.; Parviainen, H.; Roberts, S.; Reece, S.; Evans, T.

    2017-10-01

    We present ARC2 (Astrophysically Robust Correction 2), an open-source python-based systematics-correction pipeline, to correct for the Kepler prime mission long-cadence light curves. The ARC2 pipeline identifies and corrects any isolated discontinuities in the light curves and then removes trends common to many light curves. These trends are modelled using the publicly available co-trending basis vectors, within an (approximate) Bayesian framework with 'shrinkage' priors to minimize the risk of overfitting and the injection of any additional noise into the corrected light curves, while keeping any astrophysical signals intact. We show that the ARC2 pipeline's performance matches that of the standard Kepler PDC-MAP data products using standard noise metrics, and demonstrate its ability to preserve astrophysical signals using injection tests with simulated stellar rotation and planetary transit signals. Although it is not identical, the ARC2 pipeline can thus be used as an open-source alternative to PDC-MAP, whenever the ability to model the impact of the systematics removal process on other kinds of signal is important.

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

    Science.gov (United States)

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

    2013-04-01

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

  1. Clarity: An Open Source Manager for Laboratory Automation

    Science.gov (United States)

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

    2013-01-01

    Software to manage automated laboratories interfaces with hardware instruments, gives users a way to specify experimental protocols, and schedules activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity: a laboratory automation manager that is hardware agnostic, portable, extensible and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity; demonstrate an example of its implementation for the automated analysis of bacterial growth; and describe how the program can be extended to manage new hardware. Clarity is mature; well documented; actively developed; written in C# for the Common Language Infrastructure; and is free and open source software. These advantages set Clarity apart from currently available laboratory automation programs. PMID:23032169

  2. A Method for Rapid Measurement of Contrast Sensitivity on Mobile Touch-Screens

    Science.gov (United States)

    Mulligan, Jeffrey B.

    2016-01-01

    Touch-screen displays in cell phones and tablet computers are now pervasive, making them an attractive option for vision testing outside of the laboratory or clinic. Here we de- scribe a novel method in which subjects use a finger swipe to indicate the transition from visible to invisible on a grating which is swept in both contrast and frequency. Because a single image can be swiped in about a second, it is practical to use a series of images to zoom in on particular ranges of contrast or frequency, both to increase the accuracy of the measurements and to obtain an estimate of the reliability of the subject. Sensitivities to chromatic and spatio-temporal modulations are easily measured using the same method. A proto- type has been developed for Apple Computer's iPad/iPod/iPhone family of devices, implemented using an open-source scripting environment known as QuIP (QUick Image Processing, http://hsi.arc.nasa.gov/groups/scanpath/research.php). Preliminary data show good agreement with estimates obtained from traditional psychophysical methods as well as newer rapid estimation techniques. Issues relating to device calibration are also discussed.

  3. Rapid method for detection of salmonella in meat

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention relates to a rapid method for the detection of Salmonella in meat as well as to a kit for performing said method. The method provides a time-to-result of less than 8 hours.......The present invention relates to a rapid method for the detection of Salmonella in meat as well as to a kit for performing said method. The method provides a time-to-result of less than 8 hours....

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

    Science.gov (United States)

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

    2015-08-01

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

  5. Methods and compositions for rapid thermal cycling

    Science.gov (United States)

    Beer, Neil Reginald; Benett, William J.; Frank, James M.; Deotte, Joshua R.; Spadaccini, Christopher

    2015-10-27

    The rapid thermal cycling of a material is targeted. A microfluidic heat exchanger with an internal porous medium is coupled to tanks containing cold fluid and hot fluid. Fluid flows alternately from the cold tank and the hot tank into the porous medium, cooling and heating samples contained in the microfluidic heat exchanger's sample wells. A valve may be coupled to the tanks and a pump, and switching the position of the valve may switch the source and direction of fluid flowing through the porous medium. A controller may control the switching of valve positions based on the temperature of the samples and determined temperature thresholds. A sample tray for containing samples to be thermally cycled may be used in conjunction with the thermal cycling system. A surface or internal electrical heater may aid in heating the samples, or may replace the necessity for the hot tank.

  6. 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

  7. Improving Data Catalogs with Free and Open Source Software

    Science.gov (United States)

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

    2013-12-01

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

  8. Physics and 3D in Flash Simulations: Open Source Reality

    Science.gov (United States)

    Harold, J. B.; Dusenbery, P.

    2009-12-01

    Over the last decade our ability to deliver simulations over the web has steadily advanced. The improvements in speed of the Adobe Flash engine, and the development of open source tools to expand it, allow us to deliver increasingly sophisticated simulation based games through the browser, with no additional downloads required. In this paper we will present activities we are developing as part of two asteroids education projects: Finding NEO (funded through NSF and NASA SMD), and Asteroids! (funded through NSF). The first activity is Rubble!, an asteroids deflection game built on the open source Box2D physics engine. This game challenges players to push asteroids in to safe orbits before they crash in to the Earth. The Box2D engine allows us to go well beyond simple 2-body orbital calculations and incorporate “rubble piles”. These objects, which are representative of many asteroids, are composed of 50 or more individual rocks which gravitationally bind and separate in realistic ways. Even bombs can be modeled with sufficient physical accuracy to convince players of the hazards of trying to “blow up” incoming asteroids. The ability to easily build games based on underlying physical models allows us to address physical misconceptions in a natural way: by having the player operate in a world that directly collides with those misconceptions. Rubble! provides a particularly compelling example of this due to the variety of well documented misconceptions regarding gravity. The second activity is a Light Curve challenge, which uses the open source PaperVision3D tools to analyze 3D asteroid models. The goal of this activity is to introduce the player to the concept of “light curves”, measurements of asteroid brightness over time which are used to calculate the asteroid’s period. These measurements can even be inverted to generate three dimensional models of asteroids that are otherwise too small and distant to directly image. Through the use of the Paper

  9. 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.

  10. Agile Software Management for Successful Open Source Software Projects

    Science.gov (United States)

    Bermudez, L. E.

    2016-12-01

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

  11. Workshop for Open Source Universal Picture Archiving and Communication Systems (PACS)

    National Research Council Canada - National Science Library

    Tohme, Walid G

    2006-01-01

    .... The "Open Source Universal PACS Archive" workshop focused on current challenges of and open source solutions to the management of images and other clinical information in multi-center settings...

  12. Q&A. Does lack of product management impact the users of open source?

    Directory of Open Access Journals (Sweden)

    Paul Young

    2008-05-01

    Full Text Available Most commercial software companies employ product managers to handle the planning and marketing of software products, whereas few open source projects have a product manager. Does lack of product management impact the users of open source?

  13. Spatiotemporal Land Use Change Analysis Using Open-source GIS and Web Based Application

    Directory of Open Access Journals (Sweden)

    Wan Yusryzal Wan Ibrahim

    2015-05-01

    Full Text Available Spatiotemporal changes are very important information to reveal the characteristics of the urbanization process. Sharing the information is beneficial for public awareness which then improves their participation in adaptive management for spatial planning process. Open-source software and web application are freely available tools that can be the best medium used by any individual or agencies to share this important information. The objective of the paper is to discuss on the spatiotemporal land use change in Iskandar Malaysia by using open-source GIS (Quantum GIS and publish them through web application (Mash-up. Land use in 1994 to 2011 were developed and analyzed to show the landscape change of the region. Subsequently, web application was setup to distribute the findings of the study. The result show there is significant changes of land use in the study area especially on the decline of agricultural and natural land which were converted to urban land uses. Residential and industrial areas largely replaced the agriculture and natural areas particularly along the coastal zone of the region. This information is published through interactive GIS web in order to share it with the public and stakeholders. There are some limitations of web application but still not hindering the advantages of using it. The integration of open-source GIS and web application is very helpful in sharing planning information particularly in the study area that experiences rapid land use and land cover change. Basic information from this study is vital for conducting further study such as projecting future land use change and other related studies in the area.

  14. PACS for Bhutan: a cost effective open source architecture for emerging countries

    Directory of Open Access Journals (Sweden)

    Osman Ratib

    2016-07-01

    Full Text Available Abstract This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer. Messages/teaching points • Open source imaging informatics platforms can provide cost-effective alternatives for PACS • Robust and cost-effective open architecture can provide adequate solutions for emerging countries • Imaging informatics is often lacking in hospitals equipped with digital modalities

  15. The Confluence of GIS, Cloud and Open Source, Enabling Big Raster Data Applications

    Science.gov (United States)

    Plesea, L.; Emmart, C. B.; Boller, R. A.; Becker, P.; Baynes, K.

    2016-12-01

    The rapid evolution of available cloud services is profoundly changing the way applications are being developed and used. Massive object stores, service scalability, continuous integration are some of the most important cloud technology advances that directly influence science applications and GIS. At the same time, more and more scientists are using GIS platforms in their day to day research. Yet with new opportunities there are always some challenges. Given the large amount of data commonly required in science applications, usually large raster datasets, connectivity is one of the biggest problems. Connectivity has two aspects, one being the limited bandwidth and latency of the communication link due to the geographical location of the resources, the other one being the interoperability and intrinsic efficiency of the interface protocol used to connect. NASA and Esri are actively helping each other and collaborating on a few open source projects, aiming to provide some of the core technology components to directly address the GIS enabled data connectivity problems. Last year Esri contributed LERC, a very fast and efficient compression algorithm to the GDAL/MRF format, which itself is a NASA/Esri collaboration project. The MRF raster format has some cloud aware features that make it possible to build high performance web services on cloud platforms, as some of the Esri projects demonstrate. Currently, another NASA open source project, the high performance OnEarth WMTS server is being refactored and enhanced to better integrate with MRF, GDAL and Esri software. Taken together, the GDAL, MRF and OnEarth form the core of an open source CloudGIS toolkit that is already showing results. Since it is well integrated with GDAL, which is the most common interoperability component of GIS applications, this approach should improve the connectivity and performance of many science and GIS applications in the cloud.

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

    Science.gov (United States)

    Aminpour, Farzaneh; Sadoughi, Farahnaz; Ahmadi, Maryam

    2013-12-01

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

  17. Best practices for open source technology management in library and information centres

    OpenAIRE

    Vimal Kumar, V.

    2011-01-01

    Open Source technology management in library and information centers is a challenge and an opportunity. A general perception rooted among library professionals is that Open Source softwares are difficult to implement and not user friendly. Lack of awareness and opportunities for training are the main barriers for wide adoption of Open Source software in libraries. Success rate of Open Source technology implementation depend on attitude to build skill set and dedication of library staff.

  18. Location, Location, Location: How Network Embeddedness Affects Project Success in Open Source Systems

    OpenAIRE

    Rajdeep Grewal; Gary L. Lilien; Girish Mallapragada

    2006-01-01

    The community-based model for software development in open source environments is becoming a viable alternative to traditional firm-based models. To better understand the workings of open source environments, we examine the effects of network embeddedness--or the nature of the relationship among projects and developers--on the success of open source projects. We find that considerable heterogeneity exists in the network embeddedness of open source projects and project managers. We use a visua...

  19. THE PIXHAWK OPEN-SOURCE COMPUTER VISION FRAMEWORK FOR MAVS

    Directory of Open Access Journals (Sweden)

    L. Meier

    2012-09-01

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

  20. ABCD, an Open Source Software for Modern Libraries

    Directory of Open Access Journals (Sweden)

    Sangeeta Namdev Dhamdhere

    2011-12-01

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

  1. OpenFOAM: Open source CFD in research and industry

    Directory of Open Access Journals (Sweden)

    Hrvoje Jasak

    2009-12-01

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

  2. 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.

  3. An open source automatic feeder for animal experiments

    Directory of Open Access Journals (Sweden)

    Jinook Oh

    2017-04-01

    Full Text Available Automatic feeders are widely used in animal experiments to dispense an accurate amount of food reward for each trial. Several commercial automatic feeders for animal experiments are available which are specific to certain species and food types. However, it would be beneficial for researchers if they could easily build their own experimental feeders customized for their study species, food types, and other experimental considerations. In this paper, we describe an open source experimental feeder using an Arduino microcontroller. The design of the feeder is focused on simplicity to provide a straight-forward building process and allow custom modifications for various requirements. The cost for building this feeder is less than €200 and we have successfully tested our design with three different food types for pigeons, cats, and marmoset monkeys.

  4. SPATIAL DMBS ARCHITECTURE FOR A FREE AND OPEN SOURCE BIM

    Directory of Open Access Journals (Sweden)

    S. Logothetis

    2017-08-01

    Full Text Available Recent research on the field of Building Information Modelling (BIM technology, revealed that except of a few, accessible and free BIM viewers there is a lack of Free & Open Source Software (FOSS BIM software for the complete BIM process. With this in mind and considering BIM as the technological advancement of Computer-Aided Design (CAD systems, the current work proposes the use of a FOSS CAD software in order to extend its capabilities and transform it gradually into a FOSS BIM platform. Towards this undertaking, a first approach on developing a spatial Database Management System (DBMS able to store, organize and manage the overall amount of information within a single application, is presented.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-12-01

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

  6. Development of Thread-compatible Open Source Stack

    Science.gov (United States)

    Zimmermann, Lukas; Mars, Nidhal; Schappacher, Manuel; Sikora, Axel

    2017-07-01

    The Thread protocol is a recent development based on 6LoWPAN (IPv6 over IEEE 802.15.4), but with extensions regarding a more media independent approach, which - additionally - also promises true interoperability. To evaluate and analyse the operation of a Thread network a given open source 6LoWPAN stack for embedded devices (emb::6) has been extended in order to comply with the Thread specification. The implementation covers Mesh Link Establishment (MLE) and network layer functionality as well as 6LoWPAN mesh under routing mechanism based on MAC short addresses. The development has been verified on a virtualization platform and allows dynamical establishment of network topologies based on Thread’s partitioning algorithm.

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

    Science.gov (United States)

    Kempler, Steve; Pham, Long; Yang, Wenli

    2014-01-01

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

  8. Modular Open-Source Software for Item Factor Analysis.

    Science.gov (United States)

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

    2015-06-01

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

  9. Management of Astronomical Software Projects with Open Source Tools

    Science.gov (United States)

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

    2010-12-01

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

  10. USE OF OPEN SOURCE PHYSICS IN LCMS MOODLE

    Directory of Open Access Journals (Sweden)

    Vasyl M. Franchuk

    2015-02-01

    Full Text Available While designing and development of e-learning courses the LCMS MOODLE standard elements are deficient. This may be due to the fact that sometimes it is impossible to conduct demonstration experiments of physical phenomena or processes in the existing conditions of the institution, especially for laboratory work when you want to simulate a particular process without actually having physical devices and equipment. A teacher can use standard components (modules activity to build the course in LCMS MOODLE. In case the teacher has not enough standard modules for students training activities, including physics, he can add other modules that are not included in the official version of the MOODLE system. EJSApp module can be one of them. With help of EJSApp module the teacher can add Java-applets created with Java simulation in LCMS MOODLE using Library Open Source Physics.

  11. MOSFiT: Modular Open-Source Fitter for Transients

    Science.gov (United States)

    Guillochon, James; Nicholl, Matt; Villar, V. Ashley; Mockler, Brenna; Narayan, Gautham; Mandel, Kaisey S.; Berger, Edo; Williams, Peter K. G.

    2017-10-01

    MOSFiT (Modular Open-Source Fitter for Transients) downloads transient datasets from open online catalogs (e.g., the Open Supernova Catalog), generates Monte Carlo ensembles of semi-analytical light curve fits to those datasets and their associated Bayesian parameter posteriors, and optionally delivers the fitting results back to those same catalogs to make them available to the rest of the community. MOSFiT helps bridge the gap between observations and theory in time-domain astronomy; in addition to making the application of existing models and creation of new models as simple as possible, MOSFiT yields statistically robust predictions for transient characteristics, with a standard output format that includes all the setup information necessary to reproduce a given result.

  12. Source Code Management and Software Distribution using Open Source Technologies

    Science.gov (United States)

    Bly, M. J.; Allan, A.; Jenness, T.

    The Starlink Software Collection (USSC) runs on three different platforms and contains approximately 130 separate software items, totaling over 6 million lines of code. Distribution of such large software systems and installation at multiple remote sites has always been problematic due to the complex web of inter-dependencies such systems invariably generate. The rise of the Open Source movement has brought standard tools into common use to cope with such large and complex tasks. The RedHat Package Manager (RPM) software is one such which is available for many platforms. We have shown it is possible to automate the distribution and installation of the Starlink Software using RPM. We anticipate that this will vastly simplify installation and package management for Systems Administrators who must support the USSC in production data processing environments.

  13. Mahotas: Open source software for scriptable computer vision

    Directory of Open Access Journals (Sweden)

    Luis Pedro Coelho

    2013-07-01

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

  14. Integrating HCI Specialists into Open Source Software Development Projects

    Science.gov (United States)

    Hedberg, Henrik; Iivari, Netta

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Chute, Ryan M [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2008-01-01

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

  16. Spatial Dmbs Architecture for a Free and Open Source Bim

    Science.gov (United States)

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

    2017-08-01

    Recent research on the field of Building Information Modelling (BIM) technology, revealed that except of a few, accessible and free BIM viewers there is a lack of Free & Open Source Software (FOSS) BIM software for the complete BIM process. With this in mind and considering BIM as the technological advancement of Computer-Aided Design (CAD) systems, the current work proposes the use of a FOSS CAD software in order to extend its capabilities and transform it gradually into a FOSS BIM platform. Towards this undertaking, a first approach on developing a spatial Database Management System (DBMS) able to store, organize and manage the overall amount of information within a single application, is presented.

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

    Science.gov (United States)

    Erdemir, Ahmet

    2016-02-01

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

  18. Nanocall: an open source basecaller for Oxford Nanopore sequencing data.

    Science.gov (United States)

    David, Matei; Dursi, L J; Yao, Delia; Boutros, Paul C; Simpson, Jared T

    2017-01-01

    The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls. To allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ∼68% identity, directly comparable to Metrichor '1D' data. Further, Nanocall is efficient, processing ∼2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION sequencing run in real time. Metrichor provides the ability to integrate the '1D' sequencing of template and complement strands of a single DNA molecule, and create a '2D' read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data. Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license. matei.david@oicr.on.caSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  19. Comparative Analysis Study of Open Source GIS in Malaysia

    Science.gov (United States)

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

    2014-06-01

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

  20. A Case Study about Open Source Internet Software in the eThekwini ...

    African Journals Online (AJOL)

    This paper describes the use of open source software applications on the web sites of the large eThekwini municipality in Durban, South Africa. The implementation of open source was both a response to the 2003 South African Government approval of open source solutions in government departments and because open ...

  1. 76 FR 75875 - Defense Federal Acquisition Regulation Supplement; Open Source Software Public Meeting

    Science.gov (United States)

    2011-12-05

    ... Defense Acquisition Regulations System Defense Federal Acquisition Regulation Supplement; Open Source... regarding the use of open source software in DoD contracts. DATES: Public Meeting: January 12, 2012, from 10... for the discussions in the meeting. Please cite ``Public Meeting, DFARS--Open Source Software'' in all...

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

    Science.gov (United States)

    Kisworo, Marsudi Wahyu

    2016-01-01

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

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

    Science.gov (United States)

    Krishnamurthy, M.

    2008-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Luke eCampagnola

    2014-01-01

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

  6. 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

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

    Science.gov (United States)

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

    2017-04-01

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

  8. 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

    2015-06-01

    One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. TREMOR12: An Open-Source Mobile App for Tremor Quantification.

    Science.gov (United States)

    Kubben, Pieter L; Kuijf, Mark L; Ackermans, Linda P C M; Leentjes, Albert F G; Temel, Yasin

    2016-01-01

    Evaluating the effect of treatment of tremor is mostly performed with clinical rating scales. Mobile applications facilitate a more rapid, objective, and quantitative evaluation of treatment effect. Existing mobile apps do not offer raw data access, which limits algorithm development. To develop a novel open-source mobile app for tremor quantification. TREMOR12 is an open-source mobile app that samples acceleration, rotation, rotation speed, and gravity, each in 3 axes and time-stamped in a frequency up to 100 Hz. The raw measurement data can be exported as a comma-separated value file for further analysis in the TREMOR12P data processing module. The app was evaluated with 3 patients suffering from essential tremor, who were between 55 and 71 years of age. This proof-of-concept study shows that the TREMOR12 app is able to detect and register tremor characteristics such as acceleration, rotation, rotation speed, and gravity in a simple and nonburdensome way. The app is compatible with current regulatory oversight by the European Union (MEDDEV regulations) and the Food and Drug Administration (FDA) guidance on mobile medical applications. TREMOR12 offers low-cost tremor quantification for research purposes and algorithm development, and may help to improve treatment evaluation. © 2016 S. Karger AG, Basel.

  10. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data

    Energy Technology Data Exchange (ETDEWEB)

    Kyle, Jennifer E.; Crowell, Kevin L.; Casey, Cameron P.; Fujimoto, Grant M.; Kim, Sangtae; Dautel, Sydney E.; Smith, Richard D.; Payne, Samuel H.; Metz, Thomas O.

    2017-01-31

    We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.

  11. An unbroken chain: approaches to implementing Linked Open Data in libraries: comparing local, open-source, collaborative and commercial systems

    NARCIS (Netherlands)

    Greenall, R.; Koster, L.

    2014-01-01

    This paper compares methods for libraries to interact with the Web of data by assessing the benefits and risks associated with local development, free-and-open-source software, collaborative and commercial solutions. Through a number of case studies, we provide insight into how each approach can be

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

    Science.gov (United States)

    Johansson, Björn; Sudzina, Frantisek

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

  13. 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).

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

    Science.gov (United States)

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

    2015-12-01

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

  15. Open source software engineering for geoscientific modeling applications

    Science.gov (United States)

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

    2012-12-01

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

  16. An open source tool to analyse heat waves using flow analogues and weather regimes

    Science.gov (United States)

    Radanovics, Sabine; Jézéquel, Aglaé; Alvarez-Castro, Carmen; Yiou, Pascal; Hempelmann, Nils; Ehbrecht, Carsten; Nangini, Cathy; Vautard, Robert

    2017-04-01

    Studies on the relation of atmospheric circulation patterns and heat waves using flow analogues or weather regimes often miss an assessment of the uncertainties related to internal climate variability and the analysis method itself because of the limited length of the data sets used. However, considering this type of uncertainty is important when interpreting changes found in a transient climate using this type of methods. We used several hundreds of years long preindustrial control runs of CMIP5 climate models to address this issue in a constant model climate. Several heat waves over central Europe as simulated by the climate model were selected and then reconstructed using circulation analogues, that is by searching for days with similar pressure fields in the simulation and recombining the temperatures of these similar days to form uchronic events. The variance of these uchronic events is supposed to vary with the rarity of the original event. We therefore present the relationship between the variance of the uchronic events and the distance between the original event and its analogues. Further we present the variation of the distances due to internal climate variability. Weather regimes are typical atmospheric circulation patterns obtained for example using a cluster analysis. Each day is then assigned to a cluster, the weather regime. The frequency of the weather regimes is supposed to be constant in a constant climate, but variations of these frequencies can occur due to internal climate variability. We therefore show these variations for the weather regimes associated with the heat waves. The web processing service (WPS) flyingpigeon is an open source WPS featuring processes for studying weather extremes and climate change impacts. Flyingpigeon is part of the open source project birdhouse, a collection of WPSs following the Open Geospatial Consortium (OGC) standard and available on github. The WPS allowed to first select the data sets needed from the ESGF

  17. An open source device for operant licking in rats

    Directory of Open Access Journals (Sweden)

    Matthew Longley

    2017-02-01

    Full Text Available We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors and activate output devices (e.g., LED lights, syringe pumps as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.

  18. Real-time control using open source RTOS

    Science.gov (United States)

    Irwin, Philip C.; Johnson, Richard L., Jr.

    2002-12-01

    Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

  19. 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.

  20. An open source simulation model for soil and sediment bioturbation.

    Directory of Open Access Journals (Sweden)

    Katja Schiffers

    Full Text Available Bioturbation is one of the most widespread forms of ecological engineering and has significant implications for the structure and functioning of ecosystems, yet our understanding of the processes involved in biotic mixing remains incomplete. One reason is that, despite their value and utility, most mathematical models currently applied to bioturbation data tend to neglect aspects of the natural complexity of bioturbation in favour of mathematical simplicity. At the same time, the abstract nature of these approaches limits the application of such models to a limited range of users. Here, we contend that a movement towards process-based modelling can improve both the representation of the mechanistic basis of bioturbation and the intuitiveness of modelling approaches. In support of this initiative, we present an open source modelling framework that explicitly simulates particle displacement and a worked example to facilitate application and further development. The framework combines the advantages of rule-based lattice models with the application of parameterisable probability density functions to generate mixing on the lattice. Model parameters can be fitted by experimental data and describe particle displacement at the spatial and temporal scales at which bioturbation data is routinely collected. By using the same model structure across species, but generating species-specific parameters, a generic understanding of species-specific bioturbation behaviour can be achieved. An application to a case study and comparison with a commonly used model attest the predictive power of the approach.

  1. Phenobook: an open source software for phenotypic data collection.

    Science.gov (United States)

    Crescente, Juan M; Guidobaldi, Fabio; Demichelis, Melina; Formica, Maria B; Helguera, Marcelo; Vanzetti, Leonardo S

    2017-04-01

    Research projects often involve observation, registration, and data processing starting from information obtained in field experiments. In many cases, these tasks are carried out by several persons in different places, times, and ways, adding different levels of complexity and error in data collecting. Furthermore, data processing can be time consuming, and input errors may produce unwanted results. We have developed a novel, open source software called Phenobook, an easy, flexible, and intuitive tool to organize, collect, and save experimental data for further analyses. Phenobook was conceived to collect phenotypic observations in a user-friendly, cost-effective way. It consists of a web-based software for experiment design, data input and visualization, and exportation, combined with a mobile application for remote data collecting. We provide in this article a detailed description of the developed tool. Phenobook is a software tool that can be easily implemented in collaborative research and development projects involving data collecting and forward analyses. Adopting Phenobook is expected to improve the involved processes by minimizing input errors, resulting in higher quality and reliability of the research outcomes.

  2. Manual Whisker Annotator (MWA: A Modular Open-Source Tool

    Directory of Open Access Journals (Sweden)

    Brett M. Hewitt

    2016-04-01

    Full Text Available Rodents are key to generating translational data for healthcare research. Behavioural analyses, in particular, are integral to the non-invasive monitoring of rodent health and welfare. Finding quantitative behavioural measures mitigates stress, allowing for the animal behave freely while also enabling the same animal to be studied over the time-course of its life. Locomotion and whisking are both such quantitative behavioural measures, and have been found to be significantly impacted in rodent models of neurodegenerative disease. While automatic trackers of whiskers and locomotion exist, a manual tracker is required to validate these approaches, and also to annotate complex videos where these automatic versions fail. Manually annotating whiskers for research purposes is a long and tedious task and current software does little to provide an intuitive and simple interface to carry out this task. This led to the creation of the Manual Whisker Annotator (MWA. MWA is an open source, portable whisker annotation tool developed for the Windows platform. Not only does MWA make the process much quicker, it also provides added statistical tools to analyse the data. MWA was developed in C# and WPF using the .NET framework, and could be used in any situation where annotating or tracking multiple targets is desired.

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

    Science.gov (United States)

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

  4. Digital time stamping system based on open source technologies.

    Science.gov (United States)

    Miskinis, Rimantas; Smirnov, Dmitrij; Urba, Emilis; Burokas, Andrius; Malysko, Bogdan; Laud, Peeter; Zuliani, Francesco

    2010-03-01

    A digital time stamping system based on open source technologies (LINUX-UBUNTU, OpenTSA, OpenSSL, MySQL) is described in detail, including all important testing results. The system, called BALTICTIME, was developed under a project sponsored by the European Commission under the Program FP 6. It was designed to meet the requirements posed to the systems of legal and accountable time stamping and to be applicable to the hardware commonly used by the national time metrology laboratories. The BALTICTIME system is intended for the use of governmental and other institutions as well as personal bodies. Testing results demonstrate that the time stamps issued to the user by BALTICTIME and saved in BALTICTIME's archives (which implies that the time stamps are accountable) meet all the regulatory requirements. Moreover, the BALTICTIME in its present implementation is able to issue more than 10 digital time stamps per second. The system can be enhanced if needed. The test version of the BALTICTIME service is free and available at http://baltictime. pfi.lt:8080/btws/ and http://baltictime.lnmc.lv:8080/btws/.

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

    CERN Multimedia

    CERN. Geneva

    2010-01-01

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

  6. Application of Open Source Technologies for Oceanographic Data Analysis

    Science.gov (United States)

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

    2015-12-01

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

  7. An open source device for operant licking in rats.

    Science.gov (United States)

    Longley, Matthew; Willis, Ethan L; Tay, Cindy X; Chen, Hao

    2017-01-01

    We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.

  8. Contrasting Proprietary and Free/Open Source Game Development

    Directory of Open Access Journals (Sweden)

    Marco Zamarian

    2008-10-01

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

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

    Science.gov (United States)

    Panayides, A; Eleftheriou, I; Pantziaris, M

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    A. Panayides

    2013-01-01

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

  11. The OPAL Project: Open source Procedure for Assessment of Loss using Global Earthquake Modelling software

    Science.gov (United States)

    Daniell, James

    2010-05-01

    This paper provides a comparison between Earthquake Loss Estimation (ELE) software packages and their application using an "Open Source Procedure for Assessment of Loss using Global Earthquake Modelling software" (OPAL). The OPAL procedure has been developed to provide a framework for optimisation of a Global Earthquake Modelling process through: 1) Overview of current and new components of earthquake loss assessment (vulnerability, hazard, exposure, specific cost and technology); 2) Preliminary research, acquisition and familiarisation with all available ELE software packages; 3) Assessment of these 30+ software packages in order to identify the advantages and disadvantages of the ELE methods used; and 4) Loss analysis for a deterministic earthquake (Mw7.2) for the Zeytinburnu district, Istanbul, Turkey, by applying 3 software packages (2 new and 1 existing): a modified displacement-based method based on DBELA (Displacement Based Earthquake Loss Assessment), a capacity spectrum based method HAZUS (HAZards United States) and the Norwegian HAZUS-based SELENA (SEismic Loss EstimatioN using a logic tree Approach) software which was adapted for use in order to compare the different processes needed for the production of damage, economic and social loss estimates. The modified DBELA procedure was found to be more computationally expensive, yet had less variability, indicating the need for multi-tier approaches to global earthquake loss estimation. Similar systems planning and ELE software produced through the OPAL procedure can be applied to worldwide applications, given exposure data. Keywords: OPAL, displacement-based, DBELA, earthquake loss estimation, earthquake loss assessment, open source, HAZUS

  12. In vitro eye irritation testing using the open source reconstructed hemicornea - a ring trial.

    Science.gov (United States)

    Mewes, Karsten R; Engelke, Maria; Zorn-Kruppa, Michaela; Bartok, Melinda; Tandon, Rashmi; Brandner, Johanna M; Petersohn, Dirk

    2017-01-01

    The aim of the present ring trial was to test whether two new methodological approaches for the in vitro classification of eye irritating chemicals can be reliably transferred from the developers' laboratories to other sites. Both test methods are based on the well-established open source reconstructed 3D hemicornea models. In the first approach, the initial depth of injury after chemical treatment in the hemicornea model is derived from the quantitative analysis of histological sections. In the second approach, tissue viability, as a measure for corneal damage after chemical treatment, is analyzed separately for epithelium and stroma of the hemicornea model. The three independent laboratories that participated in the ring trial produced their own hemicornea models according to the test producer's instructions, thus supporting the open source concept. A total of 9 chemicals with different physicochemical and eye-irritating properties were tested to assess the between-laboratory reproducibility (BLR), the predictive performance, as well as possible limitations of the test systems. The BLR was 62.5% for the first and 100% for the second method. Both methods enabled to discriminate Cat. 1 chemicals from all non-Cat. 1 substances, which qualifies them to be used in a top-down approach. However, the selectivity between No Cat. and Cat. 2 chemicals still needs optimization.

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

    Science.gov (United States)

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

    2013-03-15

    ADMET (absorption, distribution, metabolism, excretion, and toxicity)-related failure of drug candidates is a major issue for the pharmaceutical industry today. Prediction of PD-PK-T properties using in silico tools has become very important in pharmaceutical research to reduce cost and enhance efficiency. PaDEL-DDPredictor is an in silico tool for rapid prediction of PD-PK-T properties of compounds from their chemical structures. It is free and open-source software that, has both graphical user interface and command line interface, can work on all major platforms (Windows, Linux, and MacOS) and supports more than 90 different molecular file formats. The software can be downloaded from http://padel.nus.edu.sg/software/padelddpredictor. Copyright © 2012 Wiley Periodicals, Inc.

  14. MARVIN: a medical research application framework based on open source software.

    Science.gov (United States)

    Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

    2008-08-01

    This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

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

    Science.gov (United States)

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

    2013-01-01

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

  16. MANTA – An Open-Source, High Density Electrophysiology Recording Suite for MATLAB

    Directory of Open Access Journals (Sweden)

    Bernhard eEnglitz

    2013-05-01

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

  17. Free and Open Source Chemistry Software in Research of Quantitative Structure-Toxicity Relationship of Pesticides

    Directory of Open Access Journals (Sweden)

    Rastija Vesna

    2017-01-01

    Full Text Available Pesticides are toxic chemicals aimed for the destroying pest on crops. Numerous data evidence about toxicity of pesticides on aquatic organisms. Since pesticides with similar properties tend to have similar biological activities, toxicity may be predicted from structure. Their structure feature and properties are encoded my means of molecular descriptors. Molecular descriptors can capture quite simple two-dimensional (2D chemical structures to highly complex three-dimensional (3D chemical structures. Quantitative structure-toxicity relationship (QSTR method uses linear regression analyses for correlation toxicity of chemical with their structural feature using molecular descriptors. Molecular descriptors were calculated using open source software PaDEL and in-house built PyMOL plugin (PyDescriptor. PyDescriptor is a new script implemented with the commonly used visualization software PyMOL for calculation of a large and diverse set of easily interpretable molecular descriptors encoding pharmacophoric patterns and atomic fragments. PyDescriptor has several advantages like free and open source, can work on all major platforms (Windows, Linux, MacOS. QSTR method allows prediction of toxicity of pesticides without experimental assay. In the present work, QSTR analysis for toxicity of a dataset of mixtures of 5 classes of pesticides comprising has been performed.

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

    Science.gov (United States)

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

    2014-12-01

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

  19. RAPID METHOD FOR DETERMINATION OF RADIOSTRONTIUM IN EMERGENCY MILK SAMPLES

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, S.; Culligan, B.

    2008-07-17

    A new rapid separation method for radiostrontium in emergency milk samples was developed at the Savannah River Site (SRS) Environmental Bioassay Laboratory (Aiken, SC, USA) that will allow rapid separation and measurement of Sr-90 within 8 hours. The new method uses calcium phosphate precipitation, nitric acid dissolution of the precipitate to coagulate residual fat/proteins and a rapid strontium separation using Sr Resin (Eichrom Technologies, Darien, IL, USA) with vacuum-assisted flow rates. The method is much faster than previous method that use calcination or cation exchange pretreatment, has excellent chemical recovery, and effectively removes beta interferences. When a 100 ml sample aliquot is used, the method has a detection limit of 0.5 Bq/L, well below generic emergency action levels.

  20. Pengembangan Model Aplikasi Administrasi Pelayanan Kesehatan di Puskemas dengan Cloud Computing Berbasiskan Open Source

    Directory of Open Access Journals (Sweden)

    Honni Honni

    2013-12-01

    Full Text Available Puskemas as community health centers becomes one of the main focuses of development on the agenda of the Government of Indonesia beside education. Therefore, we purpose to develop an affordable online system of health care administration based on open source using cloud computing approach. It can be used for collecting data of patients, diseases, and treatment of patients at Puskesmas. The methods used are literature study related to cloud computing, survey design and data collection infrastructure of information technology thatcan be applied to online health services, analysis of survey data on actual conditions in some centers and other health care centers in Jakarta, then making model of online health services such as physician consulting, prescribing and disease diagnosis. The result is a web-based application system of health care administration of Puskesmas, which utilizes cloud computing technology and development architectures that are both modular and dynamic. The application model combines the benefits of open-source applications with a flexible design system. It also supports mobile devices to improve the quality of patient care. Web-based network structure allows both online and inter-section between institutions which can be accessed anytime, anywhere, through mobile devices.Development application model is also adapted to the function of the business processes and administrative processes that exist in Puskesmas throughout Indonesia. Each model is also expected to be integrated to optimize efficiency and has been adapted to the service system of Dinas Kesehatan and Health Ministery.

  1. A completely open source based computing system for computer generation of Fourier holograms

    Science.gov (United States)

    Jackin, B. J.; Palanisamy, P. K.

    2009-10-01

    Computer generated holograms are usually generated using commercial software like MATLAB, MATHCAD, Mathematica, etc. This work is an approach in doing the same using freely distributed open source packages and Operating System. A Fourier hologram is generated using this method and tested for simulated and optical reconstruction. The reconstructed images are in good agreement with the objects chosen. The significance of using such a system is also discussed. Program summaryProgram title: FHOLO Catalogue identifier: AEDS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 176 336 No. of bytes in distributed program, including test data, etc.: 4 294 872 Distribution format: tar.gz Programming language: C++ Computer: any X86 micro computer Operating system: Linux (Debian Etch) RAM: 512 MB Classification: 18 Nature of problem: To generate a Fourier Hologram in micro computer only by using open source operating system and packages. Running time: Depends on the matrix size. 10 sec for a matrix of size 256×256.

  2. FLIM-FRET analyzer: open source software for automation of lifetime-based FRET analysis.

    Science.gov (United States)

    Kim, Jiho; Tsoy, Yury; Persson, Jan; Grailhe, Regis

    2017-01-01

    Despite the broad use of FRET techniques, available methods for analyzing protein-protein interaction are subject to high labor and lack of systematic analysis. We propose an open source software allowing the quantitative analysis of fluorescence lifetime imaging (FLIM) while integrating the steady-state fluorescence intensity information for protein-protein interaction studies. Our developed open source software is dedicated to fluorescence lifetime imaging microscopy (FLIM) data obtained from Becker & Hickl SPC-830. FLIM-FRET analyzer includes: a user-friendly interface enabling automated intensity-based segmentation into single cells, time-resolved fluorescence data fitting to lifetime value for each segmented objects, batch capability, and data representation with donor lifetime versus acceptor/donor intensity quantification as a measure of protein-protein interactions. The FLIM-FRET analyzer software is a flexible application for lifetime-based FRET analysis. The application, the C#. NET source code, and detailed documentation are freely available at the following URL: http://FLIM-analyzer.ip-korea.org.

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

    Science.gov (United States)

    Cardinal, Rudolf N

    2017-04-26

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

  4. The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.

    Science.gov (United States)

    Enquobahrie, Andinet; Cheng, Patrick; Gary, Kevin; Ibanez, Luis; Gobbi, David; Lindseth, Frank; Yaniv, Ziv; Aylward, Stephen; Jomier, Julien; Cleary, Kevin

    2007-11-01

    This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.

  5. Open Source Software Tools for Anomaly Detection Analysis

    Science.gov (United States)

    2014-04-01

    RapidMiner provides data mining and machine learning procedures including: data loading and transformation (extract, transform, load [ ETL ]), data...accessed September 1, 2012). 7. RapidMiner – Data Mining, ETL , OLAP, BI. Sourceforge. Geeknet, Inc. http://sourceforge.net/projects/rapidminer...for Developing KDD-Applications Supported by Index- Structures ETL extract, transform, load GIS geographic/geospatial information system GUI

  6. Why Selecting an Open Source ERP over Proprietary ERP? : A focus on SMEs and Suppliers perspective

    OpenAIRE

    Huq, Nasimul; Shah, Syed Mushtaq Ali

    2010-01-01

    Introduction: Open Source ERP is considered as a viable alternative of proprietary ERP paradigm. Open Source ERP is getting more and more acceptance among Small and Medium Sized Enterprises (SMEs) recently. Majority of Proprietary ERP vendors are changing their strategy nowadays and extend their focus on SMEs, even though SMEs are not that interested in Proprietary ERP systems. The factors that may motivate SMEs to select an Open Source ERP over proprietary ERP are not identified empirically ...

  7. A Systems Thinking Model for Open Source Software Development in Social Media

    OpenAIRE

    Mustaquim, Moyen

    2010-01-01

    In this paper a social media model, based on systems thinking methodology is proposed to understand the behavior of the open source software development community working in social media.The proposed model is focused on relational influences of two different systems- social media and the open source community. This model can be useful for taking decisions which are complicated and where solutions are not apparent.Based on the proposed model, an efficient way of working in open source developm...

  8. Development of a code clone search tool for open source repositories

    OpenAIRE

    Xia, Pei; Yoshida, Norihiro; Manabe, Yuki; Inoue, Katsuro

    2011-01-01

    Finding code clones in the open source systems is one of important and demanding features for efficient and safe reuse of existing open source software. In this paper, we propose a novel search model, open code clone search, to explore code clones in open source repositories on the Internet. Based on this search model, we have designed and implemented a prototype system named Open CCFinder. This system takes a query code fragment as its input, and returns the code fragments containing the cod...

  9. What Constitutes Open Source? A Study of the Vista Electronic Medical Record Software

    Science.gov (United States)

    Noll, John

    Strictly speaking, Open Source Software is any program that is covered by an Open Source Software license. However, the notion of Open Source Software Development conjures images of high-quality, market dominating products developed by armies of volunteer programmers, who work only for the joy of programming. Certainly, banner projects like Apache, the Linux kernel, and Mozilla/Firefox resemble this notion, even if they do employ significant numbers of paid programmers.

  10. A universal, rapid, and inexpensive method for genomic DNA ...

    Indian Academy of Sciences (India)

    MOHAMMED BAQUR SAHIB A. AL-SHUHAIB

    Abstract. There is no 'one' procedure for extracting DNA from the whole blood of both mammals and birds, since each species has a unique property that require different methods to release its own DNA. Therefore, to obtain genomic DNA, a universal, rapid, and noncostly method was developed. A very simple biological ...

  11. Rapid, cost-effective liquid chromatograghic method for the ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... 1Department of Medicinal Chemistry and Quality Control, National Institute for Pharmaceutical Research and Development, Abuja,. Nigeria. ... A rapid and cost effective method for the analysis of metronidazole in biological samples was ... effective HPLC method of assaying metronidazole both in.

  12. A universal, rapid, and inexpensive method for genomic DNA ...

    Indian Academy of Sciences (India)

    ... of both mammals and birds, since each species has a unique property that require different methods to release its own DNA. Therefore, to obtain genomic DNA, a universal, rapid, and noncostly method was developed. A very simple biological basis is followed in this procedure, in which, when the bloodis placed in water, ...

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

    Science.gov (United States)

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

    2016-12-01

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

  14. Analýza trhu Open-source CRM systémů

    OpenAIRE

    Sklenář, Ondřej

    2012-01-01

    The thesis analyzes the market of open source CRM systems. The aim is to map the market of CRM systems and compared 3 selected systems. At first, the concepts open source and CRM are explained theoretically. After that is described market of open source CRM systems. The last chapter is a comparison of selected 3 OS CRM systems according to established criteria. The contribution of the work lies in the mapping market of open source CRM systems, as these topics have not yet been processed.

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

    Science.gov (United States)

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

    2011-09-28

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

  16. Il software didattico Open Source entra nella BSD e in ESSEDIQUADRO

    Directory of Open Access Journals (Sweden)

    Valeria Candiani

    2004-01-01

    Full Text Available Discussion of obtaining information related to open source educational software, with particular reference to ESSEDIQUADRO, the National Service of Documents on Educational Software.

  17. Performance-Based Comparative Assessment of Open Source Web Vulnerability Scanners

    National Research Council Canada - National Science Library

    Mansour Alsaleh; Noura Alomar; Monirah Alshreef; Abdulrahman Alarifi; AbdulMalik Al-Salman

    2017-01-01

    ... their detection effectiveness. Despite the advantages of dynamic testing approaches, the literature lacks studies that systematically evaluate the performance of open source web vulnerability scanners...

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

    Science.gov (United States)

    Zender, C. S.

    2009-12-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

  20. Methods for Rapid Screening in Woody Plant Herbicide Development

    Directory of Open Access Journals (Sweden)

    William Stanley

    2014-07-01

    Full Text Available Methods for woody plant herbicide screening were assayed with the goal of reducing resources and time required to conduct preliminary screenings for new products. Rapid screening methods tested included greenhouse seedling screening, germinal screening, and seed screening. Triclopyr and eight experimental herbicides from Dow AgroSciences (DAS 313, 402, 534, 548, 602, 729, 779, and 896 were tested on black locust, loblolly pine, red maple, sweetgum, and water oak. Screening results detected differences in herbicide and species in all experiments in much less time (days to weeks than traditional field screenings and consumed significantly less resources (<500 mg acid equivalent per herbicide per screening. Using regression analysis, various rapid screening methods were linked into a system capable of rapidly and inexpensively assessing herbicide efficacy and spectrum of activity. Implementation of such a system could streamline early-stage herbicide development leading to field trials, potentially freeing resources for use in development of beneficial new herbicide products.

  1. Methods and systems for rapid prototyping of high density circuits

    Science.gov (United States)

    Palmer, Jeremy A [Albuquerque, NM; Davis, Donald W [Albuquerque, NM; Chavez, Bart D [Albuquerque, NM; Gallegos, Phillip L [Albuquerque, NM; Wicker, Ryan B [El Paso, TX; Medina, Francisco R [El Paso, TX

    2008-09-02

    A preferred embodiment provides, for example, a system and method of integrating fluid media dispensing technology such as direct-write (DW) technologies with rapid prototyping (RP) technologies such as stereolithography (SL) to provide increased micro-fabrication and micro-stereolithography. A preferred embodiment of the present invention also provides, for example, a system and method for Rapid Prototyping High Density Circuit (RPHDC) manufacturing of solderless connectors and pilot devices with terminal geometries that are compatible with DW mechanisms and reduce contact resistance where the electrical system is encapsulated within structural members and manual electrical connections are eliminated in favor of automated DW traces. A preferred embodiment further provides, for example, a method of rapid prototyping comprising: fabricating a part layer using stereolithography and depositing thermally curable media onto the part layer using a fluid dispensing apparatus.

  2. A rapid ultrasound particle agglutination method for HIV antibody detection: Comparison with conventional rapid HIV tests.

    Science.gov (United States)

    Bystryak, Simon; Ossina, Natalya

    2017-11-01

    We present the results of the feasibility and preliminary studies on analytical performance of a rapid test for detection of human immunodeficiency virus (HIV) antibodies in human serum or plasma that is an important advance in detecting HIV infection. Current methods for rapid testing of antibodies against HIV are qualitative and exhibit poor sensitivity (limit of detection). In this paper, we describe an ultrasound particle agglutination (UPA) method that leads to a significant increase of the sensitivity of conventional latex agglutination tests for HIV antibody detection in human serum or plasma. The UPA method is based on the use of: 1) a dual mode ultrasound, wherein a first single-frequency mode is used to accelerate the latex agglutination process, and then a second swept-frequency mode of sonication is used to disintegrate non-specifically bound aggregates; and 2) a numerical assessment of results of the agglutination process. The numerical assessment is carried out by optical detection and analysis of moving patterns in the resonator cell during the swept-frequency mode. The single-step UPA method is rapid and more sensitive than the three commercial rapid HIV test kits analyzed in the study: analytical sensitivity of the new UPA method was found to be 510-, 115-, and 80-fold higher than that for Capillus™, Multispot™ and Uni-Gold™ Recombigen HIV antibody rapid test kits, respectively. The newly developed UPA method opens up additional possibilities for detection of a number of clinically significant markers in point-of-care settings. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. 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.

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

    Science.gov (United States)

    Di Leo, M.; Di Stefano, M.

    2013-12-01

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

  5. Temporal bone radiology report classification using open source machine learning and natural langue processing libraries.

    Science.gov (United States)

    Masino, Aaron J; Grundmeier, Robert W; Pennington, Jeffrey W; Germiller, John A; Crenshaw, E Bryan

    2016-06-06

    Radiology reports are a rich resource for biomedical research. Prior to utilization, trained experts must manually review reports to identify discrete outcomes. The Audiological and Genetic Database (AudGenDB) is a public, de-identified research database that contains over 16,000 radiology reports. Because the reports are unlabeled, it is difficult to select those with specific abnormalities. We implemented a classification pipeline using a human-in-the-loop machine learning approach and open source libraries to label the reports with one or more of four abnormality region labels: inner, middle, outer, and mastoid, indicating the presence of an abnormality in the specified ear region. Trained abstractors labeled radiology reports taken from AudGenDB to form a gold standard. These were split into training (80 %) and test (20 %) sets. We applied open source libraries to normalize and convert every report to an n-gram feature vector. We trained logistic regression, support vector machine (linear and Gaussian), decision tree, random forest, and naïve Bayes models for each ear region. The models were evaluated on the hold-out test set. Our gold-standard data set contained 726 reports. The best classifiers were linear support vector machine for inner and outer ear, logistic regression for middle ear, and decision tree for mastoid. Classifier test set accuracy was 90 %, 90 %, 93 %, and 82 % for the inner, middle, outer and mastoid regions, respectively. The logistic regression method was very consistent, achieving accuracy scores within 2.75 % of the best classifier across regions and a receiver operator characteristic area under the curve of 0.92 or greater across all regions. Our results indicate that the applied methods achieve accuracy scores sufficient to support our objective of extracting discrete features from radiology reports to enhance cohort identification in AudGenDB. The models described here are available in several free, open source libraries that

  6. RAPID SEPARATION METHOD FOR ACTINIDES IN EMERGENCY SOIL SAMPLES

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, S.; Culligan, B.; Noyes, G.

    2009-11-09

    A new rapid method for the determination of actinides in soil and sediment samples has been developed at the Savannah River Site Environmental Lab (Aiken, SC, USA) that can be used for samples up to 2 grams in emergency response situations. The actinides in soil method utilizes a rapid sodium hydroxide fusion method, a lanthanum fluoride soil matrix removal step, and a streamlined column separation process with stacked TEVA, TRU and DGA Resin cartridges. Lanthanum was separated rapidly and effectively from Am and Cm on DGA Resin. Vacuum box technology and rapid flow rates are used to reduce analytical time. Alpha sources are prepared using cerium fluoride microprecipitation for counting by alpha spectrometry. The method showed high chemical recoveries and effective removal of interferences. This new procedure was applied to emergency soil samples received in the NRIP Emergency Response exercise administered by the National Institute for Standards and Technology (NIST) in April, 2009. The actinides in soil results were reported within 4-5 hours with excellent quality.

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

    Science.gov (United States)

    van Rooij, Shahron Williams

    2007-01-01

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

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

    Science.gov (United States)

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

    2003-01-01

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

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

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    Science.gov (United States)

    Fagan, Jody Condit; Keach, Jennifer A.

    2010-01-01

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

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

    Science.gov (United States)

    Samuels, Ruth Gallegos; Griffy, Henry

    2012-01-01

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

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

    Science.gov (United States)

    Derringer, Pam

    2009-01-01

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

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

    Science.gov (United States)

    van Rooij, S. Williams

    2012-01-01

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

  14. OPEN-SOURCE MOODLE SOFTWARE ADAPTATION SUPPORTING MEDICAL UNIVERSITY ACADEMIC PROCESS

    Directory of Open Access Journals (Sweden)

    A. V. Semenets

    2014-01-01

    Full Text Available An open-source software application is an important part of the modern approach to the medical education. The experience of the Moodle learning management system in Ternopil State Medical University by I. Ya. Horbachevsky implementation, adaptation and support was presented. Examples of application of the version control system to the open-source software adaptation and support also was shown.

  15. Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

    Science.gov (United States)

    Wang, Shuo; Wang, Jing; Gao, Yanjing

    2017-01-01

    An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2013-09-30

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

  18. IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis.

    Science.gov (United States)

    Trevisan, Júlio; Angelov, Plamen P; Scott, Andrew D; Carmichael, Paul L; Martin, Francis L

    2013-04-15

    IRootLab is a free and open-source MATLAB toolbox for vibrational biospectroscopy (VBS) data analysis. It offers an object-oriented programming class library, graphical user interfaces (GUIs) and automatic MATLAB code generation. The class library contains a large number of methods, concepts and visualizations for VBS data analysis, some of which are introduced in the toolbox. The GUIs provide an interface to the class library, including a module to merge several spectral files into a dataset. Automatic code allows developers to quickly write VBS data analysis scripts and is a unique resource among tools for VBS. Documentation includes a manual, tutorials, Doxygen-generated reference and a demonstration showcase. IRootLab can handle some of the most popular file formats used in VBS. License: GNU-LGPL. Official website: http://irootlab.googlecode.com/. Supplementary data are available at Bioinformatics online.

  19. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

    Energy Technology Data Exchange (ETDEWEB)

    Felberg, Lisa E. [Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley California 94720; Brookes, David H. [Department of Chemistry, University of California Berkeley, Berkeley California 94720; Yap, Eng-Hui [Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx New York 10461; Jurrus, Elizabeth [Division of Computational and Statistical Analytics, Pacific Northwest National Laboratory, Richland Washington 99352; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City Utah 84112; Baker, Nathan A. [Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland Washington 99352; Division of Applied Mathematics, Brown University, Providence Rhode Island 02912; Head-Gordon, Teresa [Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley California 94720; Department of Chemistry, University of California Berkeley, Berkeley California 94720; Department of Bioengineering, University of California Berkeley, Berkeley California 94720; Chemical Sciences Division, Lawrence Berkeley National Labs, Berkeley California 94720

    2016-11-02

    We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.

  20. PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome.

    Science.gov (United States)

    Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan L

    2015-05-01

    G protein-coupled receptors (GPCRs) are essential mediators of cellular signaling and are important targets of drug action. Of the approximately 350 nonolfactory human GPCRs, more than 100 are still considered to be 'orphans' because their endogenous ligands remain unknown. Here, we describe a unique open-source resource that allows interrogation of the druggable human GPCRome via a G protein-independent β-arrestin-recruitment assay. We validate this unique platform at more than 120 nonorphan human GPCR targets, demonstrate its utility for discovering new ligands for orphan human GPCRs and describe a method (parallel receptorome expression and screening via transcriptional output, with transcriptional activation following arrestin translocation (PRESTO-Tango)) for the simultaneous and parallel interrogation of the entire human nonolfactory GPCRome.