Development of a written music-recognition system using Java and open source technologies

NASA Astrophysics Data System (ADS)

Loibner, Gernot; Schwarzl, Andreas; Kovač, Matthias; Paulus, Dietmar; Pölzleitner, Wolfgang

2005-10-01

We report on the development of a software system to recognize and interpret printed music. The overall goal is to scan printed music sheets, analyze and recognize the notes, timing, and written text, and derive the all necessary information to use the computers MIDI sound system to play the music. This function is primarily useful for musicians who want to digitize printed music for editing purposes. There exist a number of commercial systems that offer such a functionality. However, on testing these systems, we were astonished on how weak they behave in their pattern recognition parts. Although we submitted very clear and rather flawless scanning input, none of these systems was able to e.g. recognize all notes, staff lines, and systems. They all require a high degree of interaction, post-processing, and editing to get a decent digital version of the hard copy material. In this paper we focus on the pattern recognition area. In a first approach we tested more or less standard methods of adaptive thresholding, blob detection, line detection, and corner detection to find the notes, staff lines, and candidate objects subject to OCR. Many of the objects on this type of material can be learned in a training phase. None of the commercial systems we saw offers the option to train special characters or unusual signatures. A second goal in this project is to use a modern software engineering platform. We were interested in how well Java and open source technologies are suitable for pattern recognition and machine vision. The scanning of music served as a case-study.

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

PubMed Central

2011-01-01

Background The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints, only a few open source implementations are available. The aim of this work is to introduce a library for exactly defined molecular decompositions, with a strong focus on the application of these features in machine learning and data mining. It provides several options such as search depth, distance cut-offs, atom- and pharmacophore typing. Furthermore, it provides the functionality to combine, to compare, or to export the fingerprints into several formats. Results We provide a Java 1.6 library for the decomposition of chemical graphs based on the open source Chemistry Development Kit toolkit. We reimplemented popular fingerprinting algorithms such as depth-first search fingerprints, extended connectivity fingerprints, autocorrelation fingerprints (e.g. CATS2D), radial fingerprints (e.g. Molprint2D), geometrical Molprint, atom pairs, and pharmacophore fingerprints. We also implemented custom fingerprints such as the all-shortest path fingerprint that only includes the subset of shortest paths from the full set of paths of the depth-first search fingerprint. As an application of jCompoundMapper, we provide a command-line executable binary. We measured the conversion speed and number of features for each encoding and described the composition of the features in detail. The quality of the encodings was tested using the default parametrizations in combination with a support vector machine on the Sutherland QSAR data sets. Additionally, we benchmarked the fingerprint encodings on the large-scale Ames toxicity benchmark using a large-scale linear support vector machine. The results were promising and could often compete with literature results. On the large Ames benchmark, for example, we obtained an AUC ROC performance of 0.87 with a reimplementation of

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

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

An open-source java platform for automated reaction mapping.

PubMed

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

2010-09-27

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

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

PubMed

Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

2016-01-01

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

jmzML, an open-source Java API for mzML, the PSI standard for MS data.

PubMed

Côté, Richard G; Reisinger, Florian; Martens, Lennart

2010-04-01

We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

Java simulations of embedded control systems.

PubMed

Farias, Gonzalo; Cervin, Anton; Arzén, Karl-Erik; Dormido, Sebastián; Esquembre, Francisco

2010-01-01

This paper introduces a new Open Source Java library suited for the simulation of embedded control systems. The library is based on the ideas and architecture of TrueTime, a toolbox of Matlab devoted to this topic, and allows Java programmers to simulate the performance of control processes which run in a real time environment. Such simulations can improve considerably the learning and design of multitasking real-time systems. The choice of Java increases considerably the usability of our library, because many educators program already in this language. But also because the library can be easily used by Easy Java Simulations (EJS), a popular modeling and authoring tool that is increasingly used in the field of Control Education. EJS allows instructors, students, and researchers with less programming capabilities to create advanced interactive simulations in Java. The paper describes the ideas, implementation, and sample use of the new library both for pure Java programmers and for EJS users. The JTT library and some examples are online available on http://lab.dia.uned.es/jtt.

Java Simulations of Embedded Control Systems

PubMed Central

Farias, Gonzalo; Cervin, Anton; Årzén, Karl-Erik; Dormido, Sebastián; Esquembre, Francisco

2010-01-01

This paper introduces a new Open Source Java library suited for the simulation of embedded control systems. The library is based on the ideas and architecture of TrueTime, a toolbox of Matlab devoted to this topic, and allows Java programmers to simulate the performance of control processes which run in a real time environment. Such simulations can improve considerably the learning and design of multitasking real-time systems. The choice of Java increases considerably the usability of our library, because many educators program already in this language. But also because the library can be easily used by Easy Java Simulations (EJS), a popular modeling and authoring tool that is increasingly used in the field of Control Education. EJS allows instructors, students, and researchers with less programming capabilities to create advanced interactive simulations in Java. The paper describes the ideas, implementation, and sample use of the new library both for pure Java programmers and for EJS users. The JTT library and some examples are online available on http://lab.dia.uned.es/jtt. PMID:22163674

Java Source Code Analysis for API Migration to Embedded Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winter, Victor; McCoy, James A.; Guerrero, Jonathan

Embedded systems form an integral part of our technological infrastructure and oftentimes play a complex and critical role within larger systems. From the perspective of reliability, security, and safety, strong arguments can be made favoring the use of Java over C in such systems. In part, this argument is based on the assumption that suitable subsets of Java’s APIs and extension libraries are available to embedded software developers. In practice, a number of Java-based embedded processors do not support the full features of the JVM. For such processors, source code migration is a mechanism by which key abstractions offered bymore » APIs and extension libraries can made available to embedded software developers. The analysis required for Java source code-level library migration is based on the ability to correctly resolve element references to their corresponding element declarations. A key challenge in this setting is how to perform analysis for incomplete source-code bases (e.g., subsets of libraries) from which types and packages have been omitted. This article formalizes an approach that can be used to extend code bases targeted for migration in such a manner that the threats associated the analysis of incomplete code bases are eliminated.« less

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

PubMed Central

O'Boyle, Noel M; Hutchison, Geoffrey R

2008-01-01

Background Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs). Results We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. Conclusion By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit. PMID:19055766

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

PubMed

Kopanitsa, Georgy; Taranik, Maxim

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

PubMed

Marchetti, Luca; Manca, Vincenzo

2015-04-15

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Instrument Control (iC) - An Open-Source Software to Automate Test Equipment.

PubMed

Pernstich, K P

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming.

JSXGraph--Dynamic Mathematics with JavaScript

ERIC Educational Resources Information Center

Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

2010-01-01

Since Java applets seem to be on the retreat in web application, other approaches for displaying interactive mathematics in the web browser are needed. One such alternative could be our open-source project JSXGraph. It is a cross-browser library for displaying interactive geometry, function plotting, graphs, and data visualization in a web…

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.

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

PubMed

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

2007-02-22

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

Instrument Control (iC) – An Open-Source Software to Automate Test Equipment

PubMed Central

Pernstich, K. P.

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming. PMID:26900522

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

PubMed Central

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E.; Rost, Burkhard; Goldberg, Tatyana

2016-01-01

Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: msa@bio.sh PMID:27412096

Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

Cybersecurity has become a great concern as threats of service interruption, unauthorized access, stealing and altering of information, and spreading of viruses have become more prevalent and serious. Application layer access control of applications is a critical component in the overall security solution that also includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. An access control solution, based on an open-source access manager augmented with custom software components, was developed to provide protection to both Web-based and Javabased client and server applications. The DISA Security Service (DISA-SS) provides common access control capabilities for AMMOS software applications through a set of application programming interfaces (APIs) and network- accessible security services for authentication, single sign-on, authorization checking, and authorization policy management. The OpenAM access management technology designed for Web applications can be extended to meet the needs of Java thick clients and stand alone servers that are commonly used in the JPL AMMOS environment. The DISA-SS reusable components have greatly reduced the effort for each AMMOS subsystem to develop its own access control strategy. The novelty of this work is that it leverages an open-source access management product that was designed for Webbased applications to provide access control for Java thick clients and Java standalone servers. Thick clients and standalone servers are still commonly used in businesses and government, especially for applications that require rich graphical user interfaces and high-performance visualization that cannot be met by thin clients running on Web browsers

PDDL4J: a planning domain description library for java

NASA Astrophysics Data System (ADS)

Pellier, D.; Fiorino, H.

2018-01-01

PDDL4J (Planning Domain Description Library for Java) is an open source toolkit for Java cross-platform developers meant (1) to provide state-of-the-art planners based on the Pddl language, and (2) to facilitate research works on new planners. In this article, we present an overview of the Automated Planning concepts and languages. We present some planning systems and their most significant applications. Then, we detail the Pddl4j toolkit with an emphasis on the available informative structures, heuristics and search algorithms.

Developing a GIS for CO2 analysis using lightweight, open source components

NASA Astrophysics Data System (ADS)

Verma, R.; Goodale, C. E.; Hart, A. F.; Kulawik, S. S.; Law, E.; Osterman, G. B.; Braverman, A.; Nguyen, H. M.; Mattmann, C. A.; Crichton, D. J.; Eldering, A.; Castano, R.; Gunson, M. R.

2012-12-01

There are advantages to approaching the realm of geographic information systems (GIS) using lightweight, open source components in place of a more traditional web map service (WMS) solution. Rapid prototyping, schema-less data storage, the flexible interchange of components, and open source community support are just some of the benefits. In our effort to develop an application supporting the geospatial and temporal rendering of remote sensing carbon-dioxide (CO2) data for the CO2 Virtual Science Data Environment project, we have connected heterogeneous open source components together to form a GIS. Utilizing widely popular open source components including the schema-less database MongoDB, Leaflet interactive maps, the HighCharts JavaScript graphing library, and Python Bottle web-services, we have constructed a system for rapidly visualizing CO2 data with reduced up-front development costs. These components can be aggregated together, resulting in a configurable stack capable of replicating features provided by more standard GIS technologies. The approach we have taken is not meant to replace the more established GIS solutions, but to instead offer a rapid way to provide GIS features early in the development of an application and to offer a path towards utilizing more capable GIS technology in the future.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

PubMed

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

2016-11-15

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

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

NASA Astrophysics Data System (ADS)

Fienen, M. N.; Lowry, C.

2013-12-01

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

AtomicJ: An open source software for analysis of force curves

NASA Astrophysics Data System (ADS)

Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

2014-06-01

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

A Telemetry Browser Built with Java Components

NASA Astrophysics Data System (ADS)

Poupart, E.

In the context of CNES balloon scientific campaigns and telemetry survey field, a generic telemetry processing product, called TelemetryBrowser in the following, was developed reusing COTS, Java Components for most of them. Connection between those components relies on a software architecture based on parameter producers and parameter consumers. The first one transmit parameter values to the second one which has registered to it. All of those producers and consumers can be spread over the network thanks to Corba, and over every kind of workstation thanks to Java. This gives a very powerful mean to adapt to constraints like network bandwidth, or workstations processing or memory. It's also very useful to display and correlate at the same time information coming from multiple and various sources. An important point of this architecture is that the coupling between parameter producers and parameter consumers is reduced to the minimum and that transmission of information on the network is made asynchronously. So, if a parameter consumer goes down or runs slowly, there is no consequence on the other consumers, because producers don't wait for their consumers to finish their data processing before sending it to other consumers. An other interesting point is that parameter producers, also called TelemetryServers in the following are generated nearly automatically starting from a telemetry description using Flavori component. Keywords Java components, Corba, distributed application, OpenORBii, software reuse, COTS, Internet, Flavor. i Flavor (Formal Language for Audio-Visual Object Representation) is an object-oriented media representation language being developed at Columbia University. It is designed as an extension of Java and C++ and simplifies the development of applications that involve a significant media processing component (encoding, decoding, editing, manipulation, etc.) by providing bitstream representation semantics. (flavor.sourceforge.net) ii Open

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

PubMed

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.

Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics.

PubMed

van den Broek, Karina; Kuhn, Hubert; Zielesny, Achim

2018-05-21

Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated "all-in-one" simulation systems.

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination

PubMed Central

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-01-01

Abstract Motivation Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. General features Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Availability Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. PMID:29025122

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

PubMed Central

2013-01-01

Background Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. Results We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patient’s clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website (http://www.abctb.org.au) using Deep Zoom open source technology. Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Conclusions Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5330903258483934 PMID:23402499

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

PubMed

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

2013-02-12

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

NASA World Wind, Open Source 4D Geospatial Visualization Platform: *.NET & Java*

NASA Astrophysics Data System (ADS)

Hogan, P.; Coughlan, J.

2006-12-01

NASA World Wind has only one goal, to provide the maximum opportunity for geospatial information to be experienced, be it education, science, research, business, or government. The benefits to understanding for information delivered in the context of its 4D virtual reality are extraordinary. The NASA World Wind visualization platform is open source and therefore lends itself well to being extended to service *any* requirements, be they proprietary and commercial or simply available. Data accessibility is highly optimized using standard formats including internationally certified open standards (W*S). Although proprietary applications can be built based on World Wind, and proprietary data delivered that leverage World Wind, there is nothing proprietary about the visualization platform itself or the multiple planetary data sets readily available, including global animations of live weather. NASA World Wind is being used by NASA research teams as well as being a formal part of high school and university curriculum. The National Guard uses World Wind for emergency response activities and State governments have incorporated high resolution imagery for GIS management as well as for their cross-agency emergency response activities. The U.S. federal government uses NASA World Wind for a myriad of GIS and security-related issues (NSA, NGA, DOE, FAA, etc.).

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

runtime library Swift server runtime Java servlet framework HTTP Web server Web browser Figure 2: The Swift architecture introduced an open-ended...On the server, the Java application code links against Swift’s server-side run-time library, which in turn sits on top of the standard Java servlet ...AFRL-RI-RS-TR-2010-9 Final Technical Report January 2010 ACCOUNTABLE INFORMATION FLOW FOR JAVA -BASED WEB APPLICATIONS

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.

PubMed

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-10-01

Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. © The Author 2017; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

OOSTethys - Open Source Software for the Global Earth Observing Systems of Systems

NASA Astrophysics Data System (ADS)

Bridger, E.; Bermudez, L. E.; Maskey, M.; Rueda, C.; Babin, B. L.; Blair, R.

2009-12-01

An open source software project is much more than just picking the right license, hosting modular code and providing effective documentation. Success in advancing in an open collaborative way requires that the process match the expected code functionality to the developer's personal expertise and organizational needs as well as having an enthusiastic and responsive core lead group. We will present the lessons learned fromOOSTethys , which is a community of software developers and marine scientists who develop open source tools, in multiple languages, to integrate ocean observing systems into an Integrated Ocean Observing System (IOOS). OOSTethys' goal is to dramatically reduce the time it takes to install, adopt and update standards-compliant web services. OOSTethys has developed servers, clients and a registry. Open source PERL, PYTHON, JAVA and ASP tool kits and reference implementations are helping the marine community publish near real-time observation data in interoperable standard formats. In some cases publishing an OpenGeospatial Consortium (OGC), Sensor Observation Service (SOS) from NetCDF files or a database or even CSV text files could take only minutes depending on the skills of the developer. OOSTethys is also developing an OGC standard registry, Catalog Service for Web (CSW). This open source CSW registry was implemented to easily register and discover SOSs using ISO 19139 service metadata. A web interface layer over the CSW registry simplifies the registration process by harvesting metadata describing the observations and sensors from the “GetCapabilities” response of SOS. OPENIOOS is the web client, developed in PERL to visualize the sensors in the SOS services. While the number of OOSTethys software developers is small, currently about 10 around the world, the number of OOSTethys toolkit implementers is larger and growing and the ease of use has played a large role in spreading the use of interoperable standards compliant web services widely

Open Source, Openness, and Higher Education

ERIC Educational Resources Information Center

Wiley, David

2006-01-01

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

Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

Computation in Classical Mechanics with Easy Java Simulations (EJS)

NASA Astrophysics Data System (ADS)

Cox, Anne J.

2006-12-01

Let your students enjoy creating animations and incorporating some computational physics into your Classical Mechanics course. This talk will demonstrate the use of an Open Source Physics package, Easy Java Simulations (EJS), in an already existing sophomore/junior level Classical Mechanics course. EJS allows for incremental introduction of computational physics into existing courses because it is easy to use (for instructors and students alike) and it is open source. Students can use this tool for numerical solutions to problems (as they can with commercial systems: Mathcad and Mathematica), but they can also generate their own animations. For example, students in Classical Mechanics use Lagrangian mechanics to solve a problem, and then use EJS not only to numerically solve the differential equations, but to show the associated motion (and check their answers). EJS, developed by Francisco Esquembre (http://fem.um.es/Ejs/), is built on the OpenSource Physics framework (http://www.opensourcephysics.org/) supported through NSF DUE0442581.

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

NASA Astrophysics Data System (ADS)

Udell, C.; Selker, J. S.

2017-12-01

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

Shale characterization in mass transport complex as a potential source rock: An example from onshore West Java Basin, Indonesia

NASA Astrophysics Data System (ADS)

Nugraha, A. M. S.; Widiarti, R.; Kusumah, E. P.

2017-12-01

This study describes a deep-water slump facies shale of the Early Miocene Jatiluhur/Cibulakan Formation to understand its potential as a source rock in an active tectonic region, the onshore West Java. The formation is equivalent with the Gumai Formation, which has been well-known as another prolific source rock besides the Oligocene Talang Akar Formation in North West Java Basin, Indonesia. The equivalent shale formation is expected to have same potential source rock towards the onshore of Central Java. The shale samples were taken onshore, 150 km away from the basin. The shale must be rich of organic matter, have good quality of kerogen, and thermally matured to be categorized as a potential source rock. Investigations from petrography, X-Ray diffractions (XRD), and backscattered electron show heterogeneous mineralogy in the shales. The mineralogy consists of clay minerals, minor quartz, muscovite, calcite, chlorite, clinopyroxene, and other weathered minerals. This composition makes the shale more brittle. Scanning Electron Microscope (SEM) analysis indicate secondary porosities and microstructures. Total Organic Carbon (TOC) shows 0.8-1.1 wt%, compared to the basinal shale 1.5-8 wt%. The shale properties from this outcropped formation indicate a good potential source rock that can be found in the subsurface area with better quality and maturity.

Open Source Software Development

DTIC Science & Technology

2011-01-01

Software, 2002, 149(1), 3-17. 3. DiBona , C., Cooper, D., and Stone, M. (Eds.), Open Sources 2.0, 2005, O’Reilly Media, Sebastopol, CA. Also see, C... DiBona , S. Ockman, and M. Stone (Eds.). Open Sources: Vocides from the Open Source Revolution, 1999. O’Reilly Media, Sebastopol, CA. 4. Ducheneaut, N

Introduction to an Open Source Internet-Based Testing Program for Medical Student Examinations

PubMed Central

2009-01-01

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education. PMID:20046457

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

NASA Astrophysics Data System (ADS)

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

2007-05-01

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

Open Source Vision

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

Increasingly, colleges and universities are turning to open source as a way to meet their technology infrastructure and application needs. Open source has changed life for visionary CIOs and their campus communities nationwide. The author discusses what these technologists see as the benefits--and the considerations.

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

PubMed

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

2017-10-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Open-source colorimeter.

PubMed

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

2013-04-19

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

Open-Source Colorimeter

PubMed Central

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

2013-01-01

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

An Open Source Tool to Test Interoperability

NASA Astrophysics Data System (ADS)

Bermudez, L. E.

2012-12-01

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

Open source libraries and frameworks for biological data visualisation: A guide for developers

PubMed Central

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. PMID:25475079

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

Open source posturography.

PubMed

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.

jFuzz: A Concolic Whitebox Fuzzer for Java

NASA Technical Reports Server (NTRS)

Jayaraman, Karthick; Harvison, David; Ganesh, Vijay; Kiezun, Adam

2009-01-01

We present jFuzz, a automatic testing tool for Java programs. jFuzz is a concolic whitebox fuzzer, built on the NASA Java PathFinder, an explicit-state Java model checker, and a framework for developing reliability and analysis tools for Java. Starting from a seed input, jFuzz automatically and systematically generates inputs that exercise new program paths. jFuzz uses a combination of concrete and symbolic execution, and constraint solving. Time spent on solving constraints can be significant. We implemented several well-known optimizations and name-independent caching, which aggressively normalizes the constraints to reduce the number of calls to the constraint solver. We present preliminary results due to the optimizations, and demonstrate the effectiveness of jFuzz in creating good test inputs. The source code of jFuzz is available as part of the NASA Java PathFinder. jFuzz is intended to be a research testbed for investigating new testing and analysis techniques based on concrete and symbolic execution. The source code of jFuzz is available as part of the NASA Java PathFinder.

NASA World Wind, Open Source 4D Geospatial Visualization Platform: *.NET & Java* for EDUCATION

NASA Astrophysics Data System (ADS)

Hogan, P.; Kuehnel, F.

2006-12-01

NASA World Wind has only one goal, to provide the maximum opportunity for geospatial information to be experienced, be it education, science, research, business, or government. The benefits to understanding for information delivered in the context of its 4D virtual reality are extraordinary. The NASA World Wind visualization platform is open source and therefore lends itself well to being extended to service *any* requirements, be they proprietary and commercial or simply available. Data accessibility is highly optimized using standard formats including internationally certified open standards (W*S). Although proprietary applications can be built based on World Wind, and proprietary data delivered that leverage World Wind, there is nothing proprietary about the visualization platform itself or the multiple planetary data sets readily available, including global animations of live weather. NASA World Wind is being used by NASA research teams as well as being a formal part of high school and university curriculum. The National Guard uses World Wind for emergency response activities and State governments have incorporated high resolution imagery for GIS management as well as for their cross-agency emergency response activities. The U.S. federal government uses NASA World Wind for a myriad of GIS and security-related issues (NSA, NGA, DOE, FAA, etc.).

How Is Open Source Special?

ERIC Educational Resources Information Center

Kapor, Mitchell

2005-01-01

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

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

ERIC Educational Resources Information Center

Committee for Economic Development, 2006

2006-01-01

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

An Open Source Web Map Server Implementation For California and the Digital Earth: Lessons Learned

NASA Technical Reports Server (NTRS)

Sullivan, D. V.; Sheffner, E. J.; Skiles, J. W.; Brass, J. A.; Condon, Estelle (Technical Monitor)

2000-01-01

This paper describes an Open Source implementation of the Open GIS Consortium's Web Map interface. It is based on the very popular Apache WWW Server, the Sun Microsystems Java ServIet Development Kit, and a C language shared library interface to a spatial datastore. This server was initially written as a proof of concept, to support a National Aeronautics and Space Administration (NASA) Digital Earth test bed demonstration. It will also find use in the California Land Science Information Partnership (CaLSIP), a joint program between NASA and the state of California. At least one WebMap enabled server will be installed in every one of the state's 58 counties. This server will form a basis for a simple, easily maintained installation for those entities that do not yet require one of the larger, more expensive, commercial offerings.

The Commercial Open Source Business Model

NASA Astrophysics Data System (ADS)

Riehle, Dirk

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

FloorspaceJS - A New, Open Source, Web-Based Geometry Editor for Building Energy Modeling (BEM): Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Macumber, Daniel L; Horowitz, Scott G; Schott, Marjorie

Across most industries, desktop applications are being rapidly migrated to web applications for a variety of reasons. Web applications are inherently cross platform, mobile, and easier to distribute than desktop applications. Fueling this trend are a wide range of free, open source libraries and frameworks that make it incredibly easy to develop powerful web applications. The building energy modeling community is just beginning to pick up on these larger trends, with a small but growing number of building energy modeling applications starting on or moving to the web. This paper presents a new, open source, web based geometry editor formore » Building Energy Modeling (BEM). The editor is written completely in JavaScript and runs in a modern web browser. The editor works on a custom JSON file format and is designed to be integrated into a variety of web and desktop applications. The web based editor is available to use as a standalone web application at: https://nrel.github.io/openstudio-geometry-editor/. An example integration is demonstrated with the OpenStudio desktop application. Finally, the editor can be easily integrated with a wide range of possible building energy modeling web applications.« less

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

PubMed

Bernal-Rusiel, Jorge L; Rannou, Nicolas; Gollub, Randy L; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView , a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

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

Open source libraries and frameworks for biological data visualisation: a guide for developers.

PubMed

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-04-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Petroleum systems of the Northwest Java Province, Java and offshore southeast Sumatra, Indonesia

USGS Publications Warehouse

Bishop, Michele G.

2000-01-01

Mature, synrift lacustrine shales of Eocene to Oligocene age and mature, late-rift coals and coaly shales of Oligocene to Miocene age are source rocks for oil and gas in two important petroleum systems of the onshore and offshore areas of the Northwest Java Basin. Biogenic gas and carbonate-sourced gas have also been identified. These hydrocarbons are trapped primarily in anticlines and fault blocks involving sandstone and carbonate reservoirs. These source rocks and reservoir rocks were deposited in a complex of Tertiary rift basins formed from single or multiple half-grabens on the south edge of the Sunda Shelf plate. The overall transgressive succession was punctuated by clastic input from the exposed Sunda Shelf and marine transgressions from the south. The Northwest Java province may contain more than 2 billion barrels of oil equivalent in addition to the 10 billion barrels of oil equivalent already identified.

The Open Source Snowpack modelling ecosystem

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Creating Open Source Conversation

ERIC Educational Resources Information Center

Sheehan, Kate

2009-01-01

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

Open-source software: not quite endsville.

PubMed

Stahl, Matthew T

2005-02-01

Open-source software will never achieve ubiquity. There are environments in which it simply does not flourish. By its nature, open-source development requires free exchange of ideas, community involvement, and the efforts of talented and dedicated individuals. However, pressures can come from several sources that prevent this from happening. In addition, openness and complex licensing issues invite misuse and abuse. Care must be taken to avoid the pitfalls of open-source software.

Open-source hardware for medical devices.

PubMed

Niezen, Gerrit; Eslambolchilar, Parisa; Thimbleby, Harold

2016-04-01

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

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

PubMed

Deibel, Eric

2014-01-01

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

Open-source hardware for medical devices

PubMed Central

2016-01-01

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

Terra Harvest Open Source Environment (THOSE): a universal unattended ground sensor controller

NASA Astrophysics Data System (ADS)

Gold, Joshua; Klawon, Kevin; Humeniuk, David; Landoll, Darren

2011-06-01

Under the Terra Harvest Program, the Defense Intelligence Agency (DIA) has the objective of developing a universal Controller for the Unattended Ground Sensor (UGS) community. The mission is to define, implement, and thoroughly document an open architecture that universally supports UGS missions, integrating disparate systems, peripherals, etc. The Controller's inherent interoperability with numerous systems enables the integration of both legacy and future Unattended Ground Sensor System (UGSS) components, while the design's open architecture supports rapid third-party development to ensure operational readiness. The successful accomplishment of these objectives by the program's Phase 3b contractors is demonstrated via integration of the companies' respective plug-'n-play contributions that include various peripherals, such as sensors, cameras, etc., and their associated software drivers. In order to independently validate the Terra Harvest architecture, L-3 Nova Engineering, along with its partner, the University of Dayton Research Institute (UDRI), is developing the Terra Harvest Open Source Environment (THOSE), a Java based system running on an embedded Linux Operating System (OS). The Use Cases on which the software is developed support the full range of UGS operational scenarios such as remote sensor triggering, image capture, and data exfiltration. The Team is additionally developing an ARM microprocessor evaluation platform that is both energyefficient and operationally flexible. The paper describes the overall THOSE architecture, as well as the implementation strategy for some of the key software components. Preliminary integration/test results and the Team's approach for transitioning the THOSE design and source code to the Government are also presented.

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

Open Source Molecular Modeling

PubMed Central

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

2016-01-01

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

U.S. Tsunami Information technology (TIM) Modernization:Developing a Maintainable and Extensible Open Source Earthquake and Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Lisowski, S.; Baker, B.; Hagerty, M.; Lomax, A.; Leifer, J. M.; Thies, D. A.; Schnackenberg, A.; Barrows, J.

2015-12-01

Tsunami Information technology Modernization (TIM) is a National Oceanic and Atmospheric Administration (NOAA) project to update and standardize the earthquake and tsunami monitoring systems currently employed at the U.S. Tsunami Warning Centers in Ewa Beach, Hawaii (PTWC) and Palmer, Alaska (NTWC). While this project was funded by NOAA to solve a specific problem, the requirements that the delivered system be both open source and easily maintainable have resulted in the creation of a variety of open source (OS) software packages. The open source software is now complete and this is a presentation of the OS Software that has been funded by NOAA for benefit of the entire seismic community. The design architecture comprises three distinct components: (1) The user interface, (2) The real-time data acquisition and processing system and (3) The scientific algorithm library. The system follows a modular design with loose coupling between components. We now identify the major project constituents. The user interface, CAVE, is written in Java and is compatible with the existing National Weather Service (NWS) open source graphical system AWIPS. The selected real-time seismic acquisition and processing system is open source SeisComp3 (sc3). The seismic library (libseismic) contains numerous custom written and wrapped open source seismic algorithms (e.g., ML/mb/Ms/Mwp, mantle magnitude (Mm), w-phase moment tensor, bodywave moment tensor, finite-fault inversion, array processing). The seismic library is organized in a way (function naming and usage) that will be familiar to users of Matlab. The seismic library extends sc3 so that it can be called by the real-time system, but it can also be driven and tested outside of sc3, for example, by ObsPy or Earthworm. To unify the three principal components we have developed a flexible and lightweight communication layer called SeismoEdex.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

PubMed

Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart

2011-08-05

The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.

Geothermal and volcanism in west Java

NASA Astrophysics Data System (ADS)

Setiawan, I.; Indarto, S.; Sudarsono; Fauzi I, A.; Yuliyanti, A.; Lintjewas, L.; Alkausar, A.; Jakah

2018-02-01

Indonesian active volcanoes extend from Sumatra, Jawa, Bali, Lombok, Flores, North Sulawesi, and Halmahera. The volcanic arc hosts 276 volcanoes with 29 GWe of geothermal resources. Considering a wide distribution of geothermal potency, geothermal research is very important to be carried out especially to tackle high energy demand in Indonesia as an alternative energy sources aside from fossil fuel. Geothermal potency associated with volcanoes-hosted in West Java can be found in the West Java segment of Sunda Arc that is parallel with the subduction. The subduction of Indo-Australian oceanic plate beneath the Eurasian continental plate results in various volcanic products in a wide range of geochemical and mineralogical characteristics. The geochemical and mineralogical characteristics of volcanic and magmatic rocks associated with geothermal systems are ill-defined. Comprehensive study of geochemical signatures, mineralogical properties, and isotopes analysis might lead to the understanding of how large geothermal fields are found in West Java compared to ones in Central and East Java. The result can also provoke some valuable impacts on Java tectonic evolution and can suggest the key information for geothermal exploration enhancement.

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

PubMed Central

Bernal-Rusiel, Jorge L.; Rannou, Nicolas; Gollub, Randy L.; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E.; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution. PMID:28507515

Java, Indonesia

NASA Image and Video Library

1996-01-20

STS072-737-012 (11-20 Jan. 1996) --- The astronauts photographed this view of Java, an Indonesian island. Java lies between the Java Sea at top and the Indian Ocean at bottom (north is located at top center). A line of volcanoes on the southern edge of the island, trending from central to eastern areas, is highlighted by a ring of clouds. Off the southern coast of Java is the Java Trench where the Australian plate, to the south, is diving under the Eurasia plate to the north. According to anthropologists, Java has one of the highest populations in Indonesia because the soil is enriched by volcanic ash. Merapi volcano, at left edge, second volcano to the right, rises to 9,550 feet and erupts frequently. Madura Island, partially obscured by clouds, can be seen on the upper eastern end of Java.

Free for All: Open Source Software

ERIC Educational Resources Information Center

Schneider, Karen

2008-01-01

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

An Open Source Simulation System

NASA Technical Reports Server (NTRS)

Slack, Thomas

2005-01-01

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

The Efficient Utilization of Open Source Information

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baty, Samuel R.

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 keymore » 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.« less

Open-Source GIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2012-01-01

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

An Open-Source and Java-Technologies Approach to Web Applications

DTIC Science & Technology

2003-09-01

program for any purpose (Freedom 0). • The freedom to study how the program works, and adapt it to individual needs (Freedom 1). Access to the source...manage information for many purposes. Today a key technology that allows developers to make Web applications is server-side programming to generate a

Access Control of Web and Java Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.; Johnson, Bryan

2011-01-01

Cyber security has gained national and international attention as a result of near continuous headlines from financial institutions, retail stores, government offices and universities reporting compromised systems and stolen data. Concerns continue to rise as threats of service interruption, and spreading of viruses become ever more prevalent and serious. Controlling access to application layer resources is a critical component in a layered security solution that includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. In this paper we discuss the development of an application-level access control solution, based on an open-source access manager augmented with custom software components, to provide protection to both Web-based and Java-based client and server applications.

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

PubMed

Wenig, Philip; Odermatt, Juergen

2010-07-30

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

Paleofacies of Eocene Lower Ngimbang Source Rocks in Cepu Area, East Java Basin based on Biomarkers and Carbon-13 Isotopes

NASA Astrophysics Data System (ADS)

Devi, Elok A.; Rachman, Faisal; Satyana, Awang H.; Fahrudin; Setyawan, Reddy

2018-02-01

The Eocene Lower Ngimbang carbonaceous shales are geochemically proven hydrocarbon source rocks in the East Java Basin. Sedimentary facies of source rock is important for the source evaluation that can be examined by using biomarkers and carbon-13 isotopes data. Furthermore, paleogeography of the source sedimentation can be reconstructed. The case study was conducted on rock samples of Lower Ngimbang from two exploration wells drilled in Cepu area, East Java Basin, Kujung-1 and Ngimbang-1 wells. The biomarker data include GC and GC-MS data of normal alkanes, isoprenoids, triterpanes, and steranes. Carbon-13 isotope data include saturate and aromatic fractions. Various crossplots of biomarker and carbon-13 isotope data of the Lower Ngimbang source samples from the two wells show that the source facies of Lower Ngimbang shales changed from transitional/deltaic setting at Kujung-1 well location to marginal marine setting at Ngimbang-1 well location. This reveals that the Eocene paleogeography of the Cepu area was composed of land area in the north and marine setting to the south. Biomarkers and carbon-13 isotopes are powerful data for reconstructing paleogeography and paleofacies. In the absence of fossils in some sedimentary facies, these geochemical data are good alternatives.

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

PubMed Central

2011-01-01

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

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

NASA Technical Reports Server (NTRS)

Fiene, Bruce F.

1994-01-01

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

JAMSS: proteomics mass spectrometry simulation in Java.

PubMed

Smith, Rob; Prince, John T

2015-03-01

Countless proteomics data processing algorithms have been proposed, yet few have been critically evaluated due to lack of labeled data (data with known identities and quantities). Although labeling techniques exist, they are limited in terms of confidence and accuracy. In silico simulators have recently been used to create complex data with known identities and quantities. We propose Java Mass Spectrometry Simulator (JAMSS): a fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous in silico simulators in terms of its ease to install, minimal parameters, graphical user interface, multithreading capability, retention time shift model and reproducibility. The simulator creates mzML 1.1.0. It is open source software licensed under the GPLv3. The software and source are available at https://github.com/optimusmoose/JAMSS. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The 2017 Bioinformatics Open Source Conference (BOSC)

PubMed Central

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. PMID:29118973

The 2017 Bioinformatics Open Source Conference (BOSC).

PubMed

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.

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

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

Open source molecular modeling.

PubMed

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

2016-09-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Health figures: an open source JavaScript library for health data visualization.

PubMed

Ledesma, Andres; Al-Musawi, Mohammed; Nieminen, Hannu

2016-03-22

The way we look at data has a great impact on how we can understand it, particularly when the data is related to health and wellness. Due to the increased use of self-tracking devices and the ongoing shift towards preventive medicine, better understanding of our health data is an important part of improving the general welfare of the citizens. Electronic Health Records, self-tracking devices and mobile applications provide a rich variety of data but it often becomes difficult to understand. We implemented the hFigures library inspired on the hGraph visualization with additional improvements. The purpose of the library is to provide a visual representation of the evolution of health measurements in a complete and useful manner. We researched the usefulness and usability of the library by building an application for health data visualization in a health coaching program. We performed a user evaluation with Heuristic Evaluation, Controlled User Testing and Usability Questionnaires. In the Heuristics Evaluation the average response was 6.3 out of 7 points and the Cognitive Walkthrough done by usability experts indicated no design or mismatch errors. In the CSUQ usability test the system obtained an average score of 6.13 out of 7, and in the ASQ usability test the overall satisfaction score was 6.64 out of 7. We developed hFigures, an open source library for visualizing a complete, accurate and normalized graphical representation of health data. The idea is based on the concept of the hGraph but it provides additional key features, including a comparison of multiple health measurements over time. We conducted a usability evaluation of the library as a key component of an application for health and wellness monitoring. The results indicate that the data visualization library was helpful in assisting users in understanding health data and its evolution over time.

Using OpenOffice as a Portable Interface to JAVA-Based Applications

NASA Astrophysics Data System (ADS)

Comeau, T.; Garrett, B.; Richon, J.; Romelfanger, F.

2004-07-01

STScI previously used Microsoft Word and Microsoft Access, a Sybase ODBC driver, and the Adobe Acrobat PDF writer, along with a substantial amount of Visual Basic, to generate a variety of documents for the internal Space Telescope Grants Administration System (STGMS). While investigating an upgrade to Microsoft Office XP, we began considering alternatives, ultimately selecting an open source product, OpenOffice.org. This reduces the total number of products required to operate the internal STGMS system, simplifies the build system, and opens the possibility of moving to a non-Windows platform. We describe the experience of moving from Microsoft Office to OpenOffice.org, and our other internal uses of OpenOffice.org in our development environment.

Improving Data Catalogs with Free and Open Source Software

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Open-Source Syringe Pump Library

PubMed Central

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

2014-01-01

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

Open-Source 3D-Printable Optics Equipment

PubMed Central

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

2013-01-01

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

Open-source 3D-printable optics equipment.

PubMed

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

2013-01-01

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

Tactical Web Services: Using XML and Java Web Services to Conduct Real-Time Net-Centric Sonar Visualization

DTIC Science & Technology

2004-09-01

Rosetti USN U.S. Navy Chesterton, IN 6. Erik Chaum NUWC Newport, RI 7. David Bellino NPRI Newport, RI 8. Dick Nadolink NUWC Newport, RI...found at (http://www.parallelgraphics.com/products/cortona). G. JFREECHART JFreeChart is an open source Java API created by David Gilbert and...www.xj3d.org/. Accessed 3 September 2004. Hunter, David , Kurt Cagle, and Chris Dix, eds. Beginning XML, Second Edition. Indianapolis, IN

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

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

2011-01-01

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

Hydrocarbon potential assessment of Ngimbang formation, Rihen field of Northeast Java Basin

NASA Astrophysics Data System (ADS)

Pandito, R. H.; Haris, A.; Zainal, R. M.; Riyanto, A.

2017-07-01

The assessment of Ngimbang formation at Rihen field of Northeast Java Basin has been conducted to identify the hydrocarbon potential by analyzing the response of passive seismic on the proven reservoir zone and proposing a tectonic evolution model. In the case of petroleum exploration in Northeast Java basin, the Ngimbang formation cannot be simply overemphasized. East Java Basin has been well known as one of the mature basins producing hydrocarbons in Indonesia. This basin was stratigraphically composed of several formations from the old to the young i.e., the basement, Ngimbang, Kujung, Tuban, Ngerayong, Wonocolo, Kawengan and Lidah formation. All of these formations have proven to become hydrocarbon producer. The Ngrayong formation, which is geologically dominated by channels, has become a production formation. The Kujung formation that has been known with the reef build up has produced more than 102 million barrel of oil. The Ngimbang formation so far has not been comprehensively assessed in term its role as a source rock and a reservoir. In 2013, one exploratory well has been drilled at Ngimbang formation and shown a gas discovery, which is indicated on Drill Stem Test (DST) reading for more than 22 MMSCFD of gas. This discovery opens new prospect in exploring the Ngimbang formation.

The 2016 Bioinformatics Open Source Conference (BOSC).

PubMed

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.

Investigating Along-Strike Variations of Source Parameters for Relocated Thrust Earthquakes Along the Sumatra-Java Subduction Zone

NASA Astrophysics Data System (ADS)

El Hariri, M.; Bilek, S. L.; Deshon, H. R.; Engdahl, E. R.

2009-12-01

Some earthquakes generate anomalously large tsunami waves relative to their surface wave magnitudes (Ms). This class of events, known as tsunami earthquakes, is characterized by having a long rupture duration and low radiated energy at long periods. These earthquakes are relatively rare. There have been only 9 documented cases, including 2 in the Java subduction zone (1994 Mw=7.8 and the 2006 Mw=7.7). Several models have been proposed to explain the unexpectedly large tsunami, such as displacement along high-angle splay faults, landslide-induced tsunami due to coseismic shaking, or large seismic slip within low rigidity sediments or weaker material along the shallowest part of the subduction zone. Slow slip has also been suggested along portions of the 2004 Mw=9.2 Sumatra-Andaman earthquake zone. In this study we compute the source parameters of 90 relocated shallow thrust events (Mw 5.1-7.8) along the Sumatra-Java subduction zone including the two Java tsunami earthquakes. Events are relocated using a modification to the Engdahl, van der Hilst and Buland (EHB) earthquake relocation method that incorporates an automated frequency-dependent phase detector. This allows for the use of increased numbers of phase arrival times, especially depth phases, and improves hypocentral locations. Source time functions, rupture duration and depth estimates are determined using multi-station deconvolution of broadband teleseismic P and SH waves. We seek to correlate any along-strike variation in rupture characteristics with tectonic features and rupture characteristics of the previous slow earthquakes along this margin to gain a better understanding of the conditions resulting in slow ruptures. Preliminary results from the analysis of these events show that in addition to depth-dependent variations there are also along-strike variations in rupture duration. We find that along the Java segment, the longer duration event locates in a highly coupled region corresponding to the

Developing an Open Source Option for NASA Software

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Open-Source Data and the Study of Homicide.

PubMed

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.

40 CFR Table 3 to Subpart Wwww of... - Organic HAP Emissions Limits for Existing Open Molding Sources, New Open Molding Sources Emitting...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic Composites... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and...

The 2016 Bioinformatics Open Source Conference (BOSC)

PubMed Central

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

2016-01-01

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

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

The state and profile of open source software projects in health and medical informatics.

PubMed

Janamanchi, Balaji; Katsamakas, Evangelos; Raghupathi, Wullianallur; Gao, Wei

2009-07-01

Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

ImgLib2--generic image processing in Java.

PubMed

Pietzsch, Tobias; Preibisch, Stephan; Tomancák, Pavel; Saalfeld, Stephan

2012-11-15

ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins. ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib. Supplementary data are available at Bioinformatics Online. saalfeld@mpi-cbg.de

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PubMed

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

2016-02-01

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

A Study of Clinically Related Open Source Software Projects

PubMed Central

Hogarth, Michael A.; Turner, Stuart

2005-01-01

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the ‘fit’ of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects. PMID:16779056

Open Source 2010: Reflections on 2007

ERIC Educational Resources Information Center

Wheeler, Brad

2007-01-01

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

BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction.

PubMed

Jonnalagadda, Siddhartha; Gonzalez, Graciela

2010-11-13

BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%. The BioSimplify tool and test corpus can be downloaded from https://biosimplify.sourceforge.net.

The successes and challenges of open-source biopharmaceutical innovation.

PubMed

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.

Predictors of Errors of Novice Java Programmers

ERIC Educational Resources Information Center

Bringula, Rex P.; Manabat, Geecee Maybelline A.; Tolentino, Miguel Angelo A.; Torres, Edmon L.

2012-01-01

This descriptive study determined which of the sources of errors would predict the errors committed by novice Java programmers. Descriptive statistics revealed that the respondents perceived that they committed the identified eighteen errors infrequently. Thought error was perceived to be the main source of error during the laboratory programming…

OpenHealth Platform for Interactive Contextualization of Population Health Open Data.

PubMed

Almeida, Jonas S; Hajagos, Janos; Crnosija, Ivan; Kurc, Tahsin; Saltz, Mary; Saltz, Joel

The financial incentives for data science applications leading to improved health outcomes, such as DSRIP (bit.ly/dsrip), are well-aligned with the broad adoption of Open Data by State and Federal agencies. This creates entirely novel opportunities for analytical applications that make exclusive use of the pervasive Web Computing platform. The framework described here explores this new avenue to contextualize Health data in a manner that relies exclusively on the native JavaScript interpreter and data processing resources of the ubiquitous Web Browser. The OpenHealth platform is made publicly available, and is publicly hosted with version control and open source, at https://github.com/mathbiol/openHealth. The different data/analytics workflow architectures explored are accompanied with live applications ranging from DSRIP, such as Hospital Inpatient Prevention Quality Indicators at http://bit.ly/pqiSuffolk, to The Cancer Genome Atlas (TCGA) as illustrated by http://bit.ly/tcgascopeGBM.

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

PubMed Central

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

2016-01-01

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

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

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

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

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

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

Science.gov Websites

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

PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees.

PubMed

Fuchsberger, Christian; Falchi, Mario; Forer, Lukas; Pramstaller, Peter P

2008-01-15

PedVizApi is a Java API (application program interface) for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data. An extensive demo application and a R interface is provided. http://www.pedvizapi.org

The r-Java 2.0 code: nuclear physics

NASA Astrophysics Data System (ADS)

Kostka, M.; Koning, N.; Shand, Z.; Ouyed, R.; Jaikumar, P.

2014-08-01

Aims: We present r-Java 2.0, a nucleosynthesis code for open use that performs r-process calculations, along with a suite of other analysis tools. Methods: Equipped with a straightforward graphical user interface, r-Java 2.0 is capable of simulating nuclear statistical equilibrium (NSE), calculating r-process abundances for a wide range of input parameters and astrophysical environments, computing the mass fragmentation from neutron-induced fission and studying individual nucleosynthesis processes. Results: In this paper we discuss enhancements to this version of r-Java, especially the ability to solve the full reaction network. The sophisticated fission methodology incorporated in r-Java 2.0 that includes three fission channels (beta-delayed, neutron-induced, and spontaneous fission), along with computation of the mass fragmentation, is compared to the upper limit on mass fission approximation. The effects of including beta-delayed neutron emission on r-process yield is studied. The role of Coulomb interactions in NSE abundances is shown to be significant, supporting previous findings. A comparative analysis was undertaken during the development of r-Java 2.0 whereby we reproduced the results found in the literature from three other r-process codes. This code is capable of simulating the physical environment of the high-entropy wind around a proto-neutron star, the ejecta from a neutron star merger, or the relativistic ejecta from a quark nova. Likewise the users of r-Java 2.0 are given the freedom to define a custom environment. This software provides a platform for comparing proposed r-process sites.

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

PubMed

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

2012-01-01

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

CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PubMed Central

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

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery. PMID:22815713

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.

PubMed

Aiyetan, Paul; Thomas, Stefani N; Zhang, Zhen; Zhang, Hui

2015-12-12

Selected and multiple reaction monitoring involves monitoring a multiplexed assay of proteotypic peptides and associated transitions in mass spectrometry runs. To describe peptide and associated transitions as stable, quantifiable, and reproducible representatives of proteins of interest, experimental and analytical validation is required. However, inadequate and disparate analytical tools and validation methods predispose assay performance measures to errors and inconsistencies. Implemented as a freely available, open-source tool in the platform independent Java programing language, MRMPlus computes analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for "Tier 2" assays - that is, non-clinical assays sufficient enough to measure changes due to both biological and experimental perturbations. Computed measures include; limit of detection, lower limit of quantification, linearity, carry-over, partial validation of specificity, and upper limit of quantification. MRMPlus streamlines assay development analytical workflow and therefore minimizes error predisposition. MRMPlus may also be used for performance estimation for targeted assays not described by the Assay Development Working Group. MRMPlus' source codes and compiled binaries can be freely downloaded from https://bitbucket.org/paiyetan/mrmplusgui and https://bitbucket.org/paiyetan/mrmplusgui/downloads respectively.

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

ERIC Educational Resources Information Center

Hirst, Tony

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

Learning from hackers: open-source clinical trials.

PubMed

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.

Seismic hazard analysis with PSHA method in four cities in Java.

NASA Astrophysics Data System (ADS)

Elistyawati, Y.; Palupi, I. R.; Suharsono

2016-11-01

In this study the tectonic earthquakes was observed through the peak ground acceleration through the PSHA method by dividing the area of the earthquake source. This study applied the earthquake data from 1965 - 2015 that has been analyzed the completeness of the data, location research was the entire Java with stressed in four large cities prone to earthquakes. The results were found to be a hazard map with a return period of 500 years, 2500 years return period, and the hazard curve were four major cities (Jakarta, Bandung, Yogyakarta, and the city of Banyuwangi). Results Java PGA hazard map 500 years had a peak ground acceleration within 0 g ≥ 0.5 g, while the return period of 2500 years had a value of 0 to ≥ 0.8 g. While, the PGA hazard curves on the city's most influential source of the earthquake was from sources such as fault Cimandiri backgroud, for the city of Bandung earthquake sources that influence the seismic source fault dent background form. In other side, the city of Yogyakarta earthquake hazard curve of the most influential was the source of the earthquake background of the Opak fault, and the most influential hazard curve of Banyuwangi earthquake was the source of Java and Sumba megatruts earthquake.

FPV: fast protein visualization using Java 3D.

PubMed

Can, Tolga; Wang, Yujun; Wang, Yuan-Fang; Su, Jianwen

2003-05-22

Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

The SAMI2 Open Source Project

NASA Astrophysics Data System (ADS)

Huba, J. D.; Joyce, G.

2001-05-01

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

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

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

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

Java Application Shell: A Framework for Piecing Together Java Applications

NASA Technical Reports Server (NTRS)

Miller, Philip; Powers, Edward I. (Technical Monitor)

2001-01-01

This session describes the architecture of Java Application Shell (JAS), a Swing-based framework for developing interactive Java applications. Java Application Shell is being developed by Commerce One, Inc. for NASA Goddard Space Flight Center Code 588. The purpose of JAS is to provide a framework for the development of Java applications, providing features that enable the development process to be more efficient, consistent and flexible. Fundamentally, JAS is based upon an architecture where an application is considered a collection of 'plugins'. In turn, a plug-in is a collection of Swing actions defined using XML and packaged in a jar file. Plug-ins may be local to the host platform or remotely-accessible through HTTP. Local and remote plugins are automatically discovered by JAS upon application startup; plugins may also be loaded dynamically without having to re-start the application. Using Extensible Markup Language (XML) to define actions, as opposed to hardcoding them in application logic, allows easier customization of application-specific operations by separating application logic from presentation. Through XML, a developer defines an action that may appear on any number of menus, toolbars, and buttons. Actions maintain and propagate enable/disable states and specify icons, tool-tips, titles, etc. Furthermore, JAS allows actions to be implemented using various scripting languages through the use of IBM's Bean Scripting Framework. Scripted action implementation is seamless to the end-user. In addition to action implementation, scripts may be used for application and unit-level testing. In the case of application-level testing, JAS has hooks to assist a script in simulating end-user input. JAS also provides property and user preference management, JavaHelp, Undo/Redo, Multi-Document Interface, Single-Document Interface, printing, and logging. Finally, Jini technology has also been included into the framework by means of a Jini services browser and the

A clinic compatible, open source electrophysiology system.

PubMed

Hermiz, John; Rogers, Nick; Kaestner, Erik; Ganji, Mehran; Cleary, Dan; Snider, Joseph; Barba, David; Dayeh, Shadi; Halgren, Eric; Gilja, Vikash

2016-08-01

Open source electrophysiology (ephys) recording systems have several advantages over commercial systems such as customization and affordability enabling more researchers to conduct ephys experiments. Notable open source ephys systems include Open-Ephys, NeuroRighter and more recently Willow, all of which have high channel count (64+), scalability, and advanced software to develop on top of. However, little work has been done to build an open source ephys system that is clinic compatible, particularly in the operating room where acute human electrocorticography (ECoG) research is performed. We developed an affordable (<; $10,000) and open system for research purposes that features power isolation for patient safety, compact and water resistant enclosures and 256 recording channels sampled up to 20ksam/sec, 16-bit. The system was validated by recording ECoG with a high density, thin film device for an acute, awake craniotomy study at UC San Diego, Thornton Hospital Operating Room.

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

PubMed Central

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

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

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

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

The case for open-source software in drug discovery.

PubMed

DeLano, Warren L

2005-02-01

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

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

NASA Astrophysics Data System (ADS)

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.

Freeing Worldview's development process: Open source everything!

NASA Astrophysics Data System (ADS)

Gunnoe, T.

2016-12-01

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

Model Checking Real Time Java Using Java PathFinder

NASA Technical Reports Server (NTRS)

Lindstrom, Gary; Mehlitz, Peter C.; Visser, Willem

2005-01-01

The Real Time Specification for Java (RTSJ) is an augmentation of Java for real time applications of various degrees of hardness. The central features of RTSJ are real time threads; user defined schedulers; asynchronous events, handlers, and control transfers; a priority inheritance based default scheduler; non-heap memory areas such as immortal and scoped, and non-heap real time threads whose execution is not impeded by garbage collection. The Robust Software Systems group at NASA Ames Research Center has JAVA PATHFINDER (JPF) under development, a Java model checker. JPF at its core is a state exploring JVM which can examine alternative paths in a Java program (e.g., via backtracking) by trying all nondeterministic choices, including thread scheduling order. This paper describes our implementation of an RTSJ profile (subset) in JPF, including requirements, design decisions, and current implementation status. Two examples are analyzed: jobs on a multiprogramming operating system, and a complex resource contention example involving autonomous vehicles crossing an intersection. The utility of JPF in finding logic and timing errors is illustrated, and the remaining challenges in supporting all of RTSJ are assessed.

Java-based cryptosystem for PACS and tele-imaging

NASA Astrophysics Data System (ADS)

Tjandra, Donny; Wong, Stephen T. C.; Yu, Yuan-Pin

1998-07-01

Traditional PACS systems are based on two-tier client server architectures, and require the use of costly, high-end client workstations for image viewing. Consequently, PACS systems using the two-tier architecture do not scale well as data increases in size and complexity. Furthermore, use of dedicated viewing workstations incurs costs in deployment and maintenance. To address these issues, the use of digital library technologies, such as the World Wide Web, Java, and CORBA, is being explored to distribute PACS data to serve a broader range of healthcare providers in an economic and efficient manner. Integration of PACS systems with digital library technologies allows access to medical information through open networks such as the Internet. However, use of open networks to transmit medical data introduces problems with maintaining privacy and integrity of patient information. Cryptography and digital timestamping is used to protect sensitive information from unauthorized access or tampering. A major concern when using cryptography and digital timestamping is the performance degradation associated with the mathematical calculations needed to encrypt/decrypt an image dataset, or to calculate the hash value of an image. The performance issue is compounded by the extra layer associated with the CORBA middleware, and the use of programming languages interpreted at the client side, such as Java. This paper study the extent to which Java-based cryptography and digital timestamping affects performance in a PACS system integrated with digital library technologies.

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

PubMed

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

2017-08-01

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

Add Java extensions to your wiki: Java applets can bring dynamic functionality to your wiki pages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scarberry, Randall E.

Virtually everyone familiar with today’s world wide web has encountered the free online encyclopedia Wikipedia many times. What you may not know is that Wikipedia is driven by an excellent open-source product called MediaWiki which is available to anyone for free. This has led to a proliferation of wiki sites devoted to just about any topic one can imagine. Users of a wiki can add content -- all that is required of them is that they type in their additions into their web browsers using the simple markup language called wikitext. Even better, the developers of wikitext made it extensible.more » With a little server-side development of your own, you can add your own custom syntax. Users aware of your extensions can then utilize them on their wiki pages with a few simple keystrokes. These extensions can be custom decorations, formatting, web applications, and even instances of the venerable old Java applet. One example of a Java applet extension is the Jmol extension (REF), used to embed a 3-D molecular viewer. This article will walk you through the deployment of a fairly elaborate applet via a MediaWiki extension. By no means exhaustive -- an entire book would be required for that -- it will demonstrate how to give the applet resize handles using using a little Javascript and CSS coding and some popular Javascript libraries. It even describes how a user may customize the extension somewhat using a wiki template. Finally, it explains a rudimentary persistence mechanism which allows applets to save data directly to the wiki pages on which they reside.« less

Simulation for Dynamic Situation Awareness and Prediction III

DTIC Science & Technology

2010-03-01

source Java ™ library for capturing and sending network packets; 4) Groovy – an open source, Java -based scripting language (version 1.6 or newer). Open...DMOTH Analyzer application. Groovy is an open source dynamic scripting language for the Java Virtual Machine. It is consistent with Java syntax...between temperature, pressure, wind and relative humidity, and 3) a precipitation editing algorithm. The Editor can be used to prepare scripted changes

An Analysis of Open Source Security Software Products Downloads

ERIC Educational Resources Information Center

Barta, Brian J.

2014-01-01

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

Open-Source Unionism: New Workers, New Strategies

ERIC Educational Resources Information Center

Schmid, Julie M.

2004-01-01

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

Open source OCR framework using mobile devices

NASA Astrophysics Data System (ADS)

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

2008-02-01

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

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

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.

2017-12-01

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

The Emergence of Open-Source Software in North America

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

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

a Framework for AN Open Source Geospatial Certification Model

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

An Evolving Worldview: Making Open Source Easy

NASA Technical Reports Server (NTRS)

Rice, Zachary

2017-01-01

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. New developers are able to track upcoming features, collaborate on them and make their own contributions. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. A focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straight forward commands to clone, configure, install and run. This presentation will emphasis our focus to simplify and standardize Worldview's open source code so more people are able to contribute. The more people who contribute, the better the application will become over time.

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

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

7 Questions to Ask Open Source Vendors

ERIC Educational Resources Information Center

Raths, David

2012-01-01

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

Interim Open Source Software (OSS) Policy

EPA Pesticide Factsheets

This interim Policy establishes a framework to implement the requirements of the Office of Management and Budget's (OMB) Federal Source Code Policy to achieve efficiency, transparency and innovation through reusable and open source software.

Starch Product of Wild Plants Species Jalawure (Tacca leontopetaloides L.) Kuntze as The Source of Food Security in The South Coastal West Java

NASA Astrophysics Data System (ADS)

Wardah; Sambas, E. N.; Ridwan; Ariani, D.

2017-04-01

Majority of people of South coast of West Java, from Sukabumi, Cianjur, Garut are fishermen. Natural conditions are very dry and the area of land for agriculture, particularly rice cultivation is minimal. So that the condition of the society is more directed to high enough levels of food insecurity. Because coastal areas tend to have a longer dry season from rainfall. Results of research conducted in the years 2013 - 2016 in the area of Pelabuhan Ratu, Cidaun (Cianjur), Coastal area of Jayanti, Ranca Buaya, Mekar Mukti, and along the coast until Pameungpeuk, Leuweung Sancang, is known that jalawure plant which grows wild at South-coast region of West Java is precisely the alternative solution to address food insecurity. The results of the starch flour is a source of carbohydrate that is high enough to be used as a substitute for rice and wheat. Another potential source of jalawure nutrition is also recommended for diabetics consumption.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

An Open Source Model for Open Access Journal Publication

PubMed Central

Blesius, Carl R.; Williams, Michael A.; Holzbach, Ana; Huntley, Arthur C.; Chueh, Henry

2005-01-01

We describe an electronic journal publication infrastructure that allows a flexible publication workflow, academic exchange around different forms of user submissions, and the exchange of articles between publishers and archives using a common XML based standard. This web-based application is implemented on a freely available open source software stack. This publication demonstrates the Dermatology Online Journal's use of the platform for non-biased independent open access publication. PMID:16779183

Open Source in Education

ERIC Educational Resources Information Center

Lakhan, Shaheen E.; Jhunjhunwala, Kavita

2008-01-01

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

Open source Modeling and optimization tools for Planning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peles, S.

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 tomore » 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.« less

Open source bioimage informatics for cell biology.

PubMed

Swedlow, Jason R; Eliceiri, Kevin W

2009-11-01

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

Open source bioimage informatics for cell biology

PubMed Central

Swedlow, Jason R.; Eliceiri, Kevin W.

2009-01-01

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery. PMID:19833518

Open Source, Open Standards, and Health Care Information Systems

PubMed Central

2011-01-01

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

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

PubMed

Reynolds, Carl J; Wyatt, Jeremy C

2011-02-17

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

Validation of a semi-automatic protocol for the assessment of the tear meniscus central area based on open-source software

NASA Astrophysics Data System (ADS)

Pena-Verdeal, Hugo; Garcia-Resua, Carlos; Yebra-Pimentel, Eva; Giraldez, Maria J.

2017-08-01

Purpose: Different lower tear meniscus parameters can be clinical assessed on dry eye diagnosis. The aim of this study was to propose and analyse the variability of a semi-automatic method for measuring lower tear meniscus central area (TMCA) by using open source software. Material and methods: On a group of 105 subjects, one video of the lower tear meniscus after fluorescein instillation was generated by a digital camera attached to a slit-lamp. A short light beam (3x5 mm) with moderate illumination in the central portion of the meniscus (6 o'clock) was used. Images were extracted from each video by a masked observer. By using an open source software based on Java (NIH ImageJ), a further observer measured in a masked and randomized order the TMCA in the short light beam illuminated area by two methods: (1) manual method, where TMCA images was "manually" measured; (2) semi-automatic method, where TMCA images were transformed in an 8-bit-binary image, then holes inside this shape were filled and on the isolated shape, the area size was obtained. Finally, both measurements, manual and semi-automatic, were compared. Results: Paired t-test showed no statistical difference between both techniques results (p = 0.102). Pearson correlation between techniques show a significant positive near to perfect correlation (r = 0.99; p < 0.001). Conclusions: This study showed a useful tool to objectively measure the frontal central area of the meniscus in photography by free open source software.

Monitoring Java Programs with Java PathExplorer

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Rosu, Grigore; Clancy, Daniel (Technical Monitor)

2001-01-01

We present recent work on the development Java PathExplorer (JPAX), a tool for monitoring the execution of Java programs. JPAX can be used during program testing to gain increased information about program executions, and can potentially furthermore be applied during operation to survey safety critical systems. The tool facilitates automated instrumentation of a program's late code which will then omit events to an observer during its execution. The observer checks the events against user provided high level requirement specifications, for example temporal logic formulae, and against lower level error detection procedures, for example concurrency related such as deadlock and data race algorithms. High level requirement specifications together with their underlying logics are defined in the Maude rewriting logic, and then can either be directly checked using the Maude rewriting engine, or be first translated to efficient data structures and then checked in Java.

Model Checking JAVA Programs Using Java Pathfinder

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Pressburger, Thomas

2000-01-01

This paper describes a translator called JAVA PATHFINDER from JAVA to PROMELA, the "programming language" of the SPIN model checker. The purpose is to establish a framework for verification and debugging of JAVA programs based on model checking. This work should be seen in a broader attempt to make formal methods applicable "in the loop" of programming within NASA's areas such as space, aviation, and robotics. Our main goal is to create automated formal methods such that programmers themselves can apply these in their daily work (in the loop) without the need for specialists to manually reformulate a program into a different notation in order to analyze the program. This work is a continuation of an effort to formally verify, using SPIN, a multi-threaded operating system programmed in Lisp for the Deep-Space 1 spacecraft, and of previous work in applying existing model checkers and theorem provers to real applications.

Specvis: Free and open-source software for visual field examination.

PubMed

Dzwiniel, Piotr; Gola, Mateusz; Wójcik-Gryciuk, Anna; Waleszczyk, Wioletta J

2017-01-01

Visual field impairment affects more than 100 million people globally. However, due to the lack of the access to appropriate ophthalmic healthcare in undeveloped regions as a result of associated costs and expertise this number may be an underestimate. Improved access to affordable diagnostic software designed for visual field examination could slow the progression of diseases, such as glaucoma, allowing for early diagnosis and intervention. We have developed Specvis, a free and open-source application written in Java programming language that can run on any personal computer to meet this requirement (http://www.specvis.pl/). Specvis was tested on glaucomatous, retinitis pigmentosa and stroke patients and the results were compared to results using the Medmont M700 Automated Static Perimeter. The application was also tested for inter-test intrapersonal variability. The results from both validation studies indicated low inter-test intrapersonal variability, and suitable reliability for a fast and simple assessment of visual field impairment. Specvis easily identifies visual field areas of zero sensitivity and allows for evaluation of its levels throughout the visual field. Thus, Specvis is a new, reliable application that can be successfully used for visual field examination and can fill the gap between confrontation and perimetry tests. The main advantages of Specvis over existing methods are its availability (free), affordability (runs on any personal computer), and reliability (comparable to high-cost solutions).

Specvis: Free and open-source software for visual field examination

PubMed Central

Dzwiniel, Piotr; Gola, Mateusz; Wójcik-Gryciuk, Anna

2017-01-01

Visual field impairment affects more than 100 million people globally. However, due to the lack of the access to appropriate ophthalmic healthcare in undeveloped regions as a result of associated costs and expertise this number may be an underestimate. Improved access to affordable diagnostic software designed for visual field examination could slow the progression of diseases, such as glaucoma, allowing for early diagnosis and intervention. We have developed Specvis, a free and open-source application written in Java programming language that can run on any personal computer to meet this requirement (http://www.specvis.pl/). Specvis was tested on glaucomatous, retinitis pigmentosa and stroke patients and the results were compared to results using the Medmont M700 Automated Static Perimeter. The application was also tested for inter-test intrapersonal variability. The results from both validation studies indicated low inter-test intrapersonal variability, and suitable reliability for a fast and simple assessment of visual field impairment. Specvis easily identifies visual field areas of zero sensitivity and allows for evaluation of its levels throughout the visual field. Thus, Specvis is a new, reliable application that can be successfully used for visual field examination and can fill the gap between confrontation and perimetry tests. The main advantages of Specvis over existing methods are its availability (free), affordability (runs on any personal computer), and reliability (comparable to high-cost solutions). PMID:29028825

Open Source Cloud-Based Technologies for Bim

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Managing multicentre clinical trials with open source.

PubMed

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.

Open source data assimilation framework for hydrological modeling

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

From open source communications to knowledge

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Developing open-source codes for electromagnetic geophysics using industry support

NASA Astrophysics Data System (ADS)

Key, K.

2017-12-01

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

Java Mission Evaluation Workstation System

NASA Technical Reports Server (NTRS)

Pettinger, Ross; Watlington, Tim; Ryley, Richard; Harbour, Jeff

2006-01-01

The Java Mission Evaluation Workstation System (JMEWS) is a collection of applications designed to retrieve, display, and analyze both real-time and recorded telemetry data. This software is currently being used by both the Space Shuttle Program (SSP) and the International Space Station (ISS) program. JMEWS was written in the Java programming language to satisfy the requirement of platform independence. An object-oriented design was used to satisfy additional requirements and to make the software easily extendable. By virtue of its platform independence, JMEWS can be used on the UNIX workstations in the Mission Control Center (MCC) and on office computers. JMEWS includes an interactive editor that allows users to easily develop displays that meet their specific needs. The displays can be developed and modified while viewing data. By simply selecting a data source, the user can view real-time, recorded, or test data.

Analysis of variables affecting unemployment rate and detecting for cluster in West Java, Central Java, and East Java in 2012

NASA Astrophysics Data System (ADS)

Samuel, Putra A.; Widyaningsih, Yekti; Lestari, Dian

2016-02-01

The objective of this study is modeling the Unemployment Rate (UR) in West Java, Central Java, and East Java, with rate of disease, infant mortality rate, educational level, population size, proportion of married people, and GDRP as the explanatory variables. Spatial factors are also considered in the modeling since the closer the distance, the higher the correlation. This study uses the secondary data from BPS (Badan Pusat Statistik). The data will be analyzed using Moran I test, to obtain the information about spatial dependence, and using Spatial Autoregressive modeling to obtain the information, which variables are significant affecting UR and how great the influence of the spatial factors. The result is, variables proportion of married people, rate of disease, and population size are related significantly to UR. In all three regions, the Hotspot of unemployed will also be detected districts/cities using Spatial Scan Statistics Method. The results are 22 districts/cities as a regional group with the highest unemployed (Most likely cluster) in the study area; 2 districts/cities as a regional group with the highest unemployed in West Java; 1 district/city as a regional groups with the highest unemployed in Central Java; 15 districts/cities as a regional group with the highest unemployed in East Java.

Spatial modeling for estimation of earthquakes economic loss in West Java

NASA Astrophysics Data System (ADS)

Retnowati, Dyah Ayu; Meilano, Irwan; Riqqi, Akhmad; Hanifa, Nuraini Rahma

2017-07-01

Indonesia has a high vulnerability towards earthquakes. The low adaptive capacity could make the earthquake become disaster that should be concerned. That is why risk management should be applied to reduce the impacts, such as estimating the economic loss caused by hazard. The study area of this research is West Java. The main reason of West Java being vulnerable toward earthquake is the existence of active faults. These active faults are Lembang Fault, Cimandiri Fault, Baribis Fault, and also Megathrust subduction zone. This research tries to estimates the value of earthquakes economic loss from some sources in West Java. The economic loss is calculated by using HAZUS method. The components that should be known are hazard (earthquakes), exposure (building), and the vulnerability. Spatial modeling is aimed to build the exposure data and make user get the information easier by showing the distribution map, not only in tabular data. As the result, West Java could have economic loss up to 1,925,122,301,868,140 IDR ± 364,683,058,851,703.00 IDR, which is estimated from six earthquake sources with maximum possibly magnitude. However, the estimation of economic loss value in this research is the worst case earthquakes occurrence which is probably over-estimated.

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

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.

Jannovar: a java library for exome annotation.

PubMed

Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

2014-05-01

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

Java Programming Language

NASA Technical Reports Server (NTRS)

Shaykhian, Gholam Ali

2007-01-01

The Java seminar covers the fundamentals of Java programming language. No prior programming experience is required for participation in the seminar. The first part of the seminar covers introductory concepts in Java programming including data types (integer, character, ..), operators, functions and constants, casts, input, output, control flow, scope, conditional statements, and arrays. Furthermore, introduction to Object-Oriented programming in Java, relationships between classes, using packages, constructors, private data and methods, final instance fields, static fields and methods, and overloading are explained. The second part of the seminar covers extending classes, inheritance hierarchies, polymorphism, dynamic binding, abstract classes, protected access. The seminar conclude by introducing interfaces, properties of interfaces, interfaces and abstract classes, interfaces and cailbacks, basics of event handling, user interface components with swing, applet basics, converting applications to applets, the applet HTML tags and attributes, exceptions and debugging.

Meteorological Error Budget Using Open Source Data

DTIC Science & Technology

2016-09-01

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...Error Budget Using Open-Source Data 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) J Cogan, J Smith, P Haines

Building Energy Management Open Source Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.more » (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

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

PubMed

Mathôt, Sebastiaan; Schreij, Daniel; Theeuwes, Jan

2012-06-01

In the present article, we introduce OpenSesame, a graphical experiment builder for the social sciences. OpenSesame is free, open-source, and cross-platform. It features a comprehensive and intuitive graphical user interface and supports Python scripting for complex tasks. Additional functionality, such as support for eyetrackers, input devices, and video playback, is available through plug-ins. OpenSesame can be used in combination with existing software for creating experiments.

Web Server Security on Open Source Environments

NASA Astrophysics Data System (ADS)

Gkoutzelis, Dimitrios X.; Sardis, Manolis S.

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

OpenEIS. Developer Guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lutes, Robert G.; Neubauer, Casey C.; Haack, Jereme N.

2015-03-31

The Department of Energy’s (DOE’s) Building Technologies Office (BTO) is supporting the development of an open-source software tool for analyzing building energy and operational data: OpenEIS (open energy information system). This tool addresses the problems of both owners of building data and developers of tools to analyze this data. Building owners and managers have data but lack the tools to analyze it while tool developers lack data in a common format to ease development of reusable data analysis tools. This document is intended for developers of applications and explains the mechanisms for building analysis applications, accessing data, and displaying datamore » using a visualization from the included library. A brief introduction to the visualizations can be used as a jumping off point for developers familiar with JavaScript to produce their own. Several example applications are included which can be used along with this document to implement algorithms for performing energy data analysis.« less

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

ERIC Educational Resources Information Center

Wang, Jing

2013-01-01

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

Open-Source RTOS Space Qualification: An RTEMS Case Study

NASA Technical Reports Server (NTRS)

Zemerick, Scott

2017-01-01

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

Technology collaboration by means of an open source government

NASA Astrophysics Data System (ADS)

Berardi, Steven M.

2009-05-01

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

Evaluating Open Source Portals

ERIC Educational Resources Information Center

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

2008-01-01

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

OpenDrift - an open source framework for ocean trajectory modeling

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Supporting openEHR Java desktop application developers.

PubMed

Kashfi, Hajar; Torgersson, Olof

2011-01-01

The openEHR community suggests that an appropriate approach for creating a graphical user interface for an openEHR-based application is to generate forms from the underlying archetypes and templates. However, current generation techniques are not mature enough to be able to produce high quality interfaces with good usability. Therefore, developing efficient ways to combine manually designed and developed interfaces to openEHR backends is an interesting alternative. In this study, a framework for binding a pre-designed graphical user interface to an openEHR-based backend is proposed. The proposed framework contributes to the set of options available for developers. In particular we believe that the approach of combining user interface components with an openEHR backend in the proposed way might be useful in situations where the quality of the user interface is essential and for creating small scale and experimental systems.

Open Source as Appropriate Technology for Global Education

ERIC Educational Resources Information Center

Carmichael, Patrick; Honour, Leslie

2002-01-01

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

Opening up Architectures of Software-Intensive Systems: A Functional Decomposition to Support System Comprehension

DTIC Science & Technology

2007-10-01

Architecture ................................................................................ 14 Figure 2. Eclipse Java Model...16 Figure 3. Eclipse Java Model at the Source Code Level...24 Figure 9. Java Source Code

Open Source Library Management Systems: A Multidimensional Evaluation

ERIC Educational Resources Information Center

Balnaves, Edmund

2008-01-01

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

An Evolving Worldview: Making Open Source Easy

NASA Astrophysics Data System (ADS)

Rice, Z.

2017-12-01

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. Community developers are able to track upcoming features, collaborate on them and make their own contributions. Developers who discover issues are able to address those issues and submit a fix. This reduces the time it takes for a project developer to reproduce an issue or develop a new feature. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. After witnessing potential outside contributors struggle, a focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straightforward commands to clone, configure, install and run. This presentation will emphasize our focus to simplify and standardize Worldview's open source code so that more people are able to contribute. The more people who contribute, the better the application will become over time.

Implementation of a near-real time cross-border web-mapping platform on airborne particulate matter (PM) concentration with open-source software

NASA Astrophysics Data System (ADS)

Knörchen, Achim; Ketzler, Gunnar; Schneider, Christoph

2015-01-01

Although Europe has been growing together for the past decades, cross-border information platforms on environmental issues are still scarce. With regard to the establishment of a web-mapping tool on airborne particulate matter (PM) concentration for the Euregio Meuse-Rhine located in the border region of Belgium, Germany and the Netherlands, this article describes the research on methodical and technical backgrounds implementing such a platform. An open-source solution was selected for presenting the data in a Web GIS (OpenLayers/GeoExt; both JavaScript-based), applying other free tools for data handling (Python), data management (PostgreSQL), geo-statistical modelling (Octave), geoprocessing (GRASS GIS/GDAL) and web mapping (MapServer). The multilingual, made-to-order online platform provides access to near-real time data on PM concentration as well as additional background information. In an open data section, commented configuration files for the Web GIS client are being made available for download. Furthermore, all geodata generated by the project is being published under public domain and can be retrieved in various formats or integrated into Desktop GIS as Web Map Services (WMS).

Open source electronic health records and chronic disease management.

PubMed

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.

Open source electronic health records and chronic disease management

PubMed Central

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

2014-01-01

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

JSBML: a flexible Java library for working with SBML.

PubMed

Dräger, Andreas; Rodriguez, Nicolas; Dumousseau, Marine; Dörr, Alexander; Wrzodek, Clemens; Le Novère, Nicolas; Zell, Andreas; Hucka, Michael

2011-08-01

The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.

Open-source, community-driven microfluidics with Metafluidics.

PubMed

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.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

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

Open Source Initiative Powers Real-Time Data Streams

NASA Technical Reports Server (NTRS)

2014-01-01

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

Empowerment model of biomass in west java

NASA Astrophysics Data System (ADS)

Mulyana, C.; Fitriani, N. I.; Saad, A.; Yuliah, Y.

2017-06-01

Scarcity of fossil energy accelerates the search of renewable energy sources as the substitution. In West Java, biomass has potential to be developed into bio-briquette because the resources are abundant. The objectives of this research are mapping the potency of biomass as bio-briquette in West Java, and making the model of the empowerment biomass potential involving five fundamental step which are raw material, pre-processing process, conversion mechanism, products, and end user. The main object of this model focused on 3 forms which are solid, liquid, and gas which was made by involving the community component as the owner biomass, district government, academics and researcher communities, related industries as users of biomass, and the central government as the policy holders and investors as a funder. In the model was described their respective roles and mutual relationship one with another so that the bio-briquette as a substitute of fossil fuels can be realized. Application of this model will provide the benefits in renewability energy sources, environmental, socio economical and energy security.

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

2005-04-01

The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

Open-source tools for data mining.

PubMed

Zupan, Blaz; Demsar, Janez

2008-03-01

With a growing volume of biomedical databases and repositories, the need to develop a set of tools to address their analysis and support knowledge discovery is becoming acute. The data mining community has developed a substantial set of techniques for computational treatment of these data. In this article, we discuss the evolution of open-source toolboxes that data mining researchers and enthusiasts have developed over the span of a few decades and review several currently available open-source data mining suites. The approaches we review are diverse in data mining methods and user interfaces and also demonstrate that the field and its tools are ready to be fully exploited in biomedical research.

Late Holocene carbon and nitrogen input into the Java Sea recorded in sediment cores off rivers from Java and Kalimantan

NASA Astrophysics Data System (ADS)

Herbeck, Lucia; Kwiatkowski, Cornelia; Mohtadi, Mahyar; Jennerjahn, Tim

2014-05-01

terrestrial input into the Java Sea was limited to approx. 15 km off the river mouth. Both cores off Kalimantan and the core off Java close to the Bengawan Solo had similar Corg contents (~0.8%) and molar C/N-ratios (11-19). δ13Corg of -24‰ and low carbonate contents (~7%) indicate an even higher contribution of terrigenous organic matter off the Kalimantan rivers than off the Bengawan Solo, where δ13Corg of -22‰ and CaCO3 contents of ~17% rather point to marine phytoplankton as major organic matter source. Our preliminary results indicate a higher input of terrigenous organic matter from Kalimantan than from Java and show little evidence for anthropogenic impact on organic matter inputs into the Java Sea during the late Holocene.

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

NASA Astrophysics Data System (ADS)

Francoeur, H.; Callaghan, S.; Perry, S.; Jordan, T.

2004-12-01

The Southern California Earthquake Center undergraduate IT intern program (SCEC UseIT) conducts IT research to benefit collaborative earth science research. Through this program, interns have developed real-time, interactive, 3D visualization software using open-source tools. Dubbed LA3D, a distribution of this software is now in use by the seismic community. LA3D enables the user to interactively view Southern California datasets and models of importance to earthquake scientists, such as faults, earthquakes, fault blocks, digital elevation models, and seismic hazard maps. LA3D is now being extended to support visualizations anywhere on the planet. The new software, called SCEC-VIDEO (Virtual Interactive Display of Earth Objects), makes use of a modular, plugin-based software architecture which supports easy development and integration of new data sets. Currently SCEC-VIDEO is in beta testing, with a full open-source release slated for the future. Both LA3D and SCEC-VIDEO were developed using a wide variety of software technologies. These, which included relational databases, web services, software management technologies, and 3-D graphics in Java, were necessary to integrate the heterogeneous array of data sources which comprise our software. Currently the interns are working to integrate new technologies and larger data sets to increase software functionality and value. In addition, both LA3D and SCEC-VIDEO allow the user to script and create movies. Thus program interns with computer science backgrounds have been writing software while interns with other interests, such as cinema, geology, and education, have been making movies that have proved of great use in scientific talks, media interviews, and education. Thus, SCEC UseIT incorporates a wide variety of scientific and human resources to create products of value to the scientific and outreach communities. The program plans to continue with its interdisciplinary approach, increasing the relevance of the

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

PubMed

Neinstein, Aaron; Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-03-01

Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management

PubMed Central

Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-01-01

Objective Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. Materials and Methods An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Results Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application (“app”), Blip, to visualize the data. Tidepool’s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. Discussion By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. Conclusion The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool’s open source, cloud model for health data interoperability is applicable to other healthcare use cases. PMID:26338218

Development of an Open Source, Air-Deployable Weather Station

NASA Astrophysics Data System (ADS)

Krejci, A.; Lopez Alcala, J. M.; Nelke, M.; Wagner, J.; Udell, C.; Higgins, C. W.; Selker, J. S.

2017-12-01

We created a packaged weather station intended to be deployed in the air on tethered systems. The device incorporates lightweight sensors and parts and runs for up to 24 hours off of lithium polymer batteries, allowing the entire package to be supported by a thin fiber. As the fiber does not provide a stable platform, additional data (pitch and roll) from typical weather parameters (e.g. temperature, pressure, humidity, wind speed, and wind direction) are determined using an embedded inertial motion unit. All designs are open sourced including electronics, CAD drawings, and descriptions of assembly and can be found on the OPEnS lab website at http://www.open-sensing.org/lowcost-weather-station/. The Openly Published Environmental Sensing Lab (OPEnS: Open-Sensing.org) expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting-edge technology. New OPEnS labs are now being established in India, France, Switzerland, the Netherlands, and Ghana.

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

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

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

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

PubMed

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

2007-11-01

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

Implementation of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Schultz, Matthew; Jin, Hao-Qiang; Yan, Jerry

2000-01-01

A number of features make Java an attractive but a debatable choice for High Performance Computing (HPC). In order to gauge the applicability of Java to the Computational Fluid Dynamics (CFD) we have implemented NAS Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would move Java closer to Fortran in the competition for CFD applications.

The HYPE Open Source Community

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Using Open Source Software in Visual Simulation Development

DTIC Science & Technology

2005-09-01

increased the use of the technology in training activities. Using open source/free software tools in the process can expand these possibilities...resulting in even greater cost reduction and allowing the flexibility needed in a training environment. This thesis presents a configuration and architecture...to be used when developing training visual simulations using both personal computers and open source tools. Aspects of the requirements needed in a

THE OPEN SOURCING OF EPANET

EPA Science Inventory

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

Potential Development Essential Oil Production of Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Alighiri, D.; Eden, W. T.; Supardi, K. I.; Masturi; Purwinarko, A.

2017-04-01

Indonesia is the source of raw essential oil in the world. Essential oils are used in various types of industries such as food and beverage, flavour, fragrance, perfumery, pharmaceuticals, and cosmetics. However, the development of Indonesian essential oil industry has not been encouraging for the production of essential oils, further it is unable to meet global demand. Besides that, the quality of volatile oil resulted cannot meet the international market standards. Based on the facts, the potential of Indonesian essential oils needs to be developed to provide added value, through increased production, improved quality and product diversification. One part of Indonesia having abundant of raw essential oil source is Central Java. Central Java has the quite large potential production of essential oils. Some essential oils produced from refining industry owned by the government, private and community sectors include cananga oils (Boyolali district), clove oils (Semarang district), patchouli oils (Brebes district, Pemalang district, and Klaten district). The main problem in the development of plants industries that producing essential oil in Central Java is low crops production, farming properties, quality of essential oils are diverse, providing poor-quality products and volatile oil price fluctuations. Marketing constraints of Central Java essential oils are quite complex supply chain. In general, marketing constraints of essential oils due to three factors, namely the low quality due to type of essential oil business that generally shaped small businesses with different capital and technology, domestic marketing is still a buyer-market (price determined by the buyer) because of weak bargaining position processors businessman, and prices fluctuate (domestic and foreign) due to uncontrolled domestic production and inter-country competition among manufacturers.

Parallel programming with Easy Java Simulations

NASA Astrophysics Data System (ADS)

Esquembre, F.; Christian, W.; Belloni, M.

2018-01-01

Nearly all of today's processors are multicore, and ideally programming and algorithm development utilizing the entire processor should be introduced early in the computational physics curriculum. Parallel programming is often not introduced because it requires a new programming environment and uses constructs that are unfamiliar to many teachers. We describe how we decrease the barrier to parallel programming by using a java-based programming environment to treat problems in the usual undergraduate curriculum. We use the easy java simulations programming and authoring tool to create the program's graphical user interface together with objects based on those developed by Kaminsky [Building Parallel Programs (Course Technology, Boston, 2010)] to handle common parallel programming tasks. Shared-memory parallel implementations of physics problems, such as time evolution of the Schrödinger equation, are available as source code and as ready-to-run programs from the AAPT-ComPADRE digital library.

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

PubMed

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

2014-11-01

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

The validity of open-source data when assessing jail suicides.

PubMed

Thomas, Amanda L; Scott, Jacqueline; Mellow, Jeff

2018-05-09

The Bureau of Justice Statistics' Deaths in Custody Reporting Program is the primary source for jail suicide research, though the data is restricted from general dissemination. This study is the first to examine whether jail suicide data obtained from publicly available sources can help inform our understanding of this serious public health problem. Of the 304 suicides that were reported through the DCRP in 2009, roughly 56 percent (N = 170) of those suicides were identified through the open-source search protocol. Each of the sources was assessed based on how much information was collected on the incident and the types of variables available. A descriptive analysis was then conducted on the variables that were present in both data sources. The four variables present in each data source were: (1) demographic characteristics of the victim, (2) the location of occurrence within the facility, (3) the location of occurrence by state, and (4) the size of the facility. Findings demonstrate that the prevalence and correlates of jail suicides are extremely similar in both open-source and official data. However, for almost every variable measured, open-source data captured as much information as official data did, if not more. Further, variables not found in official data were identified in the open-source database, thus allowing researchers to have a more nuanced understanding of the situational characteristics of the event. This research provides support for the argument in favor of including open-source data in jail suicide research as it illustrates how open-source data can be used to provide additional information not originally found in official data. In sum, this research is vital in terms of possible suicide prevention, which may be directly linked to being able to manipulate environmental factors.

Managing Digital Archives Using Open Source Software Tools

NASA Astrophysics Data System (ADS)

Barve, S.; Dongare, S.

2007-10-01

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

Integrating an Automatic Judge into an Open Source LMS

ERIC Educational Resources Information Center

Georgouli, Katerina; Guerreiro, Pedro

2011-01-01

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

The open-source movement: an introduction for forestry professionals

Treesearch

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....

Open source tools for ATR development and performance evaluation

NASA Astrophysics Data System (ADS)

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

2002-07-01

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

Open Source Hbim for Cultural Heritage: a Project Proposal

NASA Astrophysics Data System (ADS)

Diara, F.; Rinaudo, F.

2018-05-01

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

Designing and developing portable large-scale JavaScript web applications within the Experiment Dashboard framework

NASA Astrophysics Data System (ADS)

Andreeva, J.; Dzhunov, I.; Karavakis, E.; Kokoszkiewicz, L.; Nowotka, M.; Saiz, P.; Tuckett, D.

2012-12-01

Improvements in web browser performance and web standards compliance, as well as the availability of comprehensive JavaScript libraries, provides an opportunity to develop functionally rich yet intuitive web applications that allow users to access, render and analyse data in novel ways. However, the development of such large-scale JavaScript web applications presents new challenges, in particular with regard to code sustainability and team-based work. We present an approach that meets the challenges of large-scale JavaScript web application design and development, including client-side model-view-controller architecture, design patterns, and JavaScript libraries. Furthermore, we show how the approach leads naturally to the encapsulation of the data source as a web API, allowing applications to be easily ported to new data sources. The Experiment Dashboard framework is used for the development of applications for monitoring the distributed computing activities of virtual organisations on the Worldwide LHC Computing Grid. We demonstrate the benefits of the approach for large-scale JavaScript web applications in this context by examining the design of several Experiment Dashboard applications for data processing, data transfer and site status monitoring, and by showing how they have been ported for different virtual organisations and technologies.

NASA's Earth Imagery Service as Open Source Software

NASA Astrophysics Data System (ADS)

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.

Volcanoes, Central Java, Indonesia

NASA Technical Reports Server (NTRS)

1992-01-01

The island of Java (8.0S, 112.0E), perhaps better than any other, illustrates the volcanic origin of Pacific Island groups. Seen in this single view are at least a dozen once active volcano craters. Alignment of the craters even defines the linear fault line of Java as well as the other some 1500 islands of the Indonesian Archipelago. Deep blue water of the Indian Ocean to the south contrasts to the sediment laden waters of the Java Sea to the north.

Volcanoes, Central Java, Indonesia

NASA Image and Video Library

1992-08-08

The island of Java (8.0S, 112.0E), perhaps better than any other, illustrates the volcanic origin of Pacific Island groups. Seen in this single view are at least a dozen once active volcano craters. Alignment of the craters even defines the linear fault line of Java as well as the other some 1500 islands of the Indonesian Archipelago. Deep blue water of the Indian Ocean to the south contrasts to the sediment laden waters of the Java Sea to the north.

Java PathFinder: A Translator From Java to Promela

NASA Technical Reports Server (NTRS)

Havelund, Klaus

1999-01-01

JAVA PATHFINDER, JPF, is a prototype translator from JAVA to PROMELA, the modeling language of the SPIN model checker. JPF is a product of a major effort by the Automated Software Engineering group at NASA Ames to make model checking technology part of the software process. Experience has shown that severe bugs can be found in final code using this technique, and that automated translation from a programming language to a modeling language like PROMELA can help reducing the effort required.

Using open-source programs to create a web-based portal for hydrologic information

NASA Astrophysics Data System (ADS)

Kim, H.

2013-12-01

Some hydrologic data sets, such as basin climatology, precipitation, and terrestrial water storage, are not easily obtainable and distributable due to their size and complexity. We present a Hydrologic Information Portal (HIP) that has been implemented at the University of California for Hydrologic Modeling (UCCHM) and that has been organized around the large river basins of North America. This portal can be easily accessed through a modern web browser that enables easy access and visualization of such hydrologic data sets. Some of the main features of our HIP include a set of data visualization features so that users can search, retrieve, analyze, integrate, organize, and map data within large river basins. Recent information technologies such as Google Maps, Tornado (Python asynchronous web server), NumPy/SciPy (Scientific Library for Python) and d3.js (Visualization library for JavaScript) were incorporated into the HIP to create ease in navigating large data sets. With such open source libraries, HIP can give public users a way to combine and explore various data sets by generating multiple chart types (Line, Bar, Pie, Scatter plot) directly from the Google Maps viewport. Every rendered object such as a basin shape on the viewport is clickable, and this is the first step to access the visualization of data sets.

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

PubMed

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

2014-01-01

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

AKM in Open Source Communities

NASA Astrophysics Data System (ADS)

Stamelos, Ioannis; Kakarontzas, George

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

Open source system OpenVPN in a function of Virtual Private Network

NASA Astrophysics Data System (ADS)

Skendzic, A.; Kovacic, B.

2017-05-01

Using of Virtual Private Networks (VPN) can establish high security level in network communication. VPN technology enables high security networking using distributed or public network infrastructure. VPN uses different security and managing rules inside networks. It can be set up using different communication channels like Internet or separate ISP communication infrastructure. VPN private network makes security communication channel over public network between two endpoints (computers). OpenVPN is an open source software product under GNU General Public License (GPL) that can be used to establish VPN communication between two computers inside business local network over public communication infrastructure. It uses special security protocols and 256-bit Encryption and it is capable of traversing network address translators (NATs) and firewalls. It allows computers to authenticate each other using a pre-shared secret key, certificates or username and password. This work gives review of VPN technology with a special accent on OpenVPN. This paper will also give comparison and financial benefits of using open source VPN software in business environment.

MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions.

PubMed

Klemm, Martin; Kirchner, Thomas; Gröhl, Janek; Cheray, Dominique; Nolden, Marco; Seitel, Alexander; Hoppe, Harald; Maier-Hein, Lena; Franz, Alfred M

2017-03-01

Due to rapid developments in the research areas of medical imaging, medical image processing and robotics, computer-assisted interventions (CAI) are becoming an integral part of modern patient care. From a software engineering point of view, these systems are highly complex and research can benefit greatly from reusing software components. This is supported by a number of open-source toolkits for medical imaging and CAI such as the medical imaging interaction toolkit (MITK), the public software library for ultrasound imaging research (PLUS) and 3D Slicer. An independent inter-toolkit communication such as the open image-guided therapy link (OpenIGTLink) can be used to combine the advantages of these toolkits and enable an easier realization of a clinical CAI workflow. MITK-OpenIGTLink is presented as a network interface within MITK that allows easy to use, asynchronous two-way messaging between MITK and clinical devices or other toolkits. Performance and interoperability tests with MITK-OpenIGTLink were carried out considering the whole CAI workflow from data acquisition over processing to visualization. We present how MITK-OpenIGTLink can be applied in different usage scenarios. In performance tests, tracking data were transmitted with a frame rate of up to 1000 Hz and a latency of 2.81 ms. Transmission of images with typical ultrasound (US) and greyscale high-definition (HD) resolutions of [Formula: see text] and [Formula: see text] is possible at up to 512 and 128 Hz, respectively. With the integration of OpenIGTLink into MITK, this protocol is now supported by all established open-source toolkits in the field. This eases interoperability between MITK and toolkits such as PLUS or 3D Slicer and facilitates cross-toolkit research collaborations. MITK and its submodule MITK-OpenIGTLink are provided open source under a BSD-style licence ( http://mitk.org ).

OpenMC In Situ Source Convergence Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aldrich, Garrett Allen; Dutta, Soumya; Woodring, Jonathan Lee

2016-05-07

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

Getting Open Source Software into Schools: Strategies and Challenges

ERIC Educational Resources Information Center

Hepburn, Gary; Buley, Jan

2006-01-01

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

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

PubMed

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.

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

PubMed

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).

Open Source Drug Discovery in Practice: A Case Study

PubMed Central

Årdal, Christine; Røttingen, John-Arne

2012-01-01

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

GSTARI model of BPR assets in West Java, Central Java, and East Java

NASA Astrophysics Data System (ADS)

Susanti, Susi; Sulistijowati Handajani, Sri; Indriati, Diari

2018-05-01

Bank Perkreditan Rakyat (BPR) is a financial institution in Indonesia dealing with Micro, Small, and Medium Enterprises (MSMEs). Though limited to MSMEs, the development of the BPR industry continues to increase. West Java, Central Java, and East Java have high BPR asset development are suspected to be interconnected because of their economic activities as a neighboring provincies. BPR assets are nonstationary time series data that follow the uptrend pattern. Therefore, the suitable model with the data is generalized space time autoregressive integrated (GSTARI) which considers the spatial and time interrelationships. GSTARI model used spatial order 1 and the autoregressive order is obtained of optimal lag which has the smallest value of Akaike information criterion corrected. The correlation test results showed that the location used in this study had a close relationship. Based on the results of model identification, the best model obtained is GSTAR(31)-I(1). The parameter estimation used the ordinary least squares with the selection of significant variables used the stepwise method and the normalization cross correlation weighting. The residual model fulfilled the assumption of white noise and normal multivariate, so the model was appropriate. The average RMSE and MAPE values of the model were 498.75 and 2.48%.

Open Source and These United States

DTIC Science & Technology

1999-04-01

the ability of all participants to freely access the source code and keep abreast of progress. There can be no information hoarding on an open source... developed in this way depends upon ready and reliable communications. Just as the internet has increased the ability of people to exchange information...investment is maximized through long use and reuse. This process results in systems which harnesses the collaborative abilities of its user developers

Evaluating open-source cloud computing solutions for geosciences

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Open Source GIS based integrated watershed management

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Computer Forensics Education - the Open Source Approach

NASA Astrophysics Data System (ADS)

Huebner, Ewa; Bem, Derek; Cheung, Hon

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

Implementation of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for High Performance Computing (HPC). In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for CFD applications.

APINetworks Java. A Java approach to the efficient treatment of large-scale complex networks

NASA Astrophysics Data System (ADS)

Muñoz-Caro, Camelia; Niño, Alfonso; Reyes, Sebastián; Castillo, Miriam

2016-10-01

We present a new version of the core structural package of our Application Programming Interface, APINetworks, for the treatment of complex networks in arbitrary computational environments. The new version is written in Java and presents several advantages over the previous C++ version: the portability of the Java code, the easiness of object-oriented design implementations, and the simplicity of memory management. In addition, some additional data structures are introduced for storing the sets of nodes and edges. Also, by resorting to the different garbage collectors currently available in the JVM the Java version is much more efficient than the C++ one with respect to memory management. In particular, the G1 collector is the most efficient one because of the parallel execution of G1 and the Java application. Using G1, APINetworks Java outperforms the C++ version and the well-known NetworkX and JGraphT packages in the building and BFS traversal of linear and complete networks. The better memory management of the present version allows for the modeling of much larger networks.

Model Checker for Java Programs

NASA Technical Reports Server (NTRS)

Visser, Willem

2007-01-01

Java Pathfinder (JPF) is a verification and testing environment for Java that integrates model checking, program analysis, and testing. JPF consists of a custom-made Java Virtual Machine (JVM) that interprets bytecode, combined with a search interface to allow the complete behavior of a Java program to be analyzed, including interleavings of concurrent programs. JPF is implemented in Java, and its architecture is highly modular to support rapid prototyping of new features. JPF is an explicit-state model checker, because it enumerates all visited states and, therefore, suffers from the state-explosion problem inherent in analyzing large programs. It is suited to analyzing programs less than 10kLOC, but has been successfully applied to finding errors in concurrent programs up to 100kLOC. When an error is found, a trace from the initial state to the error is produced to guide the debugging. JPF works at the bytecode level, meaning that all of Java can be model-checked. By default, the software checks for all runtime errors (uncaught exceptions), assertions violations (supports Java s assert), and deadlocks. JPF uses garbage collection and symmetry reductions of the heap during model checking to reduce state-explosion, as well as dynamic partial order reductions to lower the number of interleavings analyzed. JPF is capable of symbolic execution of Java programs, including symbolic execution of complex data such as linked lists and trees. JPF is extensible as it allows for the creation of listeners that can subscribe to events during searches. The creation of dedicated code to be executed in place of regular classes is supported and allows users to easily handle native calls and to improve the efficiency of the analysis.

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

NASA Astrophysics Data System (ADS)

Johansson, Björn; Sudzina, Frantisek

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

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

NASA Astrophysics Data System (ADS)

Kuhnert, Kristin; Quedenau, Jörn

2016-04-01

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

Reflections on the role of open source in health information system interoperability.

PubMed

Sfakianakis, S; Chronaki, C E; Chiarugi, F; Conforti, F; Katehakis, D G

2007-01-01

This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events

PubMed Central

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-01-01

Background Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. Objective To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. Software architecture DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Results Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. Discussion This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. Conclusion The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License. PMID:17472749

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events.

PubMed

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-05-01

Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. SOFTWARE ARCHITECTURE: DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License.

Open Source Clinical NLP - More than Any Single System.

PubMed

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

2014-01-01

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

Java: An Explosion on the Internet.

ERIC Educational Resources Information Center

Read, Tim; Hall, Hazel

Summer 1995 saw the release, with considerable media attention, of draft versions of Sun Microsystems' Java computer programming language and the HotJava browser. Java has been heralded as the latest "killer" technology in the Internet explosion. Sun Microsystems and numerous companies including Microsoft, IBM, and Netscape have agreed…

JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Langhirt, Eric; Livny, Miron; Ramamurthy, Ravishankar; Soloman, Marvin; Traugott, Steve

2000-01-01

A genetic algorithm code, JavaGenes, was written in Java and used to evolve pharmaceutical drug molecules and digital circuits. JavaGenes was run under the Condor cycle-scavenging batch system managing 100-170 desktop SGI workstations. Genetic algorithms mimic biological evolution by evolving solutions to problems using crossover and mutation. While most genetic algorithms evolve strings or trees, JavaGenes evolves graphs representing (currently) molecules and circuits. Java was chosen as the implementation language because the genetic algorithm requires random splitting and recombining of graphs, a complex data structure manipulation with ample opportunities for memory leaks, loose pointers, out-of-bound indices, and other hard to find bugs. Java garbage-collection memory management, lack of pointer arithmetic, and array-bounds index checking prevents these bugs from occurring, substantially reducing development time. While a run-time performance penalty must be paid, the only unacceptable performance we encountered was using standard Java serialization to checkpoint and restart the code. This was fixed by a two-day implementation of custom checkpointing. JavaGenes is minimally integrated with Condor; in other words, JavaGenes must do its own checkpointing and I/O redirection. A prototype Java-aware version of Condor was developed using standard Java serialization for checkpointing. For the prototype to be useful, standard Java serialization must be significantly optimized. JavaGenes is approximately 8700 lines of code and a few thousand JavaGenes jobs have been run. Most jobs ran for a few days. Results include proof that genetic algorithms can evolve directed and undirected graphs, development of a novel crossover operator for graphs, a paper in the journal Nanotechnology, and another paper in preparation.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Java PathFinder User Guide

NASA Technical Reports Server (NTRS)

Havelund, Klaus

1999-01-01

The JAVA PATHFINDER, JPF, is a translator from a subset of JAVA 1.0 to PROMELA, the programming language of the SPIN model checker. The purpose of JPF is to establish a framework for verification and debugging of JAVA programming based on model checking. The main goal is to automate program verification such that a programmer can apply it in the daily work without the need for a specialist to manually reformulate a program into a different notation in order to analyze the program. The system is especially suited for analyzing multi-threaded JAVA applications, where normal testing usually falls short. The system can find deadlocks and violations of boolean assertions stated by the programmer in a special assertion language. This document explains how to Use JPF.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

The 2006 July 17 Java (Indonesia) tsunami from satellite imagery and numerical modelling: a single or complex source?

NASA Astrophysics Data System (ADS)

Hébert, H.; Burg, P.-E.; Binet, R.; Lavigne, F.; Allgeyer, S.; Schindelé, F.

2012-12-01

The Mw 7.8 2006 July 17 earthquake off the southern coast of Java, Indonesia, has been responsible for a very large tsunami causing more than 700 casualties. The tsunami has been observed on at least 200 km of coastline in the region of Pangandaran (West Java), with run-up heights from 5 to more than 20 m. Such a large tsunami, with respect to the source magnitude, has been attributed to the slow character of the seismic rupture, defining the event as a so-called tsunami earthquake, but it has also been suggested that the largest run-up heights are actually the result of a second local landslide source. Here we test whether a single slow earthquake source can explain the tsunami run-up, using a combination of new detailed data in the region of the largest run-ups and comparison with modelled run-ups for a range of plausible earthquake source models. Using high-resolution satellite imagery (SPOT 5 and Quickbird), the coastal impact of the tsunami is refined in the surroundings of the high-security Permisan prison on Nusa Kambangan island, where 20 m run-up had been recorded directly after the event. These data confirm the extreme inundation lengths close to the prison, and extend the area of maximum impact further along the Nusa Kambangan island (about 20 km of shoreline), where inundation lengths reach several hundreds of metres, suggesting run-up as high as 10-15 m. Tsunami modelling has been conducted in detail for the high run-up Permisan area (Nusa Kambangan) and the PLTU power plant about 25 km eastwards, where run-up reached only 4-6 m and a video recording of the tsunami arrival is available. For the Permisan prison a high-resolution DEM was built from stereoscopic satellite imagery. The regular basin of the PLTU plant was designed using photographs and direct observations. For the earthquake's mechanism, both static (infinite) and finite (kinematic) ruptures are investigated using two published source models. The models account rather well for the sea level

Open source IPSEC software in manned and unmanned space missions

NASA Astrophysics Data System (ADS)

Edwards, Jacob

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

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

PubMed

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

2015-09-01

Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Limitations of Phased Array Beamforming in Open Rotor Noise Source Imaging

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

MicMac GIS application: free open source

NASA Astrophysics Data System (ADS)

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.

Analyzing huge pathology images with open source software.

PubMed

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

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

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 tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results 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. Conclusions 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. Virtual slides The virtual slide(s) for this article can be found here: http

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

ERIC Educational Resources Information Center

Conner, Trey; Gresham, Morgan; McCracken, Jill

2011-01-01

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

Open Source for Knowledge and Learning Management: Strategies beyond Tools

ERIC Educational Resources Information Center

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

2007-01-01

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

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

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

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

A Framework for the Systematic Collection of Open Source Intelligence

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2009-01-01

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

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

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.

Understanding the Requirements for Open Source Software

DTIC Science & Technology

2009-06-17

GNOME and K Development Environment ( KDE ) for end-user interfaces, the Eclipse and NetBeans interactive development environments for Java-based Web...17 4.1. Informal Post-hoc Assertion of OSS Requirements vs . Requirements Elicitation...18 4.2. Requirements Reading, Sense-making, and Accountability vs . Requirements Analysis

Open Source Solutions for Libraries: ABCD vs Koha

ERIC Educational Resources Information Center

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

2013-01-01

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

Modular Open-Source Software for Item Factor Analysis

ERIC Educational Resources Information Center

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

2015-01-01

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

State-of-the-practice and lessons learned on implementing open data and open source policies.

DOT National Transportation Integrated Search

2012-05-01

This report describes the current government, academic, and private sector practices associated with open data and open source application development. These practices are identified; and the potential uses with the ITS Programs Data Capture and M...

Migrations of the Mind: The Emergence of Open Source Education

ERIC Educational Resources Information Center

Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

2011-01-01

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

Data mining for clustering naming of the village at Java Island

NASA Astrophysics Data System (ADS)

Setiawan Abdullah, Atje; Nurani Ruchjana, Budi; Hidayat, Akik; Akmal; Setiana, Deni

2017-10-01

Clustering of query based data mining to identify the meaning of the naming of the village in Java island, done by exploring the database village with three categories namely: prefix in the naming of the village, syllables contained in the naming of the village, and full word naming of the village which is actually used. While syllables contained in the naming of the village are classified by the behaviour of the culture and character of each province that describes the business, feelings, circumstances, places, nature, respect, plants, fruits, and animals. Sources of data used for the clustering of the naming of the village on the island of Java was obtained from Geospatial Information Agency (BIG) in the form of a complete village name data with the coordinates in six provinces in Java, which is arranged in a hierarchy of provinces, districts / cities, districts and villages. The research method using KDD (Knowledge Discovery in Database) through the process of preprocessing, data mining and postprocessing to obtain knowledge. In this study, data mining applications to facilitate the search query based on the name of the village, using Java software. While the contours of a map is processed using ArcGIS software. The results of the research can give recommendations to stakeholders such as the Department of Tourism to describe the meaning of the classification of naming the village according to the character in each province at Java island.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Open-Source Automated Mapping Four-Point Probe.

PubMed

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.

Open-Source Automated Mapping Four-Point Probe

PubMed Central

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

2017-01-01

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. PMID:28772471

Implementation, reliability, and feasibility test of an Open-Source PACS.

PubMed

Valeri, Gianluca; Zuccaccia, Matteo; Badaloni, Andrea; Ciriaci, Damiano; La Riccia, Luigi; Mazzoni, Giovanni; Maggi, Stefania; Giovagnoni, Andrea

2015-12-01

To implement a hardware and software system able to perform the major functions of an Open-Source PACS, and to analyze it in a simulated real-world environment. A small home network was implemented, and the Open-Source operating system Ubuntu 11.10 was installed in a laptop containing the Dcm4chee suite with the software devices needed. The Open-Source PACS implemented is compatible with Linux OS, Microsoft OS, and Mac OS X; furthermore, it was used with operating systems that guarantee the operation in portable devices (smartphone, tablet) Android and iOS. An OSS PACS is useful for making tutorials and workshops on post-processing techniques for educational and training purposes.

Changes in polyphenolics during maturation of Java plum (Syzygium cumini Lam.).

PubMed

Lestario, Lydia Ninan; Howard, Luke R; Brownmiller, Cindi; Stebbins, Nathan B; Liyanage, Rohana; Lay, Jackson O

2017-10-01

Java plum (Syzygium cumini Lam.) is a rich source of polyphenolics with many purported health benefits, but the effect of maturation on polyphenolic content is unknown. Freeze-dried samples of Java plum from seven different maturity stages were analyzed for anthocyanin, flavonol, flavanonol and hydrolysable tannin composition by HPLC. Anthocyanins were first detected at the green-pink stage of maturity and increased throughout maturation with the largest increase occurring from the dark purple to black stages of maturation. Levels of gallotannins, ellagitannins, flavonols, gallic acid and ellagic acid were highest at early stages of maturation and decreased as the fruit ripened. For production of antioxidant-rich nutraceutical ingredients, fruit should be harvested immature to obtain extracts rich in hydrolysable tannins and flavonols. The exceptional anthocyanin content of black fruit may prove useful as a source of a natural colorant. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

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

PubMed

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

2017-06-01

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

T-Check in Technologies for Interoperability: Web Services and Security--Single Sign-On

DTIC Science & Technology

2007-12-01

following tools: • Apache Tomcat 6.0—a Java Servlet container to host the Web services and a simple Web client application [Apache 2007a] • Apache Axis...Eclipse. Eclipse – an open development platform. http://www.eclipse.org/ (2007) [Hunter 2001] Hunter, Jason. Java Servlet Programming, 2nd Edition...Citation SAML 1.1 Java Toolkit SAML Ping Identity’s SAML-1.1 implementation [SourceID 2006] OpenSAML SAML An open source implementation of SAML 1.1

DICOM router: an open source toolbox for communication and correction of DICOM objects.

PubMed

Hackländer, Thomas; Kleber, Klaus; Martin, Jens; Mertens, Heinrich

2005-03-01

Today, the exchange of medical images and clinical information is well defined by the digital imaging and communications in medicine (DICOM) and Health Level Seven (ie, HL7) standards. The interoperability among information systems is specified by the integration profiles of IHE (Integrating the Healthcare Enterprise). However, older imaging modalities frequently do not correctly support these interfaces and integration profiles, and some use cases are not yet specified by IHE. Therefore, corrections of DICOM objects are necessary to establish conformity. The aim of this project was to develop a toolbox that can automatically perform these recurrent corrections of the DICOM objects. The toolbox is composed of three main components: 1) a receiver to receive DICOM objects, 2) a processing pipeline to correct each object, and 3) one or more senders to forward each corrected object to predefined addressees. The toolbox is implemented under Java as an open source project. The processing pipeline is realized by means of plug ins. One of the plug ins can be programmed by the user via an external eXtensible Stylesheet Language (ie, XSL) file. Using this plug in, DICOM objects can also be converted into eXtensible Markup Language (ie, XML) documents or other data formats. DICOM storage services, DICOM CD-ROMs, and the local file system are defined as input and output channel. The toolbox is used clinically for different application areas. These are the automatic correction of DICOM objects from non-IHE-conforming modalities, the import of DICOM CD-ROMs into the picture archiving and communication system and the pseudo naming of DICOM images. The toolbox has been accepted by users in a clinical setting. Because of the open programming interfaces, the functionality can easily be adapted to future applications.

Scalar collapse in AdS with an OpenCL open source code

NASA Astrophysics Data System (ADS)

Liebling, Steven L.; Khanna, Gaurav

2017-10-01

We study the spherically symmetric collapse of a scalar field in anti-de Sitter spacetime using a newly constructed, open-source code which parallelizes over heterogeneous architectures using the open standard OpenCL. An open question for this scenario concerns how to tell, a priori, whether some form of initial data will be stable or will instead develop under the turbulent instability into a black hole in the limit of vanishing amplitude. Previous work suggested the existence of islands of stability around quasi-periodic solutions, and we use this new code to examine the stability properties of approximately quasi-periodic solutions which balance energy transfer to higher modes with energy transfer to lower modes. The evolutions provide some evidence, though not conclusively, for stability of initial data sufficiently close to quasiperiodic solutions.

OpenSim: open-source software to create and analyze dynamic simulations of movement.

PubMed

Delp, Scott L; Anderson, Frank C; Arnold, Allison S; Loan, Peter; Habib, Ayman; John, Chand T; Guendelman, Eran; Thelen, Darryl G

2007-11-01

Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.

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

ERIC Educational Resources Information Center

Kisworo, Marsudi Wahyu

2016-01-01

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

Bringing Interactivity to the Web: The JAVA Solution.

ERIC Educational Resources Information Center

Knee, Richard H.; Cafolla, Ralph

Java is an object-oriented programming language of the Internet. It's popularity lies in its ability to create interactive Web sites across platforms. The most common Java programs are applications and applets, which adhere to a set of conventions that lets them run within a Java-compatible browser. Java is becoming an essential subject matter and…

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

PubMed

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

2016-08-01

The combination of open-source software and hardware provides technically feasible methods to create low-cost, highly customized scientific research equipment. Open-source 3-D printers have proven useful for fabricating scientific tools. Here the capabilities of an open-source 3-D printer are expanded to become a highly flexible scientific platform. An automated low-cost 3-D motion control platform is presented that has the capacity to perform scientific applications, including (1) 3-D printing of scientific hardware; (2) laboratory auto-stirring, measuring, and probing; (3) automated fluid handling; and (4) shaking and mixing. The open-source 3-D platform not only facilities routine research while radically reducing the cost, but also inspires the creation of a diverse array of custom instruments that can be shared and replicated digitally throughout the world to drive down the cost of research and education further. © 2016 Society for Laboratory Automation and Screening.

OpenFOAM: Open source CFD in research and industry

NASA Astrophysics Data System (ADS)

Jasak, Hrvoje

2009-12-01

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 ofpractical 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 ofpartial 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.

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software

PubMed Central

Mejías, Andrés; Herrera, Reyes S.; Márquez, Marco A.; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-01

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)—this one designed using the intuitive graphical system of EJS—located on the user’s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented. PMID:28067801

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software.

PubMed

Mejías, Andrés; Herrera, Reyes S; Márquez, Marco A; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-05

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user's computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.

Open Source Clinical NLP – More than Any Single System

PubMed Central

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

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

Open source and DIY hardware for DNA nanotechnology labs.

PubMed

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%.

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

ERIC Educational Resources Information Center

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

2003-01-01

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

What an open source clinical trial community can learn from hackers

PubMed Central

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

2014-01-01

Summary 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. Since a similar gap has already been addressed in the software industry by the open source software movement, we examine how the social and technical principles of the movement can be used to guide the growth of an open source clinical trial community. PMID:22553248

jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

PubMed

de Leeuw, Joshua R

2015-03-01

Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

PubMed

Helt, Gregg A; Nicol, John W; Erwin, Ed; Blossom, Eric; Blanchard, Steven G; Chervitz, Stephen A; Harmon, Cyrus; Loraine, Ann E

2009-08-25

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities. Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/.

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

PubMed

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

2016-08-30

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

Open source and DIY hardware for DNA nanotechnology labs

PubMed Central

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

2015-01-01

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

NOAA's Data Catalog and the Federal Open Data Policy

NASA Astrophysics Data System (ADS)

Wengren, M. J.; de la Beaujardiere, J.

2014-12-01

The 2013 Open Data Policy Presidential Directive requires Federal agencies to create and maintain a 'public data listing' that includes all agency data that is currently or will be made publicly-available in the future. The directive requires the use of machine-readable and open formats that make use of 'common core' and extensible metadata formats according to the best practices published in an online repository called 'Project Open Data', to use open licenses where possible, and to adhere to existing metadata and other technology standards to promote interoperability. In order to meet the requirements of the Open Data Policy, the National Oceanic and Atmospheric Administration (NOAA) has implemented an online data catalog that combines metadata from all subsidiary NOAA metadata catalogs into a single master inventory. The NOAA Data Catalog is available to the public for search and discovery, providing access to the NOAA master data inventory through multiple means, including web-based text search, OGC CS-W endpoint, as well as a native Application Programming Interface (API) for programmatic query. It generates on a daily basis the Project Open Data JavaScript Object Notation (JSON) file required for compliance with the Presidential directive. The Data Catalog is based on the open source Comprehensive Knowledge Archive Network (CKAN) software and runs on the Amazon Federal GeoCloud. This presentation will cover topics including mappings of existing metadata in standard formats (FGDC-CSDGM and ISO 19115 XML ) to the Project Open Data JSON metadata schema, representation of metadata elements within the catalog, and compatible metadata sources used to feed the catalog to include Web Accessible Folder (WAF), Catalog Services for the Web (CS-W), and Esri ArcGIS.com. It will also discuss related open source technologies that can be used together to build a spatial data infrastructure compliant with the Open Data Policy.

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

ERIC Educational Resources Information Center

van Rooij, S. Williams

2012-01-01

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

JAVA PathFinder

NASA Technical Reports Server (NTRS)

Mehhtz, Peter

2005-01-01

JPF is an explicit state software model checker for Java bytecode. Today, JPF is a swiss army knife for all sort of runtime based verification purposes. This basically means JPF is a Java virtual machine that executes your program not just once (like a normal VM), but theoretically in all possible ways, checking for property violations like deadlocks or unhandled exceptions along all potential execution paths. If it finds an error, JPF reports the whole execution that leads to it. Unlike a normal debugger, JPF keeps track of every step how it got to the defect.

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

ERIC Educational Resources Information Center

Pfaffman, Jay

2008-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

High-Performance Java Codes for Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

Performance and Scalability of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for scientific applications. In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for scientific applications.

An oceanic plateau subduction offshore Eastern Java

NASA Astrophysics Data System (ADS)

Shulgin, A.; Kopp, H.; Mueller, C.; Planert, L.; Lueschen, E.; Flueh, E. R.; Djajadihardja, Y.

2010-12-01

The area offshore Java represents one of a few places globally where the early stage of subduction of an oceanic plateau is observed. We study the little investigated Roo Rise oceanic plateau on the Indian plate, subducting beneath Eurasia.Our study area is located south of eastern Java and covers the edge of the Roo Rise plateau, the Java trench and the entire forearc section. For the first time the detailed deep structure of the Roo Rise is studied, subduction of which has a significant effect on the forearc dynamics and evolution and the increase of the geohazards risks. The tsunamogenic earthquakes of 1994 and 2006 are associated with the oceanic plateau edge been subducted. We present integrated results of a refraction/wide-angle reflection tomography, gravity modeling, and multichannel reflection seismic imaging using data acquired in 2006 along a corridor centered around 113°E and composed of a 340 km long N-S profile and a 130 km long E-W oriented profile. The composite structural models reveal the previously unresolved deep geometry of the collision zone and the structure of the oceanic plateau. The crustal thickness of the Roo Rise plateau is ranging from 18 to 12 km. The structure of the upper crust of the incoming oceanic plate shows the extreme degree of fracturing in its top section, and is associated with a plate bending. The forearc Moho has a depth range from 16 to 20 km. The gravity modeling requires a sharp crustal thickness increase below Java. Within our profiles we do not recover any direct evidence for the presence of the bathymetric features on the oceanic plate currently present below the accretionary prism, responsible for the tsunamogenic earthquake triggering. However vertical variations of the forearc basement edge are observed on the trench-parallel profile, which opens a discussion on the origin of such basement undulations, together with a localized patchy uplift character of the forearc high.The complex geometry of the backstop

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Open source clustering software.

PubMed

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.

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

PubMed

Geissmann, Quentin

2013-01-01

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

Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder

NASA Technical Reports Server (NTRS)

Staats, Matt

2009-01-01

We present work on a prototype tool based on the JavaPathfinder (JPF) model checker for automatically generating tests satisfying the MC/DC code coverage criterion. Using the Eclipse IDE, developers and testers can quickly instrument Java source code with JPF annotations covering all MC/DC coverage obligations, and JPF can then be used to automatically generate tests that satisfy these obligations. The prototype extension to JPF enables various tasks useful in automatic test generation to be performed, such as test suite reduction and execution of generated tests.

The ENSDF Java Package

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sonzogni, A.A.

2005-05-24

A package of computer codes has been developed to process and display nuclear structure and decay data stored in the ENSDF (Evaluated Nuclear Structure Data File) library. The codes were written in an object-oriented fashion using the java language. This allows for an easy implementation across multiple platforms as well as deployment on web pages. The structure of the different java classes that make up the package is discussed as well as several different implementations.

Human genome and open source: balancing ethics and business.

PubMed

Marturano, Antonio

2011-01-01

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

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

The prediction of the number of clusters in a dataset, in particular microarrays, is a fundamental task in biological data analysis, usually performed via validation measures. Unfortunately, it has received very little attention and in fact there is a growing need for software tools/libraries dedicated to it. Here we present ValWorkBench, a software library consisting of eleven well known validation measures, together with novel heuristic approximations for some of them. The main objective of this paper is to provide the interested researcher with the full software documentation of an open source cluster validation platform having the main features of being easily extendible in a homogeneous way and of offering software components that can be readily re-used. Consequently, the focus of the presentation is on the architecture of the library, since it provides an essential map that can be used to access the full software documentation, which is available at the supplementary material website [1]. The mentioned main features of ValWorkBench are also discussed and exemplified, with emphasis on software abstraction design and re-usability. A comparison with existing cluster validation software libraries, mainly in terms of the mentioned features, is also offered. It suggests that ValWorkBench is a much needed contribution to the microarray software development/algorithm engineering community. For completeness, it is important to mention that previous accurate algorithmic experimental analysis of the relative merits of each of the implemented measures [19,23,25], carried out specifically on microarray data, gives useful insights on the effectiveness of ValWorkBench for cluster validation to researchers in the microarray community interested in its use for the mentioned task. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Open Source Tools for Numerical Simulation of Urban Greenhouse Gas Emissions

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Nowcasting influenza outbreaks using open-source media report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ray, Jaideep; Brownstein, John S.

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)more » 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.« less

Communal Resources in Open Source Software Development

ERIC Educational Resources Information Center

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

2008-01-01

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

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

PubMed

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.

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

PubMed

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

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

An oceanic plateau subduction: A case study offshore Eastern Java.

NASA Astrophysics Data System (ADS)

Shulgin, Alexey; Kopp, Heidrun; Mueller, Christian; Planert, Lars; Lueschen, Ewald; Flueh, Ernst; Djajadihardja, Yusuf

2010-05-01

The area offshore Java represents one of a few places globally where the early stage of subduction of an oceanic plateau is observed. Our study area is located south of eastern Java and covers the edge of the Roo Rise plateau, the Java trench and the entire forearc section. For the first time the detailed deep structure of the Roo Rise is studied, subduction of which has a significant effect on the forearc dynamics and evolution and the increase of the geohazards risks. The tsunamogenic earthquakes of 1994 and 2006 are associated with the oceanic plateau edge been subducted. We present integrated results of a refraction/wide-angle reflection tomography, gravity modeling, and multichannel reflection seismic imaging using data acquired in 2006 along a corridor centered around 113°E and composed of a 340 km long N-S profile and a 130 km long E-W oriented profile. The composite structural models reveal the previously unresolved deep geometry of the collision zone and the structure of the oceanic plateau. The crustal thickness of the Roo Rise plateau is ranging from 18 to 12 km. The structure of the upper crust of the incoming oceanic plate shows the extreme degree of fracturing in its top section, and is associated with a plate bending. The forearc Moho has a depth range from 16 to 20 km. The gravity modeling requires a sharp crustal thickness increase below Java. Within our profiles we do not recover any direct evidence for the presence of the bathymetric features on the oceanic plate currently present below the accretionary prism, responsible for the tsunamogenic earthquake triggering. However vertical variations of the forearc basement edge are observed on the trench-parallel profile, which opens a discussion on the origin of such basement undulations, together with a localized patchy uplift character of the forearc high.

Free and open-source automated 3-D microscope.

PubMed

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.

East Java Maritime Connectivity and Its Regional Development Support

NASA Astrophysics Data System (ADS)

Purboyo, H.; Ibad, M. Z.

2017-07-01

The study presents an evolution of maritime connectivity index of East Java which is associated with accessibility and mobility index of regions in East Java. The findings show that East Java increased connectivity more than three times from 1996 to 2011. Initially, the East Java is importer but then become exporter to national territory. For accessibility, the inland regions of East Java in general is higher than the coastal areas. And for mobility, inland regions initially have a small index, but in subsequent years its index is greater than the coastal areas.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Open Source Software and the Intellectual Commons.

ERIC Educational Resources Information Center

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.…

OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

PubMed Central

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net. PMID:23457446

Embracing Open Software Development in Solar Physics

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Christe, S.; Mueller, D.

2012-12-01

We discuss two ongoing software projects in solar physics that have adopted best practices of the open source software community. The first, the Helioviewer Project, is a powerful data visualization tool which includes online and Java interfaces inspired by Google Maps (tm). This effort allows users to find solar features and events of interest, and download the corresponding data. Having found data of interest, the user now has to analyze it. The dominant solar data analysis platform is an open-source library called SolarSoft (SSW). Although SSW itself is open-source, the programming language used is IDL, a proprietary language with licensing costs that are prohibative for many institutions and individuals. SSW is composed of a collection of related scripts written by missions and individuals for solar data processing and analysis, without any consistent data structures or common interfaces. Further, at the time when SSW was initially developed, many of the best software development processes of today (mirrored and distributed version control, unit testing, continuous integration, etc.) were not standard, and have not since been adopted. The challenges inherent in developing SolarSoft led to a second software project known as SunPy. SunPy is an open-source Python-based library which seeks to create a unified solar data analysis environment including a number of core datatypes such as Maps, Lightcurves, and Spectra which have consistent interfaces and behaviors. By taking advantage of the large and sophisticated body of scientific software already available in Python (e.g. SciPy, NumPy, Matplotlib), and by adopting many of the best practices refined in open-source software development, SunPy has been able to develop at a very rapid pace while still ensuring a high level of reliability. The Helioviewer Project and SunPy represent two pioneering technologies in solar physics - simple yet flexible data visualization and a powerful, new data analysis environment. We

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

ERIC Educational Resources Information Center

Derringer, Pam

2009-01-01

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

Comet: an open-source MS/MS sequence database search tool.

PubMed

Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

2013-01-01

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

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

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

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

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

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

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

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

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

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

PubMed

Hahn, Erin; Blazes, David; Lewis, Sheri

2016-01-01

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

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

PubMed Central

2011-01-01

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

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

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

Open Source Software to Control Bioflo Bioreactors

PubMed Central

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

2014-01-01

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

Visualization Software for VisIT Java Client

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billings, Jay Jay; Smith, Robert W

The VisIT Java Client (JVC) library is a lightweight thin client that is designed and written purely in the native language of Java (the Python & JavaScript versions of the library use the same concept) and communicates with any new unmodified standalone version of VisIT, a high performance computing parallel visualization toolkit, over traditional or web sockets and dynamically determines capabilities of the running VisIT instance whether local or remote.

Of Birkenstocks and Wingtips: Open Source Licenses

ERIC Educational Resources Information Center

Gandel, Paul B.; Wheeler, Brad

2005-01-01

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

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

PubMed

Erdemir, Ahmet

2016-02-01

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

jmzTab: a java interface to the mzTab data standard.

PubMed

Xu, Qing-Wei; Griss, Johannes; Wang, Rui; Jones, Andrew R; Hermjakob, Henning; Vizcaíno, Juan Antonio

2014-06-01

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches. We here present an open-source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files. In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com. © 2014 The Authors PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Freeing Crop Genetics through the Open Source Seed Initiative

PubMed Central

Luby, Claire H.; Goldman, Irwin L.

2016-01-01

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

Freeing Crop Genetics through the Open Source Seed Initiative.

PubMed

Luby, Claire H; Goldman, Irwin L

2016-04-01

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

Open Source Next Generation Visualization Software for Interplanetary Missions

NASA Technical Reports Server (NTRS)

Trimble, Jay; Rinker, George

2016-01-01

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

Social religious movement in java 19Th - 20Th century

NASA Astrophysics Data System (ADS)

Sumarno; Trilaksana, A.; Kasdi, A.

2018-01-01

Religious social movements are very interesting to be studied because this phenomenon is affecting the urban and rural communities, among the rich and the poor people, the educated and the less educated. The purpose of this study was to analyze several religious social movements in Java in the 19Th - 20Th centuries. The methods used are historical methods that include: Source feeding (main source is reference), Source Critique (source test), Interpretation of fact (analyzing the fact), and Historiography (writing research results) in the form of Journal Articles. Religious Social Symbols arise as a result of a depressed society, oppressed by the political system, or poverty as a result of colonial exploitation. For indigenous and less religious societies social pressures breed social protest movements and social revolutions. Meanwhile, in the Javanese society that has social and religious characteristics make the nature of the movement multidimensional. The form of movement is a blend of social movements that lead in the form of protests and revolutions, on the other hand formed religious movements that are politer nature because it is related to the life of the world and the hereafter. In various religious social movements in Java include the Nativist movement, Millennial/millenarianism, Messianic, Nostalgic, sectarian, and Revivalist. The movement emerged as a social impact of the Dutch colonization in the form of Cultivation which gave birth to the suffering of the people in the economic and social fields.

A Java Applet for Illustrating Internet Error Control

ERIC Educational Resources Information Center

Holliday, Mark A.

2004-01-01

This paper discusses the author's experiences developing a Java applet that illustrates how error control is implemented in the Transmission Control Protocol (TCP). One section discusses the concepts which the TCP error control Java applet is intended to convey, while the nature of the Java applet is covered in another section. The author…

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

ERIC Educational Resources Information Center

Hemphill, Thomas A.

2005-01-01

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

Is Open Source the ERP Cure-All?

ERIC Educational Resources Information Center

Panettieri, Joseph C.

2008-01-01

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

Secure Web-based Ground System User Interfaces over the Open Internet

NASA Technical Reports Server (NTRS)

Langston, James H.; Murray, Henry L.; Hunt, Gary R.

1998-01-01

A prototype has been developed which makes use of commercially available products in conjunction with the Java programming language to provide a secure user interface for command and control over the open Internet. This paper reports successful demonstration of: (1) Security over the Internet, including encryption and certification; (2) Integration of Java applets with a COTS command and control product; (3) Remote spacecraft commanding using the Internet. The Java-based Spacecraft Web Interface to Telemetry and Command Handling (Jswitch) ground system prototype provides these capabilities. This activity demonstrates the use and integration of current technologies to enable a spacecraft engineer or flight operator to monitor and control a spacecraft from a user interface communicating over the open Internet using standard World Wide Web (WWW) protocols and commercial off-the-shelf (COTS) products. The core command and control functions are provided by the COTS Epoch 2000 product. The standard WWW tools and browsers are used in conjunction with the Java programming technology. Security is provided with the current encryption and certification technology. This system prototype is a step in the direction of giving scientist and flight operators Web-based access to instrument, payload, and spacecraft data.

New Web Server - the Java Version of Tempest - Produced

NASA Technical Reports Server (NTRS)

York, David W.; Ponyik, Joseph G.

2000-01-01

A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Hypersonic simulations using open-source CFD and DSMC solvers

NASA Astrophysics Data System (ADS)

Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.

2016-11-01

Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.

Status and future plans for open source QuickPIC

NASA Astrophysics Data System (ADS)

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

JIP: Java image processing on the Internet

NASA Astrophysics Data System (ADS)

Wang, Dongyan; Lin, Bo; Zhang, Jun

1998-12-01

In this paper, we present JIP - Java Image Processing on the Internet, a new Internet based application for remote education and software presentation. JIP offers an integrate learning environment on the Internet where remote users not only can share static HTML documents and lectures notes, but also can run and reuse dynamic distributed software components, without having the source code or any extra work of software compilation, installation and configuration. By implementing a platform-independent distributed computational model, local computational resources are consumed instead of the resources on a central server. As an extended Java applet, JIP allows users to selected local image files on their computers or specify any image on the Internet using an URL as input. Multimedia lectures such as streaming video/audio and digital images are integrated into JIP and intelligently associated with specific image processing functions. Watching demonstrations an practicing the functions with user-selected input data dramatically encourages leaning interest, while promoting the understanding of image processing theory. The JIP framework can be easily applied to other subjects in education or software presentation, such as digital signal processing, business, mathematics, physics, or other areas such as employee training and charged software consumption.

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

PubMed

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

2018-05-10

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

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

NASA Astrophysics Data System (ADS)

Thaler, A. D.; Sturdivant, K.

2013-12-01

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

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

NASA Astrophysics Data System (ADS)

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

The use of open source electronic health records within the federal safety net.

PubMed

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

2014-01-01

To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). The study was conducted by the National Opinion Research Center (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 West Virginia, California and Arizona FQHC that were currently using an open source EHR. Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness.

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

PubMed

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

2017-04-18

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

Inexpensive Open-Source Data Logging in the Field

NASA Astrophysics Data System (ADS)

Wickert, A. D.

2013-12-01

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

Faculty/Student Surveys Using Open Source Software

ERIC Educational Resources Information Center

Kaceli, Sali

2004-01-01

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

Open Source Paradigm: A Synopsis of The Cathedral and the Bazaar for Health and Social Care.

PubMed

Benson, Tim

2016-07-04

Open source software (OSS) is becoming more fashionable in health and social care, although the ideas are not new. However progress has been slower than many had expected. The purpose is to summarise the Free/Libre Open Source Software (FLOSS) paradigm in terms of what it is, how it impacts users and software engineers and how it can work as a business model in health and social care sectors. Much of this paper is a synopsis of Eric Raymond's seminal book The Cathedral and the Bazaar, which was the first comprehensive description of the open source ecosystem, set out in three long essays. Direct quotes from the book are used liberally, without reference to specific passages. The first part contrasts open and closed source approaches to software development and support. The second part describes the culture and practices of the open source movement. The third part considers business models. A key benefit of open source is that users can access and collaborate on improving the software if they wish. Closed source code may be regarded as a strategic business risk that that may be unacceptable if there is an open source alternative. The sharing culture of the open source movement fits well with that of health and social care.

Soil Monitor: an open source web application for real-time soil sealing monitoring and assessment

NASA Astrophysics Data System (ADS)

Langella, Giuliano; Basile, Angelo; Giannecchini, Simone; Iamarino, Michela; Munafò, Michele; Terribile, Fabio

2016-04-01

Soil sealing is one of the most important causes of land degradation and desertification. In Europe, soil covered by impermeable materials has increased by about 80% from the Second World War till nowadays, while population has only grown by one third. There is an increasing concern at the high political levels about the need to attenuate imperviousness itself and its effects on soil functions. European Commission promulgated a roadmap (COM(2011) 571) by which the net land take would be zero by 2050. Furthermore, European Commission also published a report in 2011 providing best practices and guidelines for limiting soil sealing and imperviousness. In this scenario, we developed an open source and an open source based Soil Sealing Geospatial Cyber Infrastructure (SS-GCI) named as "Soil Monitor". This tool merges a webGIS with parallel geospatial computation in a fast and dynamic fashion in order to provide real-time assessments of soil sealing at high spatial resolution (20 meters and below) over the whole Italy. Common open source webGIS packages are used to implement both the data management and visualization infrastructures, such as GeoServer and MapStore. The high-speed geospatial computation is ensured by a GPU parallelism using the CUDA (Computing Unified Device Architecture) framework by NVIDIA®. This kind of parallelism required the writing - from scratch - all codes needed to fulfil the geospatial computation built behind the soil sealing toolbox. The combination of GPU computing with webGIS infrastructures is relatively novel and required particular attention at the Java-CUDA programming interface. As a result, Soil Monitor is smart because it can perform very high time-consuming calculations (querying for instance an Italian administrative region as area of interest) in less than one minute. The web application is embedded in a web browser and nothing must be installed before using it. Potentially everybody can use it, but the main targets are the

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

NASA Astrophysics Data System (ADS)

Liu, H. S.; Liao, H. M.

2015-08-01

Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

Spatial Information Processing: Standards-Based Open Source Visualization Technology

NASA Astrophysics Data System (ADS)

Hogan, P.

2009-12-01

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

Open-Source web-based geographical information system for health exposure assessment

PubMed Central

2012-01-01

This paper presents the design and development of an open source web-based Geographical Information System allowing users to visualise, customise and interact with spatial data within their web browser. The developed application shows that by using solely Open Source software it was possible to develop a customisable web based GIS application that provides functions necessary to convey health and environmental data to experts and non-experts alike without the requirement of proprietary software. PMID:22233606

The use of open source electronic health records within the federal safety net

PubMed Central

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

2014-01-01

Objective To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). Methods and materials The study was conducted by the National Opinion Research Center (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 West Virginia, California and Arizona FQHC that were currently using an open source EHR. Results Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. Discussion Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. Conclusions An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness. PMID:23744787

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... Regulation Supplement; Open Source Software Public Meeting AGENCY: Defense Acquisition Regulations System... initiate a dialogue with industry regarding the use of open source software in DoD contracts. DATES: Public... be held in the General Services Administration (GSA), Central Office Auditorium, 1800 F Street NW...

[The use of open source software in graphic anatomic reconstructions and in biomechanic simulations].

PubMed

Ciobanu, O

2009-01-01

The objective of this study was to obtain three-dimensional (3D) images and to perform biomechanical simulations starting from DICOM images obtained by computed tomography (CT). Open source software were used to prepare digitized 2D images of tissue sections and to create 3D reconstruction from the segmented structures. Finally, 3D images were used in open source software in order to perform biomechanic simulations. This study demonstrates the applicability and feasibility of open source software developed in our days for the 3D reconstruction and biomechanic simulation. The use of open source software may improve the efficiency of investments in imaging technologies and in CAD/CAM technologies for implants and prosthesis fabrication which need expensive specialized software.

Open-Source Intelligence in the Czech Military: Knowledge System and Process Design

DTIC Science & Technology

2002-06-01

in Open-Source Intelligence OSINT, as one of the intelligence disciplines, bears some of the general problems of intelligence " business " OSINT...ADAPTING KNOWLEDGE MANAGEMENT THEORY TO THE CZECH MILITARY INTELLIGENCE Knowledge work is the core business of the military intelligence . As...NAVAL POSTGRADUATE SCHOOL Monterey, California THESIS Approved for public release; distribution is unlimited OPEN-SOURCE INTELLIGENCE IN THE

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

PubMed

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

2015-07-08

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

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

PubMed

Sanchez, Carlos L; Romero-Cuevas, Miguel; Lopez, Diego M; Lorca, Julio; Alcazar, Francisco J; Ruiz, Sergio; Mercado, Carmen; Garcia-Fortea, Pedro

2008-01-01

Information and Communication Technologies (ICTs) are revolutionizing how healthcare systems deliver top-quality care to citizens. In this way, Open Source Software (OSS) has demonstrated to be an important strategy to spread ICTs use. Several human and technological barriers in adopting OSS for healthcare have been identified. Human barriers include user acceptance, limited support, technical skillfulness, awareness, resistance to change, etc., while Technological barriers embrace need for open standards, heterogeneous OSS developed without normalization and metrics, lack of initiatives to evaluate existing health OSS and need for quality control and functional validation. The goals of PESCA project are to create a platform of interoperable modules to evaluate, classify and validate good practices in health OSS. Furthermore, a normalization platform will provide interoperable solutions in the fields of healthcare services, health surveillance, health literature, and health education, knowledge and research. Within the platform, the first goal to achieve is the setup of the collaborative work infrastructure. The platform is being organized as a Social Network which works to evaluate five scopes of every existing open source tools for eHealth: Open Source Software, Quality, Pedagogical, Security and privacy and Internationalization/I18N. In the meantime, the knowledge collected from the networking will configure a Good Practice Repository on eHealth promoting the effective use of ICT on behalf of the citizen's health.

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

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

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

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

PubMed

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

2011-09-01

It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery. Copyright © 2011 Elsevier Ltd. All rights reserved.

Muria Volcano, Island of Java, Indonesia

NASA Technical Reports Server (NTRS)

1991-01-01

This view of the north coast of central Java, Indonesia centers on the currently inactive Muria Volcano (6.5S, 111.0E). Muria is 5,330 ft. tall and lies just north of Java's main volcanic belt which runs east - west down the spine of the island attesting to the volcanic origin of the more than 1,500 Indonesian Islands.

The Visible Human Data Sets (VHD) and Insight Toolkit (ITk): Experiments in Open Source Software

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

From its inception in 1989, the Visible Human Project was designed as an experiment in open source software. In 1994 and 1995 the male and female Visible Human data sets were released by the National Library of Medicine (NLM) as open source data sets. In 2002 the NLM released the first version of the Insight Toolkit (ITk) as open source software. PMID:14728278

Development open source microcontroller based temperature data logger

NASA Astrophysics Data System (ADS)

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.

Clarity: An Open Source Manager for Laboratory Automation

PubMed Central

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

Petroleum system of Northwest Java basin based on gravity data analysis

NASA Astrophysics Data System (ADS)

Widianto, E.

2018-01-01

Energy management in the upstream oil and gas sector becomes very important for the country’s energy security. The renewal of energy resources and reserves becomes necessary and is a must. In the oil and gas industry, gravity data is usually used only for regional surveys, but with the development of instrumentation technology and gravity software development, this method can be used for assessing oil and gas survey stages from exploration to production. This study was conducted to evaluate aspects of petroleum system and exploration play concept in the part of Northwest Java Basin, covering source rock deposition regions (source kitchen area, migration direction), development of reservoirs, structural and stratigraphic trap, based on gravity data. This study uses data from Bouguer gravity anomaly map by filtering process to produce a residual map depicting sedimentation basin configuration. The mapping generated 20 sedimentary basins in Java Island with the total hydrocarbon resources of 113 BBOE (Billion Barrel of Oil Equivalent). The petroleum system analysis was conducted in the Northwest Basin section. The final map produced illustrates the condition of petroleum system and play concept that can be used as exploration direction, expectedly reducing the risk of drilling failure.

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

PubMed

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

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

Neogene subduction beneath Java, Indonesia: Slab tearing and changes in magmatism

NASA Astrophysics Data System (ADS)

Cottam, Michael; Hall, Robert; Cross, Lanu; Clements, Benjamin; Spakman, Wim

2010-05-01

Java is a Neogene calc-alkaline volcanic island arc formed by the northwards subduction of the Indo-Australian Plate beneath Sundaland, the continental core of SE Asia. The island has a complex history of volcanism and displays unusual subduction characteristics. These characteristics are consistent with the subduction of a hole in the down going slab that was formed by the arrival of a buoyant oceanic plateau at the trench. Subduction beneath Java began in the Eocene. However, the position and character of the calc-alkaline arc has changed over time. An older Paleogene arc ceased activity in the Early Miocene. Volcanic activity resumed in the Late Miocene producing a younger arc to the north of the older arc, and continues to the present day. An episode of Late Miocene thrusting at about 7 Ma is observed throughout Java and appears to be linked to northward movement of the arc. Arc rocks display typical calc-alkaline characteristics and reflect melting of the mantle wedge and subducted sediments associated with high fluid fluxes. Between West Java and Bali the present arc-trench gap is unusually wide at about 300 km. Seismicity identifies subducted Indian Ocean lithosphere that dips north at about 20° between the trench and the arc and then dips more steeply at about 60-70° from 100 to 600 km depth. In East Java there is gap in seismicity between about 250 and 500 km. Seismic tomography shows that this gap is not an aseismic section of the subduction zone but a hole in the slab. East Java is also unusual in the presence of K-rich volcanoes, now inactive, to the north of the calc-alkaline volcanoes of the active arc. In contrast to the calc-alkaline volcanism of the main arc, these K-rich melts imply lower fluid fluxes and a different mantle source. We suggest that all these observations can be explained by the tearing of the subducting slab when a buoyant oceanic plateau arrived at the trench south of East Java at about 8 Ma. With the slab unable to subduct

Innovative Ways of Visualising Meta Data in 4D Using Open Source Libaries

NASA Astrophysics Data System (ADS)

Balhar, Jakub; Valach, Pavel; Veselka, Jonas; Voumard, Yann

2016-08-01

There are more and more data being measured by different Earth Observation satellites around the world. Ever increasing amount of these data present new challenges and opportunities for their visualization.In this paper we propose how to visualize the amount, distribution and the structure of the data in a transparent way, which will take into account time-dimensions as well. Our approach allows us to get a global overview as well detailed regional information about distribution of the products from EO observation missions.We focus on introducing our mobile-friendly and easy- to-use web mapping application for 4D visualization of the data. Apart from that we also present the Java application which can read and process the data from various data sources.

Open Source Hardware for DIY Environmental Sensing

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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

ERIC Educational Resources Information Center

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

2016-01-01

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

Integrated Web-Based Immersive Exploration of the Coordinated Canyon Experiment Data using Open Source STOQS Software

NASA Astrophysics Data System (ADS)

McCann, M. P.; Gwiazda, R.; O'Reilly, T. C.; Maier, K. L.; Lundsten, E. M.; Parsons, D. R.; Paull, C. K.

2017-12-01

The Coordinated Canyon Experiment (CCE) in Monterey Submarine Canyon has produced a wealth of oceanographic measurements whose analysis will improve understanding of turbidity current processes. Exploration of this data set, consisting of over 60 parameters from 15 platforms, is facilitated by using the open source Spatial Temporal Oceanographic Query System (STOQS) software (https://github.com/stoqs/stoqs). The Monterey Bay Aquarium Research Institute (MBARI) originally developed STOQS to help manage and visualize upper water column oceanographic measurements, but the generality of its data model permits effective use for any kind of spatial/temporal measurement data. STOQS consists of a PostgreSQL database and server-side Python/Django software; the client-side is jQuery JavaScript supporting AJAX requests to update a single page web application. The User Interface (UI) is optimized to provide a quick overview of data in spatial and temporal dimensions, as well as in parameter, platform, and data value space. A user may zoom into any feature of interest and select it, initiating a filter operation that updates the UI with an overview of all the data in the new filtered selection. When details are desired, radio buttons and checkboxes are selected to generate a number of different types of visualizations. These include color-filled temporal section and line plots, parameter-parameter plots, 2D map plots, and interactive 3D spatial visualizations. The Extensible 3D (X3D) standard and X3DOM JavaScript library provide the technology for presenting animated 3D data directly within the web browser. Most of the oceanographic measurements from the CCE (e.g. mooring mounted ADCP and CTD data) are easily visualized using established methods. However, unified integration and multiparameter display of several concurrently deployed sensors across a network of platforms is a challenge we hope to solve. Moreover, STOQS also allows display of data from a new instrument - the

Open source GIS for HIV/AIDS management

PubMed Central

Vanmeulebrouk, Bas; Rivett, Ulrike; Ricketts, Adam; Loudon, Melissa

2008-01-01

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 suitability of the technology

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

PubMed

Oyri, Karl; Murray, Peter J

2005-12-01

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

Can open-source drug R&D repower pharmaceutical innovation?

PubMed

Munos, B

2010-05-01

Open-source R&D initiatives are multiplying across biomedical research. Some of them-such as public-private partnerships-have achieved notable success in bringing new drugs to market economically, whereas others reflect the pharmaceutical industry's efforts to retool its R&D model. Is open innovation the answer to the innovation crisis? This Commentary argues that although it may likely be part of the solution, significant cultural, scientific, and regulatory barriers can prevent it from delivering on its promise.

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

EPA Science Inventory

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

The open-source neutral-mass spectrometer on Atmosphere Explorer-C, -D, and -E.

NASA Technical Reports Server (NTRS)

Nier, A. O.; Potter, W. E.; Hickman, D. R.; Mauersberger, K.

1973-01-01

The open-source mass spectrometer will be used to obtain the number densities of the neutral atmospheric gases in the mass range 1 to 48 amu at the satellite location. The ion source has been designed to allow gas particles to enter the ionizing region with the minimum practicable number of prior collisions with surfaces. This design minimizes the loss of atomic oxygen and other reactive species due to reactions with the walls of the ion source. The principal features of the open-source spectrometer and the laboratory calibration system are discussed.

The competitiveness of medicinal plants in Central Java Indonesia

NASA Astrophysics Data System (ADS)

Riptanti, E. W.; Qonita, R. A.; Fajarningsih, R. U.

2018-03-01

Indonesia hold a potential opportunity to be a pharmaceutical production country. In the other side, Indonesia facing agriculture product and market competition internationally and domestically. Improving competitiveness of specific products are aimed to hit the export market and also to be able to compete with import products in domestic market. Considering Indonesian market opportunity, therefore we perform this study aiming to examine the competitiveness of medicinal plants in Central Java area. The basic method applied in this study was descriptive and data sources are primary and secondary data. Data were analyzed using Revealed Comparative Advantage (RCA) and Trade Specialization Index (TSI) approaches. According to the study, we reveal that medicinal plant commodities in Central Java province have average score 8.52, indicating a strong comparative advantage in global markets, while the commodities appear to have average score of 0.97 at 0 to 1 range, representing a strong competitiveness. Those results are attributed to natural and environmental condition, as well as high demand of global market. This competitiveness will encourage traditional/modern medicinal industries in global market.

Utilizing Free and Open Source Software to access, view and compare in situ observations, EO products and model output data

NASA Astrophysics Data System (ADS)

Vines, Aleksander; Hamre, Torill; Lygre, Kjetil

2014-05-01

The GreenSeas project (Development of global plankton data base and model system for eco-climate early warning) aims to advance the knowledge and predictive capacities of how marine ecosystems will respond to global change. A main task has been to set up a data delivery and monitoring core service following the open and free data access policy implemented in the Global Monitoring for the Environment and Security (GMES) programme. The aim is to ensure open and free access to historical plankton data, new data (EO products and in situ measurements), model data (including estimates of simulation error) and biological, environmental and climatic indicators to a range of stakeholders, such as scientists, policy makers and environmental managers. To this end, we have developed a geo-spatial database of both historical and new in situ physical, biological and chemical parameters for the Southern Ocean, Atlantic, Nordic Seas and the Arctic, and organized related satellite-derived quantities and model forecasts in a joint geo-spatial repository. For easy access to these data, we have implemented a web-based GIS (Geographical Information Systems) where observed, derived and forcasted parameters can be searched, displayed, compared and exported. Model forecasts can also be uploaded dynamically to the system, to allow modelers to quickly compare their results with available in situ and satellite observations. We have implemented the web-based GIS(Geographical Information Systems) system based on free and open source technologies: Thredds Data Server, ncWMS, GeoServer, OpenLayers, PostGIS, Liferay, Apache Tomcat, PRTree, NetCDF-Java, json-simple, Geotoolkit, Highcharts, GeoExt, MapFish, FileSaver, jQuery, jstree and qUnit. We also wanted to used open standards to communicate between the different services and we use WMS, WFS, netCDF, GML, OPeNDAP, JSON, and SLD. The main advantage we got from using FOSS was that we did not have to invent the wheel all over again, but could use

Java and its future in biomedical computing.

PubMed Central

Rodgers, R P

1996-01-01

Java, a new object-oriented computing language related to C++, is receiving considerable attention due to its use in creating network-sharable, platform-independent software modules (known as "applets") that can be used with the World Wide Web. The Web has rapidly become the most commonly used information-retrieval tool associated with the global computer network known as the Internet, and Java has the potential to further accelerate the Web's application to medical problems. Java's potentially wide acceptance due to its Web association and its own technical merits also suggests that it may become a popular language for non-Web-based, object-oriented computing. PMID:8880677

Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.

PubMed

Mamlin, Burke W; Biondich, Paul G; Wolfe, Ben A; Fraser, Hamish; Jazayeri, Darius; Allen, Christian; Miranda, Justin; Tierney, William M

2006-01-01

Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (>95%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions.

Using Java for distributed computing in the Gaia satellite data processing

NASA Astrophysics Data System (ADS)

O'Mullane, William; Luri, Xavier; Parsons, Paul; Lammers, Uwe; Hoar, John; Hernandez, Jose

2011-10-01

In recent years Java has matured to a stable easy-to-use language with the flexibility of an interpreter (for reflection etc.) but the performance and type checking of a compiled language. When we started using Java for astronomical applications around 1999 they were the first of their kind in astronomy. Now a great deal of astronomy software is written in Java as are many business applications. We discuss the current environment and trends concerning the language and present an actual example of scientific use of Java for high-performance distributed computing: ESA's mission Gaia. The Gaia scanning satellite will perform a galactic census of about 1,000 million objects in our galaxy. The Gaia community has chosen to write its processing software in Java. We explore the manifold reasons for choosing Java for this large science collaboration. Gaia processing is numerically complex but highly distributable, some parts being embarrassingly parallel. We describe the Gaia processing architecture and its realisation in Java. We delve into the astrometric solution which is the most advanced and most complex part of the processing. The Gaia simulator is also written in Java and is the most mature code in the system. This has been successfully running since about 2005 on the supercomputer "Marenostrum" in Barcelona. We relate experiences of using Java on a large shared machine. Finally we discuss Java, including some of its problems, for scientific computing.

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

PubMed

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.