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.

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

PubMed

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

2011-03-08

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

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.

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

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PubMed Central

Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M.; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R.

2015-01-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/. PMID:26037908

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

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.

Understanding and Capturing People’s Mobile App Privacy Preferences

DTIC Science & Technology

2013-10-28

The entire apps’ metadata takes up about 500MB of storage space when stored in a MySQL database and all the binary files take approximately 300GB of...functionality that can de- compile Dalvik bytecodes to Java source code faster than other de-compilers. Given the scale of the app analysis we planned on... java libraries, such as parser, sql connectors, etc Targeted Ads 137 admob, adwhirl, greystripe… Provided by mobile behavioral ads company to

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 .

JDiffraction: A GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields

NASA Astrophysics Data System (ADS)

Piedrahita-Quintero, Pablo; Trujillo, Carlos; Garcia-Sucerquia, Jorge

2017-05-01

JDiffraction, a GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields, is presented. Angular spectrum, Fresnel transform, and Fresnel-Bluestein transform are the numerical algorithms implemented in the methods and functions of the library to compute the scalar propagation of the complex wavefield. The functionality of the library is tested with the modeling of easy to forecast numerical experiments and also with the numerical reconstruction of a digitally recorded hologram. The performance of JDiffraction is contrasted with a library written for C++, showing great competitiveness in the apparently less complex environment of JAVA language. JDiffraction also includes JAVA easy-to-use methods and functions that take advantage of the computation power of the graphic processing units to accelerate the processing times of 2048×2048 pixel images up to 74 frames per second.

Software reuse example and challenges at NSIDC

NASA Astrophysics Data System (ADS)

Billingsley, B. W.; Brodzik, M.; Collins, J. A.

2009-12-01

NSIDC has created a new data discovery and access system, Searchlight, to provide users with the data they want in the format they want. NSIDC Searchlight supports discovery and access to disparate data types with on-the-fly reprojection, regridding and reformatting. Architected to both reuse open source systems and be reused itself, Searchlight reuses GDAL and Proj4 for manipulating data and format conversions, the netCDF Java library for creating netCDF output, MapServer and OpenLayers for defining spatial criteria and the JTS Topology Suite (JTS) in conjunction with Hibernate Spatial for database interaction and rich OGC-compliant spatial objects. The application reuses popular Java and Java Script libraries including Struts 2, Spring, JPA (Hibernate), Sitemesh, JFreeChart, JQuery, DOJO and a PostGIS PostgreSQL database. Future reuse of Searchlight components is supported at varying architecture levels, ranging from the database and model components to web services. We present the tools, libraries and programs that Searchlight has reused. We describe the architecture of Searchlight and explain the strategies deployed for reusing existing software and how Searchlight is built for reuse. We will discuss NSIDC reuse of the Searchlight components to support rapid development of new data delivery systems.

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.

Windows Memory Forensic Data Visualization

DTIC Science & Technology

2014-06-12

clustering characteristics (Bastian, et al, 2009). The software is written in Java and utilizes the OpenGL library for rendering graphical content...Toolkit 2 nd ed. Burlington MA: Syngress. D3noob. (2013, February 8). Using a MYSQL database as a source of data. Message posted to http

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.

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

JavaScript: Data Visualizations

EPA Pesticide Factsheets

D3 is a JavaScript library that, in a manner similar to jQuery library, allows direct inspection and manipulation of the Document Object Model, but is intended for the primary purpose of data visualization.

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

Open Source Tools for Seismicity Analysis

NASA Astrophysics Data System (ADS)

Powers, P.

2010-12-01

The spatio-temporal analysis of seismicity plays an important role in earthquake forecasting and is integral to research on earthquake interactions and triggering. For instance, the third version of the Uniform California Earthquake Rupture Forecast (UCERF), currently under development, will use Epidemic Type Aftershock Sequences (ETAS) as a model for earthquake triggering. UCERF will be a "living" model and therefore requires robust, tested, and well-documented ETAS algorithms to ensure transparency and reproducibility. Likewise, as earthquake aftershock sequences unfold, real-time access to high quality hypocenter data makes it possible to monitor the temporal variability of statistical properties such as the parameters of the Omori Law and the Gutenberg Richter b-value. Such statistical properties are valuable as they provide a measure of how much a particular sequence deviates from expected behavior and can be used when assigning probabilities of aftershock occurrence. To address these demands and provide public access to standard methods employed in statistical seismology, we present well-documented, open-source JavaScript and Java software libraries for the on- and off-line analysis of seismicity. The Javascript classes facilitate web-based asynchronous access to earthquake catalog data and provide a framework for in-browser display, analysis, and manipulation of catalog statistics; implementations of this framework will be made available on the USGS Earthquake Hazards website. The Java classes, in addition to providing tools for seismicity analysis, provide tools for modeling seismicity and generating synthetic catalogs. These tools are extensible and will be released as part of the open-source OpenSHA Commons library.

Visualization of protein sequence features using JavaScript and SVG with pViz.js.

PubMed

Mukhyala, Kiran; Masselot, Alexandre

2014-12-01

pViz.js is a visualization library for displaying protein sequence features in a Web browser. By simply providing a sequence and the locations of its features, this lightweight, yet versatile, JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the Web is a common need in Bioinformatics. Although many Web sites have developed viewers to display these features, their implementations are usually focused on data from a specific source or use case. Some of these viewers can be adapted to fit other use cases but are not designed to be reusable. pViz makes it easy to display features as boxes aligned to a protein sequence with zooming functionality but also includes predefined renderings for secondary structure and post-translational modifications. The library is designed to further customize this view. We demonstrate such applications of pViz using two examples: a proteomic data visualization tool with an embedded viewer for displaying features on protein structure, and a tool to visualize the results of the variant_effect_predictor tool from Ensembl. pViz.js is a JavaScript library, available on github at https://github.com/Genentech/pviz. This site includes examples and functional applications, installation instructions and usage documentation. A Readme file, which explains how to use pViz with examples, is available as Supplementary Material A. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

von Laszewski, G.; Foster, I.; Gawor, J.

In this paper we report on the features of the Java Commodity Grid Kit. The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus protocols, allowing the Java CoG Kit to communicate also with the C Globus reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well as numerous additional libraries and frameworks developed by the Java community tomore » enable network, Internet, enterprise, and peer-to peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus software. In this paper we also report on the efforts to develop server side Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Globus jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

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

von Laszewski, G.; Gawor, J.; Lane, P.

In this paper we report on the features of the Java Commodity Grid Kit (Java CoG Kit). The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus Toolkit protocols, allowing the Java CoG Kit to also communicate with the services distributed as part of the C Globus Toolkit reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well asmore » numerous additional libraries and frameworks developed by the Java community to enable network, Internet, enterprise and peer-to-peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus Toolkit software. In this paper we also report on the efforts to develop serverside Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Grid jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

PubMed

Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

2012-03-01

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reuse of the Cloud Analytics and Collaboration Environment within Tactical Applications (TacApps): A Feasibility Analysis

DTIC Science & Technology

2016-03-01

Representational state transfer  Java messaging service  Java application programming interface (API)  Internet relay chat (IRC)/extensible messaging and...JBoss application server or an Apache Tomcat servlet container instance. The relational database management system can be either PostgreSQL or MySQL ... Java library called direct web remoting. This library has been part of the core CACE architecture for quite some time; however, there have not been

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.

A high-level 3D visualization API for Java and ImageJ.

PubMed

Schmid, Benjamin; Schindelin, Johannes; Cardona, Albert; Longair, Mark; Heisenberg, Martin

2010-05-21

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

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.

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing.

PubMed

Almeida, Diogo; Skov, Ida; Lund, Jesper; Mohammadnejad, Afsaneh; Silva, Artur; Vandin, Fabio; Tan, Qihua; Baumbach, Jan; Röttger, Richard

2016-10-01

Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html.

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing.

PubMed

Almeida, Diogo; Skov, Ida; Lund, Jesper; Mohammadnejad, Afsaneh; Silva, Artur; Vandin, Fabio; Tan, Qihua; Baumbach, Jan; Röttger, Richard

2016-12-18

Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html.

Update on PISCES

NASA Technical Reports Server (NTRS)

Pearson, Don; Hamm, Dustin; Kubena, Brian; Weaver, Jonathan K.

2010-01-01

An updated version of the Platform Independent Software Components for the Exploration of Space (PISCES) software library is available. A previous version was reported in Library for Developing Spacecraft-Mission-Planning Software (MSC-22983), NASA Tech Briefs, Vol. 25, No. 7 (July 2001), page 52. To recapitulate: This software provides for Web-based, collaborative development of computer programs for planning trajectories and trajectory- related aspects of spacecraft-mission design. The library was built using state-of-the-art object-oriented concepts and software-development methodologies. The components of PISCES include Java-language application programs arranged in a hierarchy of classes that facilitates the reuse of the components. As its full name suggests, the PISCES library affords platform-independence: The Java language makes it possible to use the classes and application programs with a Java virtual machine, which is available in most Web-browser programs. Another advantage is expandability: Object orientation facilitates expansion of the library through creation of a new class. Improvements in the library since the previous version include development of orbital-maneuver- planning and rendezvous-launch-window application programs, enhancement of capabilities for propagation of orbits, and development of a desktop user interface.

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.

Leveraging annotation-based modeling with Jump.

PubMed

Bergmayr, Alexander; Grossniklaus, Michael; Wimmer, Manuel; Kappel, Gerti

2018-01-01

The capability of UML profiles to serve as annotation mechanism has been recognized in both research and industry. Today's modeling tools offer profiles specific to platforms, such as Java, as they facilitate model-based engineering approaches. However, considering the large number of possible annotations in Java, manually developing the corresponding profiles would only be achievable by huge development and maintenance efforts. Thus, leveraging annotation-based modeling requires an automated approach capable of generating platform-specific profiles from Java libraries. To address this challenge, we present the fully automated transformation chain realized by Jump, thereby continuing existing mapping efforts between Java and UML by emphasizing on annotations and profiles. The evaluation of Jump shows that it scales for large Java libraries and generates profiles of equal or even improved quality compared to profiles currently used in practice. Furthermore, we demonstrate the practical value of Jump by contributing profiles that facilitate reverse engineering and forward engineering processes for the Java platform by applying it to a modernization scenario.

Software support for SBGN maps: SBGN-ML and LibSBGN.

PubMed

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

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.

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 semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies.

PubMed

Harispe, Sébastien; Ranwez, Sylvie; Janaqi, Stefan; Montmain, Jacky

2014-03-01

The semantic measures library and toolkit are robust open-source and easy to use software solutions dedicated to semantic measures. They can be used for large-scale computations and analyses of semantic similarities between terms/concepts defined in terminologies and ontologies. The comparison of entities (e.g. genes) annotated by concepts is also supported. A large collection of measures is available. Not limited to a specific application context, the library and the toolkit can be used with various controlled vocabularies and ontology specifications (e.g. Open Biomedical Ontology, Resource Description Framework). The project targets both designers and practitioners of semantic measures providing a JAVA library, as well as a command-line tool that can be used on personal computers or computer clusters. Downloads, documentation, tutorials, evaluation and support are available at http://www.semantic-measures-library.org.

Java Library for Input and Output of Image Data and Metadata

NASA Technical Reports Server (NTRS)

Deen, Robert; Levoe, Steven

2003-01-01

A Java-language library supports input and output (I/O) of image data and metadata (label data) in the format of the Video Image Communication and Retrieval (VICAR) image-processing software and in several similar formats, including a subset of the Planetary Data System (PDS) image file format. The library does the following: It provides low-level, direct access layer, enabling an application subprogram to read and write specific image files, lines, or pixels, and manipulate metadata directly. Two coding/decoding subprograms ("codecs" for short) based on the Java Advanced Imaging (JAI) software provide access to VICAR and PDS images in a file-format-independent manner. The VICAR and PDS codecs enable any program that conforms to the specification of the JAI codec to use VICAR or PDS images automatically, without specific knowledge of the VICAR or PDS format. The library also includes Image I/O plugin subprograms for VICAR and PDS formats. Application programs that conform to the Image I/O specification of Java version 1.4 can utilize any image format for which such a plug-in subprogram exists, without specific knowledge of the format itself. Like the aforementioned codecs, the VICAR and PDS Image I/O plug-in subprograms support reading and writing of metadata.

Sawja: Static Analysis Workshop for Java

NASA Astrophysics Data System (ADS)

Hubert, Laurent; Barré, Nicolas; Besson, Frédéric; Demange, Delphine; Jensen, Thomas; Monfort, Vincent; Pichardie, David; Turpin, Tiphaine

Static analysis is a powerful technique for automatic verification of programs but raises major engineering challenges when developing a full-fledged analyzer for a realistic language such as Java. Efficiency and precision of such a tool rely partly on low level components which only depend on the syntactic structure of the language and therefore should not be redesigned for each implementation of a new static analysis. This paper describes the Sawja library: a static analysis workshop fully compliant with Java 6 which provides OCaml modules for efficiently manipulating Java bytecode programs. We present the main features of the library, including i) efficient functional data-structures for representing a program with implicit sharing and lazy parsing, ii) an intermediate stack-less representation, and iii) fast computation and manipulation of complete programs. We provide experimental evaluations of the different features with respect to time, memory and precision.

A Geostationary Earth Orbit Satellite Model Using Easy Java Simulation

ERIC Educational Resources Information Center

Wee, Loo Kang; Goh, Giam Hwee

2013-01-01

We develop an Easy Java Simulation (EJS) model for students to visualize geostationary orbits near Earth, modelled using a Java 3D implementation of the EJS 3D library. The simplified physics model is described and simulated using a simple constant angular velocity equation. We discuss four computer model design ideas: (1) a simple and realistic…

CH5M3D: an HTML5 program for creating 3D molecular structures.

PubMed

Earley, Clarke W

2013-11-18

While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.

PubMed

Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

2005-03-09

Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.

HEP data analysis using jHepWork and Java.

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

Chekanov, S.; High Energy Physics

2009-03-23

A role of Java in high-energy physics (HEP) and recent progress in development of a platform-independent data-analysis framework, jHepWork, is discussed. The framework produces professional graphics and has many libraries for data manipulation.

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.

Tools for Integrating Data Access from the IRIS DMC into Research Workflows

NASA Astrophysics Data System (ADS)

Reyes, C. G.; Suleiman, Y. Y.; Trabant, C.; Karstens, R.; Weertman, B. R.

2012-12-01

Web service interfaces at the IRIS Data Management Center (DMC) provide access to a vast archive of seismological and related geophysical data. These interfaces are designed to easily incorporate data access into data processing workflows. Examples of data that may be accessed include: time series data, related metadata, and earthquake information. The DMC has developed command line scripts, MATLAB® interfaces and a Java library to support a wide variety of data access needs. Users of these interfaces do not need to concern themselves with web service details, networking, or even (in most cases) data conversion. Fetch scripts allow access to the DMC archive and are a comfortable fit for command line users. These scripts are written in Perl and are well suited for automation and integration into existing workflows on most operating systems. For metdata and event information, the Fetch scripts even parse the returned data into simple text summaries. The IRIS Java Web Services Library (IRIS-WS Library) allows Java developers the ability to create programs that access the DMC archives seamlessly. By returning the data and information as native Java objects the Library insulates the developer from data formats, network programming and web service details. The MATLAB interfaces leverage this library to allow users access to the DMC archive directly from within MATLAB (r2009b or newer), returning data into variables for immediate use. Data users and research groups are developing other toolkits that use the DMC's web services. Notably, the ObsPy framework developed at LMU Munich is a Python Toolbox that allows seamless access to data and information via the DMC services. Another example is the MATLAB-based GISMO and Waveform Suite developments that can now access data via web services. In summary, there now exist a host of ways that researchers can bring IRIS DMC data directly into their workflows. MATLAB users can use irisFetch.m, command line users can use the various Fetch scripts, Java users can use the IRIS-WS library, and Python users may request data through ObsPy. To learn more about any of these clients see http://www.iris.edu/ws/wsclients/.

Military Interoperable Digital Hospital Testbed (MIDHT)

DTIC Science & Technology

2013-10-01

activities are selected highlights completed by Northrop Grumman during the year. Cycle 4 development: - Increased the max_allowed_packet size in MySQL ...deployment with the Java install that is required by CONNECT v3.3.1.3. - Updated the MIDHT code base to work with the CONNECT v.3.3.1.3 Core Libraries...Provided TATRC the CONNECTUniversalClientGUI binaries for use with CONNECT v3.3.1.3 − Created and deployed a common Java library for the CONNECT

A knowledge discovery object model API for Java

PubMed Central

Zuyderduyn, Scott D; Jones, Steven JM

2003-01-01

Background Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized. Results This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually. Conclusions The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at . PMID:14583100

Friends of the National Library of Medicine 2015 Awards Gala Event | NIH MedlinePlus the Magazine

MedlinePlus

... please turn JavaScript on. Friends of the National Library of Medicine 2015 Awards Gala Event Past Issues / ... September 16, 2015, the Friends of the National Library of Medicine held its annual Awards Gala in ...

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

Scarberry, Randy

This is for a Java World article that was already published on Nov 21, 2006. When I originally submitted the draft, Java World wasn't in the available lists of publications. Now that it is, Hanford Library staff recommended that I resubmit so it would be counted. Original submission ID: PNNL-SA-52490

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

PubMed

Vanderkam, Dan; Aksoy, B Arman; Hodes, Isaac; Perrone, Jaclyn; Hammerbacher, Jeff

2016-08-01

P: ileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library. The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license. correspondence@hammerlab.org. © The Author 2016. Published by Oxford University Press.

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

Candey, Robert M.; Harris, Bernard T.; Chimiak, Reine A.

2005-01-01

The Space Physics Data Facility (SPDF) Web services provides a distributed programming interface to a portion of the SPDF software. (A general description of Web services is available at http://www.w3.org/ and in many current software-engineering texts and articles focused on distributed programming.) The SPDF Web services distributed programming interface enables additional collaboration and integration of the SPDF software system with other software systems, in furtherance of the SPDF mission to lead collaborative efforts in the collection and utilization of space physics data and mathematical models. This programming interface conforms to all applicable Web services specifications of the World Wide Web Consortium. The interface is specified by a Web Services Description Language (WSDL) file. The SPDF Web services software consists of the following components: 1) A server program for implementation of the Web services; and 2) A software developer s kit that consists of a WSDL file, a less formal description of the interface, a Java class library (which further eases development of Java-based client software), and Java source code for an example client program that illustrates the use of the interface.

Friends of the National Library of Medicine, Welcome to NIH MedlinePlus, the magazine | NIH MedlinePlus the Magazine

MedlinePlus

... please turn JavaScript on. Friends of the National Library of Medicine Past Issues / Winter 2017 Table of ... their health challenges. The Friends of the National Library of Medicine (FNLM) is the support group for ...

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

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.

Carbon Nanotube Growth Rate Regression using Support Vector Machines and Artificial Neural Networks

DTIC Science & Technology

2014-03-27

intensity D peak. Reprinted with permission from [38]. The SVM classifier is trained using custom written Java code leveraging the Sequential Minimal...Society Encog is a machine learning framework for Java , C++ and .Net applications that supports Bayesian Networks, Hidden Markov Models, SVMs and ANNs [13...SVM classifiers are trained using Weka libraries and leveraging custom written Java code. The data set is created as an Attribute Relationship File

Faust: Flexible Acquistion and Understanding System for Text

DTIC Science & Technology

2013-07-01

second version is still underway and it will continue in development as part of the DARPA DEFT program; it is written in Java and Clojure with MySQL and...SUTime, a Java library that recognizes and normalizes temporal expressions using deterministic patterns [101]. UIUC made another such framework... Java -based, large-scale inference engine called Tuffy. It leverages the full power of a relational optimizer in an RDBMS to perform the grounding of MLN

JMS Proxy and C/C++ Client SDK

NASA Technical Reports Server (NTRS)

Wolgast, Paul; Pechkam, Paul

2007-01-01

JMS Proxy and C/C++ Client SDK (JMS signifies "Java messaging service" and "SDK" signifies "software development kit") is a software package for developing interfaces that enable legacy programs (here denoted "clients") written in the C and C++ languages to communicate with each other via a JMS broker. This package consists of two main components: the JMS proxy server component and the client C library SDK component. The JMS proxy server component implements a native Java process that receives and responds to requests from clients. This component can run on any computer that supports Java and a JMS client. The client C library SDK component is used to develop a JMS client program running in each affected C or C++ environment, without need for running a Java virtual machine in the affected computer. A C client program developed by use of this SDK has most of the quality-of-service characteristics of standard Java-based client programs, including the following: Durable subscriptions; Asynchronous message receipt; Such standard JMS message qualities as "TimeToLive," "Message Properties," and "DeliveryMode" (as the quoted terms are defined in previously published JMS documentation); and Automatic reconnection of a JMS proxy to a restarted JMS broker.

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

High performance geospatial and climate data visualization using GeoJS

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Beezley, J. D.

2015-12-01

GeoJS (https://github.com/OpenGeoscience/geojs) is an open-source library developed to support interactive scientific and geospatial visualization of climate and earth science datasets in a web environment. GeoJS has a convenient application programming interface (API) that enables users to harness the fast performance of WebGL and Canvas 2D APIs with sophisticated Scalable Vector Graphics (SVG) features in a consistent and convenient manner. We started the project in response to the need for an open-source JavaScript library that can combine traditional geographic information systems (GIS) and scientific visualization on the web. Many libraries, some of which are open source, support mapping or other GIS capabilities, but lack the features required to visualize scientific and other geospatial datasets. For instance, such libraries are not be capable of rendering climate plots from NetCDF files, and some libraries are limited in regards to geoinformatics (infovis in a geospatial environment). While libraries such as d3.js are extremely powerful for these kinds of plots, in order to integrate them into other GIS libraries, the construction of geoinformatics visualizations must be completed manually and separately, or the code must somehow be mixed in an unintuitive way.We developed GeoJS with the following motivations:• To create an open-source geovisualization and GIS library that combines scientific visualization with GIS and informatics• To develop an extensible library that can combine data from multiple sources and render them using multiple backends• To build a library that works well with existing scientific visualizations tools such as VTKWe have successfully deployed GeoJS-based applications for multiple domains across various projects. The ClimatePipes project funded by the Department of Energy, for example, used GeoJS to visualize NetCDF datasets from climate data archives. Other projects built visualizations using GeoJS for interactively exploring data and analysis regarding 1) the human trafficking domain, 2) New York City taxi drop-offs and pick-ups, and 3) the Ebola outbreak. GeoJS supports advanced visualization features such as picking and selecting, as well as clustering. It also supports 2D contour plots, vector plots, heat maps, and geospatial graphs.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

Pure JavaScript Storyline Layout Algorithm

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

This is a JavaScript library for a storyline layout algorithm. Storylines are adept at communicating complex change by encoding time on the x-axis and using the proximity of lines in the y direction to represent interaction between entities. The library in this disclosure takes as input a list of objects containing an id, time, and state. The output is a data structure that can be used to conveniently render a storyline visualization. Most importantly, the library computes the y-coordinate of the entities over time that decreases layout artifacts including crossings, wiggles, and whitespace. This is accomplished through multi-objective, multi-stage optimizationmore » problem, where the output of one stage produces input and constraints for the next stage.« less

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.

WaveJava: Wavelet-based network computing

NASA Astrophysics Data System (ADS)

Ma, Kun; Jiao, Licheng; Shi, Zhuoer

1997-04-01

Wavelet is a powerful theory, but its successful application still needs suitable programming tools. Java is a simple, object-oriented, distributed, interpreted, robust, secure, architecture-neutral, portable, high-performance, multi- threaded, dynamic language. This paper addresses the design and development of a cross-platform software environment for experimenting and applying wavelet theory. WaveJava, a wavelet class library designed by the object-orient programming, is developed to take advantage of the wavelets features, such as multi-resolution analysis and parallel processing in the networking computing. A new application architecture is designed for the net-wide distributed client-server environment. The data are transmitted with multi-resolution packets. At the distributed sites around the net, these data packets are done the matching or recognition processing in parallel. The results are fed back to determine the next operation. So, the more robust results can be arrived quickly. The WaveJava is easy to use and expand for special application. This paper gives a solution for the distributed fingerprint information processing system. It also fits for some other net-base multimedia information processing, such as network library, remote teaching and filmless picture archiving and communications.

HYDRA Hyperspectral Data Research Application Tom Rink and Tom Whittaker

NASA Astrophysics Data System (ADS)

Rink, T.; Whittaker, T.

2005-12-01

HYDRA is a freely available, easy to install tool for visualization and analysis of large local or remote hyper/multi-spectral datasets. HYDRA is implemented on top of the open source VisAD Java library via Jython - the Java implementation of the user friendly Python programming language. VisAD provides data integration, through its generalized data model, user-display interaction and display rendering. Jython has an easy to read, concise, scripting-like, syntax which eases software development. HYDRA allows data sharing of large datasets through its support of the OpenDAP and OpenADDE server-client protocols. The users can explore and interrogate data, and subset in physical and/or spectral space to isolate key areas of interest for further analysis without having to download an entire dataset. It also has an extensible data input architecture to recognize new instruments and understand different local file formats, currently NetCDF and HDF4 are supported.

Thoth: Software for data visualization & statistics

NASA Astrophysics Data System (ADS)

Laher, R. R.

2016-10-01

Thoth is a standalone software application with a graphical user interface for making it easy to query, display, visualize, and analyze tabular data stored in relational databases and data files. From imported data tables, it can create pie charts, bar charts, scatter plots, and many other kinds of data graphs with simple menus and mouse clicks (no programming required), by leveraging the open-source JFreeChart library. It also computes useful table-column data statistics. A mature tool, having underwent development and testing over several years, it is written in the Java computer language, and hence can be run on any computing platform that has a Java Virtual Machine and graphical-display capability. It can be downloaded and used by anyone free of charge, and has general applicability in science, engineering, medical, business, and other fields. Special tools and features for common tasks in astronomy and astrophysical research are included in the software.

Auxiliary Library Explorer (ALEX) Development

DTIC Science & Technology

2016-02-01

non-empty cells. This is a laborious manual task and could probably have been avoided by using Java code to read the data directly from Excel. In fact...it might be even easier to leave the data as a comma separated variables (CSV) file and read the data in with Java , although this could create other...This is first implemented using the MakeFullDatabaseapp Java project, which performs an SQL query on the DSpace data to return a list of items for which

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

Ballard, Sanford; Hipp, James; Kraus, Brian

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

Using OPeNDAP's Data-Services Framework to Lift Mash-Ups above Blind Dates

NASA Astrophysics Data System (ADS)

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

2015-12-01

OPeNDAP's data-as-service framework (Hyrax) matches diverse sources with many end-user tools and contexts. Keys to its flexibility include: A data model embracing tabular data alongside n-dim arrays and other structures useful in geoinformatics. A REST-like protocol that supports—via suffix notation—a growing set of output forms (netCDF, XML, etc.) plus a query syntax for subsetting. Subsetting applies (via constraints on column values) to tabular data or (via constraints on indices or coordinates) to array-style data . A handler-style architecture that admits a growing set of input types. Community members may contribute handlers, making Hyrax effective as middleware, where N sources are mapped to M outputs with order N+M effort (not NxM). Hyrax offers virtual aggregations of source data, enabling granularity aimed at users, not data-collectors. OPeNDAP-access libraries exist in multiple languages, including Python, Java, and C++. Recent enhancements are increasing this framework's interoperability (i.e., its mash-up) potential. Extensions implemented as servlets—running adjacent to Hyrax—are enriching the forms of aggregation and enabling new protocols: User-specified aggregations, namely, applying a query to (huge) lists of source granules, and receiving one (large) table or zipped netCDF file. OGC (Open Geospatial Consortium) protocols, WMS and WCS. A Webification (W10n) protocol that returns JavaScript Object Notation (JSON). Extensions to OPeNDAP's query language are reducing transfer volumes and enabling new forms of inspection. Advances underway include: Functions that, for triangular-mesh sources, return sub-meshes spec'd via geospatial bounding boxes. Functions that, for data from multiple, satellite-borne sensors (with differing orbits), select observations based on coincidence. Calculations of means, histograms, etc. that greatly reduce output volumes.. Paths for communities to contribute new server functions (in Python, e.g.) that data providers may incorporate into Hyrax via installation parameters. One could say Hyrax itself is a mash-up, but we suggest it as an instrument for a mash-up artist's toolbox. This instrument can support mash-ups built on netCDF files, OGC protocols, JavaScript Web pages, and/or programs written in Python, Java, C or C++.

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

PubMed Central

Martin, Andrew C. R.

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

PubMed

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

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

Bonachea, D.; Dickens, P.; Thakur, R.

There is a growing interest in using Java as the language for developing high-performance computing applications. To be successful in the high-performance computing domain, however, Java must not only be able to provide high computational performance, but also high-performance I/O. In this paper, we first examine several approaches that attempt to provide high-performance I/O in Java - many of which are not obvious at first glance - and evaluate their performance on two parallel machines, the IBM SP and the SGI Origin2000. We then propose extensions to the Java I/O library that address the deficiencies in the Java I/O APImore » and improve performance dramatically. The extensions add bulk (array) I/O operations to Java, thereby removing much of the overhead currently associated with array I/O in Java. We have implemented the extensions in two ways: in a standard JVM using the Java Native Interface (JNI) and in a high-performance parallel dialect of Java called Titanium. We describe the two implementations and present performance results that demonstrate the benefits of the proposed extensions.« less

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

PubMed Central

2014-01-01

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow. PMID:25565494

Planetary Image Geometry Library

NASA Technical Reports Server (NTRS)

Deen, Robert C.; Pariser, Oleg

2010-01-01

The Planetary Image Geometry (PIG) library is a multi-mission library used for projecting images (EDRs, or Experiment Data Records) and managing their geometry for in-situ missions. A collection of models describes cameras and their articulation, allowing application programs such as mosaickers, terrain generators, and pointing correction tools to be written in a multi-mission manner, without any knowledge of parameters specific to the supported missions. Camera model objects allow transformation of image coordinates to and from view vectors in XYZ space. Pointing models, specific to each mission, describe how to orient the camera models based on telemetry or other information. Surface models describe the surface in general terms. Coordinate system objects manage the various coordinate systems involved in most missions. File objects manage access to metadata (labels, including telemetry information) in the input EDRs and RDRs (Reduced Data Records). Label models manage metadata information in output files. Site objects keep track of different locations where the spacecraft might be at a given time. Radiometry models allow correction of radiometry for an image. Mission objects contain basic mission parameters. Pointing adjustment ("nav") files allow pointing to be corrected. The object-oriented structure (C++) makes it easy to subclass just the pieces of the library that are truly mission-specific. Typically, this involves just the pointing model and coordinate systems, and parts of the file model. Once the library was developed (initially for Mars Polar Lander, MPL), adding new missions ranged from two days to a few months, resulting in significant cost savings as compared to rewriting all the application programs for each mission. Currently supported missions include Mars Pathfinder (MPF), MPL, Mars Exploration Rover (MER), Phoenix, and Mars Science Lab (MSL). Applications based on this library create the majority of operational image RDRs for those missions. A Java wrapper around the library allows parts of it to be used from Java code (via a native JNI interface). Future conversions of all or part of the library to Java are contemplated.

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

PubMed

Cui, Ya; Chen, Xiaowei; Luo, Huaxia; Fan, Zhen; Luo, Jianjun; He, Shunmin; Yue, Haiyan; Zhang, Peng; Chen, Runsheng

2016-06-01

We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions. BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/ rschen@ibp.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Java Image I/O for VICAR, PDS, and ISIS

NASA Technical Reports Server (NTRS)

Deen, Robert G.; Levoe, Steven R.

2011-01-01

This library, written in Java, supports input and output of images and metadata (labels) in the VICAR, PDS image, and ISIS-2 and ISIS-3 file formats. Three levels of access exist. The first level comprises the low-level, direct access to the file. This allows an application to read and write specific image tiles, lines, or pixels and to manipulate the label data directly. This layer is analogous to the C-language "VICAR Run-Time Library" (RTL), which is the image I/O library for the (C/C++/Fortran) VICAR image processing system from JPL MIPL (Multimission Image Processing Lab). This low-level library can also be used to read and write labeled, uncompressed images stored in formats similar to VICAR, such as ISIS-2 and -3, and a subset of PDS (image format). The second level of access involves two codecs based on Java Advanced Imaging (JAI) to provide access to VICAR and PDS images in a file-format-independent manner. JAI is supplied by Sun Microsystems as an extension to desktop Java, and has a number of codecs for formats such as GIF, TIFF, JPEG, etc. Although Sun has deprecated the codec mechanism (replaced by IIO), it is still used in many places. The VICAR and PDS codecs allow any program written using the JAI codec spec to use VICAR or PDS images automatically, with no specific knowledge of the VICAR or PDS formats. Support for metadata (labels) is included, but is format-dependent. The PDS codec, when processing PDS images with an embedded VIAR label ("dual-labeled images," such as used for MER), presents the VICAR label in a new way that is compatible with the VICAR codec. The third level of access involves VICAR, PDS, and ISIS Image I/O plugins. The Java core includes an "Image I/O" (IIO) package that is similar in concept to the JAI codec, but is newer and more capable. Applications written to the IIO specification can use any image format for which a plug-in exists, with no specific knowledge of the format itself.

SimPackJ/S: a web-oriented toolkit for discrete event simulation

NASA Astrophysics Data System (ADS)

Park, Minho; Fishwick, Paul A.

2002-07-01

SimPackJ/S is the JavaScript and Java version of SimPack, which means SimPackJ/S is a collection of JavaScript and Java libraries and executable programs for computer simulations. The main purpose of creating SimPackJ/S is that we allow existing SimPack users to expand simulation areas and provide future users with a freeware simulation toolkit to simulate and model a system in web environments. One of the goals for this paper is to introduce SimPackJ/S. The other goal is to propose translation rules for converting C to JavaScript and Java. Most parts demonstrate the translation rules with examples. In addition, we discuss a 3D dynamic system model and overview an approach to 3D dynamic systems using SimPackJ/S. We explain an interface between SimPackJ/S and the 3D language--Virtual Reality Modeling Language (VRML). This paper documents how to translate C to JavaScript and Java and how to utilize SimPackJ/S within a 3D web environment.

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

GeoTess: A generalized Earth model software utility

DOE PAGES

Ballard, Sanford; Hipp, James; Kraus, Brian; ...

2016-03-23

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust . The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

The Competitive Edge: Expanded Access Drives Vendors.

ERIC Educational Resources Information Center

Pepin, Theresa; And Others

1997-01-01

This report analyzes data gathered from 29 automated library system vendors who responded to a 1996 survey. The survey also requested their perceptions of Java (an object-oriented programming language) and network computers, and issues and trends to be considered by library administrators. Contact information about the vendors is provided. (Four…

lawn: An R client for the Turf JavaScript Library for Geospatial Analysis

EPA Science Inventory

lawn is an R package to provide access to the geospatial analysis capabilities in the Turf javascript library. Turf expects data in GeoJSON format. Given that many datasets are now available natively in GeoJSON providing an easier method for conducting geospatial analyses on thes...

ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models.

PubMed

Marvel, Skylar W; To, Kimberly; Grimm, Fabian A; Wright, Fred A; Rusyn, Ivan; Reif, David M

2018-03-05

Drawing integrated conclusions from diverse source data requires synthesis across multiple types of information. The ToxPi (Toxicological Prioritization Index) is an analytical framework that was developed to enable integration of multiple sources of evidence by transforming data into integrated, visual profiles. Methodological improvements have advanced ToxPi and expanded its applicability, necessitating a new, consolidated software platform to provide functionality, while preserving flexibility for future updates. We detail the implementation of a new graphical user interface for ToxPi (Toxicological Prioritization Index) that provides interactive visualization, analysis, reporting, and portability. The interface is deployed as a stand-alone, platform-independent Java application, with a modular design to accommodate inclusion of future analytics. The new ToxPi interface introduces several features, from flexible data import formats (including legacy formats that permit backward compatibility) to similarity-based clustering to options for high-resolution graphical output. We present the new ToxPi interface for dynamic exploration, visualization, and sharing of integrated data models. The ToxPi interface is freely-available as a single compressed download that includes the main Java executable, all libraries, example data files, and a complete user manual from http://toxpi.org .

bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.

PubMed

Lindenbaum, Pierre; Redon, Richard

2018-04-01

Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk). https://github.com/lindenb/jvarkit. pierre.lindenbaum@univ-nantes.fr.

Using Cesium for 3D Thematic Visualisations on the Web

NASA Astrophysics Data System (ADS)

Gede, Mátyás

2018-05-01

Cesium (http://cesiumjs.org) is an open source, WebGL-based JavaScript library for virtual globes and 3D maps. It is an excellent tool for 3D thematic visualisations, but to use its full functionality it has to be feed with its own file format, CZML. Unfortunately, this format is not yet supported by any major GIS software. This paper intro- duces a plugin for QGIS, developed by the author, which facilitates the creation of CZML file for various types of visualisations. The usability of Cesium is also examined in various hardware/software environments.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

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.

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.

An efficient framework for Java data processing systems in HPC environments

NASA Astrophysics Data System (ADS)

Fries, Aidan; Castañeda, Javier; Isasi, Yago; Taboada, Guillermo L.; Portell de Mora, Jordi; Sirvent, Raül

2011-11-01

Java is a commonly used programming language, although its use in High Performance Computing (HPC) remains relatively low. One of the reasons is a lack of libraries offering specific HPC functions to Java applications. In this paper we present a Java-based framework, called DpcbTools, designed to provide a set of functions that fill this gap. It includes a set of efficient data communication functions based on message-passing, thus providing, when a low latency network such as Myrinet is available, higher throughputs and lower latencies than standard solutions used by Java. DpcbTools also includes routines for the launching, monitoring and management of Java applications on several computing nodes by making use of JMX to communicate with remote Java VMs. The Gaia Data Processing and Analysis Consortium (DPAC) is a real case where scientific data from the ESA Gaia astrometric satellite will be entirely processed using Java. In this paper we describe the main elements of DPAC and its usage of the DpcbTools framework. We also assess the usefulness and performance of DpcbTools through its performance evaluation and the analysis of its impact on some DPAC systems deployed in the MareNostrum supercomputer (Barcelona Supercomputing Center).

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

Filtering the Net in Libraries: The Case (Mostly) in Favor.

ERIC Educational Resources Information Center

Banks, Michael A.

1998-01-01

Examines issues and decision-making involved in restricting Internet access in libraries, for the most part favoring filtering devices. Questions to consider when selecting a filtering program are provided. Some of the better filtering programs are described, and Web addresses are included for each. Security risks associated with Java and…

Uniform Data Access Using GXD

NASA Technical Reports Server (NTRS)

Vanderbilt, Peter

1999-01-01

This paper gives an overview of GXD, a framework facilitating publication and use of data from diverse data sources. GXD defines an object-oriented data model designed to represent a wide range of things including data, its metadata, resources and query results. GXD also defines a data transport language. a dialect of XML, for representing instances of the data model. This language allows for a wide range of data source implementations by supporting both the direct incorporation of data and the specification of data by various rules. The GXD software library, proto-typed in Java, includes client and server runtimes. The server runtime facilitates the generation of entities containing data encoded in the GXD transport language. The GXD client runtime interprets these entities (potentially from many data sources) to create an illusion of a globally interconnected data space, one that is independent of data source location and implementation.

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.

blastjs: a BLAST+ wrapper for Node.js.

PubMed

Page, Martin; MacLean, Dan; Schudoma, Christian

2016-02-27

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possible and therefore requires only a minimal amount of code in the client application. The library is freely available under the MIT license at https://github.com/teammaclean/blastjs.

Sirepo for Synchrotron Radiation Workshop

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

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

PubMed

Drummond, A; Strimmer, K

2001-07-01

Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.

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.

jvenn: an interactive Venn diagram viewer.

PubMed

Bardou, Philippe; Mariette, Jérôme; Escudié, Frédéric; Djemiel, Christophe; Klopp, Christophe

2014-08-29

Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.

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 the extended connectivity fingerprint. This result is comparable to the performance achieved by a non-linear support vector machine using state-of-the-art descriptors. On the Sutherland QSAR data set, the best fingerprint encodings showed a comparable or better performance on 5 of the 8 benchmarks when compared against the results of the best descriptors published in the paper of Sutherland et al. Conclusions jCompoundMapper is a library for chemical graph fingerprints with several tweaking possibilities and exporting options for open source data mining toolkits. The quality of the data mining results, the conversion speed, the LPGL software license, the command-line interface, and the exporters should be useful for many applications in cheminformatics like benchmarks against literature methods, comparison of data mining algorithms, similarity searching, and similarity-based data mining. PMID:21219648

Use of the NetBeans Platform for NASA Robotic Conjunction Assessment Risk Analysis

NASA Technical Reports Server (NTRS)

Sabey, Nickolas J.

2014-01-01

The latest Java and JavaFX technologies are very attractive software platforms for customers involved in space mission operations such as those of NASA and the US Air Force. For NASA Robotic Conjunction Assessment Risk Analysis (CARA), the NetBeans platform provided an environment in which scalable software solutions could be developed quickly and efficiently. Both Java 8 and the NetBeans platform are in the process of simplifying CARA development in secure environments by providing a significant amount of capability in a single accredited package, where accreditation alone can account for 6-8 months for each library or software application. Capabilities either in use or being investigated by CARA include: 2D and 3D displays with JavaFX, parallelization with the new Streams API, and scalability through the NetBeans plugin architecture.

Efficient methods and readily customizable libraries for managing complexity of large networks.

PubMed

Dogrusoz, Ugur; Karacelik, Alper; Safarli, Ilkin; Balci, Hasan; Dervishi, Leonard; Siper, Metin Can

2018-01-01

One common problem in visualizing real-life networks, including biological pathways, is the large size of these networks. Often times, users find themselves facing slow, non-scaling operations due to network size, if not a "hairball" network, hindering effective analysis. One extremely useful method for reducing complexity of large networks is the use of hierarchical clustering and nesting, and applying expand-collapse operations on demand during analysis. Another such method is hiding currently unnecessary details, to later gradually reveal on demand. Major challenges when applying complexity reduction operations on large networks include efficiency and maintaining the user's mental map of the drawing. We developed specialized incremental layout methods for preserving a user's mental map while managing complexity of large networks through expand-collapse and hide-show operations. We also developed open-source JavaScript libraries as plug-ins to the web based graph visualization library named Cytsocape.js to implement these methods as complexity management operations. Through efficient specialized algorithms provided by these extensions, one can collapse or hide desired parts of a network, yielding potentially much smaller networks, making them more suitable for interactive visual analysis. This work fills an important gap by making efficient implementations of some already known complexity management techniques freely available to tool developers through a couple of open source, customizable software libraries, and by introducing some heuristics which can be applied upon such complexity management techniques to ensure preserving mental map of users.

MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

PubMed

Yang, Chunguang G; Granite, Stephen J; Van Eyk, Jennifer E; Winslow, Raimond L

2006-11-01

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

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

Essiari, Abdelilah; Mudumbai, Srilehka; Thompson, Mary

Akenti is an authorization service for distributed resources. The authorization policy is kept in distributed certificates signed by one or more stakeholders for the resources. The package consists of the following components: Java GUI tools to create and sign the policy certificates C++ libraries to do make acess decisions based on the policy certificates A standalone authorization server that make access decisions C interfaces to the libraries and server

IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java

PubMed Central

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

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM’s image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis. PMID:25612319

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

PubMed

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

2015-01-01

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

Conditions Database for the Belle II Experiment

NASA Astrophysics Data System (ADS)

Wood, L.; Elsethagen, T.; Schram, M.; Stephan, E.

2017-10-01

The Belle II experiment at KEK is preparing for first collisions in 2017. Processing the large amounts of data that will be produced will require conditions data to be readily available to systems worldwide in a fast and efficient manner that is straightforward for both the user and maintainer. The Belle II conditions database was designed with a straightforward goal: make it as easily maintainable as possible. To this end, HEP-specific software tools were avoided as much as possible and industry standard tools used instead. HTTP REST services were selected as the application interface, which provide a high-level interface to users through the use of standard libraries such as curl. The application interface itself is written in Java and runs in an embedded Payara-Micro Java EE application server. Scalability at the application interface is provided by use of Hazelcast, an open source In-Memory Data Grid (IMDG) providing distributed in-memory computing and supporting the creation and clustering of new application interface instances as demand increases. The IMDG provides fast and efficient access to conditions data via in-memory caching.

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

Real-time Java simulations of multiple interference dielectric filters

NASA Astrophysics Data System (ADS)

Kireev, Alexandre N.; Martin, Olivier J. F.

2008-12-01

An interactive Java applet for real-time simulation and visualization of the transmittance properties of multiple interference dielectric filters is presented. The most commonly used interference filters as well as the state-of-the-art ones are embedded in this platform-independent applet which can serve research and education purposes. The Transmittance applet can be freely downloaded from the site http://cpc.cs.qub.ac.uk. Program summaryProgram title: Transmittance Catalogue identifier: AEBQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5778 No. of bytes in distributed program, including test data, etc.: 90 474 Distribution format: tar.gz Programming language: Java Computer: Developed on PC-Pentium platform Operating system: Any Java-enabled OS. Applet was tested on Windows ME, XP, Sun Solaris, Mac OS RAM: Variable Classification: 18 Nature of problem: Sophisticated wavelength selective multiple interference filters can include some tens or even hundreds of dielectric layers. The spectral response of such a stack is not obvious. On the other hand, there is a strong demand from application designers and students to get a quick insight into the properties of a given filter. Solution method: A Java applet was developed for the computation and the visualization of the transmittance of multilayer interference filters. It is simple to use and the embedded filter library can serve educational purposes. Also, its ability to handle complex structures will be appreciated as a useful research and development tool. Running time: Real-time simulations

Sirepo - Warp

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

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

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.

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.

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

Distributed Planning in a Mixed-Initiative Environment

DTIC Science & Technology

2008-06-01

Knowledge Sources Control Remote Blackboard Remote Knowledge Sources Remot e Data Remot e Data Java Distributed Blackboard Figure 3 - Distributed...an interface agent or planning agent and the second type is a critic agent. Agents in the DEEP architecture extend and use the Java Agent...chosen because it is fully implemented in Java , and supports these requirements. 2.3.3 Interface Agents Interface agents are the interfaces through

A geostationary Earth orbit satellite model using Easy Java Simulation

NASA Astrophysics Data System (ADS)

Wee, Loo Kang; Hwee Goh, Giam

2013-01-01

We develop an Easy Java Simulation (EJS) model for students to visualize geostationary orbits near Earth, modelled using a Java 3D implementation of the EJS 3D library. The simplified physics model is described and simulated using a simple constant angular velocity equation. We discuss four computer model design ideas: (1) a simple and realistic 3D view and associated learning in the real world; (2) comparative visualization of permanent geostationary satellites; (3) examples of non-geostationary orbits of different rotation senses, periods and planes; and (4) an incorrect physics model for conceptual discourse. General feedback from the students has been relatively positive, and we hope teachers will find the computer model useful in their own classes.

A High-Availability, Distributed Hardware Control System Using Java

NASA Technical Reports Server (NTRS)

Niessner, Albert F.

2011-01-01

Two independent coronagraph experiments that require 24/7 availability with different optical layouts and different motion control requirements are commanded and controlled with the same Java software system executing on many geographically scattered computer systems interconnected via TCP/IP. High availability of a distributed system requires that the computers have a robust communication messaging system making the mix of TCP/IP (a robust transport), and XML (a robust message) a natural choice. XML also adds the configuration flexibility. Java then adds object-oriented paradigms, exception handling, heavily tested libraries, and many third party tools for implementation robustness. The result is a software system that provides users 24/7 access to two diverse experiments with XML files defining the differences

StrBioLib: a Java library for development of custom computationalstructural biology applications

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

Chandonia, John-Marc

2007-05-14

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure predictionmore » program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov« less

StrBioLib: a Java library for development of custom computational structural biology applications.

PubMed

Chandonia, John-Marc

2007-08-01

StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/

Having Java in the Library Doesn't Necessarily Require a Coffee Cart: Using an Object-Oriented Programming Language to Streamline Circulation Services for a Distance Education University

ERIC Educational Resources Information Center

Godbee, Sara; de Jong, Mark

2007-01-01

The University of Maryland University College (UMUC) serves a dispersed patron base, and its library has developed, over time, a circulation system for distributing physical research materials to its patrons throughout the United States. This article discusses the development of this system and its associated interface/database management system…

STILTS -- Starlink Tables Infrastructure Library Tool Set

NASA Astrophysics Data System (ADS)

Taylor, Mark

STILTS is a set of command-line tools for processing tabular data. It has been designed for, but is not restricted to, use on astronomical data such as source catalogues. It contains both generic (format-independent) table processing tools and tools for processing VOTable documents. Facilities offered include crossmatching, format conversion, format validation, column calculation and rearrangement, row selection, sorting, plotting, statistical calculations and metadata display. Calculations on cell data can be performed using a powerful and extensible expression language. The package is written in pure Java and based on STIL, the Starlink Tables Infrastructure Library. This gives it high portability, support for many data formats (including FITS, VOTable, text-based formats and SQL databases), extensibility and scalability. Where possible the tools are written to accept streamed data so the size of tables which can be processed is not limited by available memory. As well as the tutorial and reference information in this document, detailed on-line help is available from the tools themselves. STILTS is available under the GNU General Public Licence.

Awards and Recognition

MedlinePlus

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phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

Math Description Engine Software Development Kit

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Smith, Stephanie L.; Dexter, Dan E.; Hodgson, Terry R.

2010-01-01

The Math Description Engine Software Development Kit (MDE SDK) can be used by software developers to make computer-rendered graphs more accessible to blind and visually-impaired users. The MDE SDK generates alternative graph descriptions in two forms: textual descriptions and non-verbal sound renderings, or sonification. It also enables display of an animated trace of a graph sonification on a visual graph component, with color and line-thickness options for users having low vision or color-related impairments. A set of accessible graphical user interface widgets is provided for operation by end users and for control of accessible graph displays. Version 1.0 of the MDE SDK generates text descriptions for 2D graphs commonly seen in math and science curriculum (and practice). The mathematically rich text descriptions can also serve as a virtual math and science assistant for blind and sighted users, making graphs more accessible for everyone. The MDE SDK has a simple application programming interface (API) that makes it easy for programmers and Web-site developers to make graphs accessible with just a few lines of code. The source code is written in Java for cross-platform compatibility and to take advantage of Java s built-in support for building accessible software application interfaces. Compiled-library and NASA Open Source versions are available with API documentation and Programmer s Guide at http:/ / prim e.jsc.n asa. gov.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, N.; Bossant, M.; Dupont, E.

2014-06-01

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

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

Soppera, N., E-mail: nicolas.soppera@oecd.org; Bossant, M.; Dupont, E.

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

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).

Identification of rice supply chain risk to DKI Jakarta through Cipinang primary rice market

NASA Astrophysics Data System (ADS)

Sugiarto, D.; Ariwibowo, A.; Mardianto, I.; Surjasa, D.

2018-01-01

This paper identifies several sources of risks in DKI Jakarta rice supply chain that through Cipinang Primary Rice Market (CPRM). Secondary data from several sources were collected and analysed using pareto chart and time series analysis. Based on the pareto analysis, it was known that there was a change in the order of suppliers whereas in 2011, 80% of the supply came only from Cirebon, Karawang and Bandung (West Java Province). While in 2015 the main source of supply changed to Cirebon, Central Java and Karawang. Linear trend equation using decomposition model for Cirebon and Karawang showed trend of decreasing monthly supply while Central Java had a positive trend. Harvest area of wetland paddy in Cirebon and Karawang showed a negative trend in the last 6 years. The data also showed that West Java Province was the province with the largest rice crop area affected by plant organism attack and drought disaster in 2015. DKI Jakarta had several potential supply chain risks from rice supply, drought risk and pests risk where the province of West Java, which previously could become a major supplier began to require supply assistance from other provinces, especially Central Java.

An Interface Transformation Strategy for AF-IPPS

DTIC Science & Technology

2012-12-01

Representational State Transfer (REST) and Java Enterprise Edition ( Java EE) to implement a reusable “translation service.” For SOAP and REST protocols, XML and...of best-of-breed open source software. The product baseline is summarized in the following table: Product Function Description Java Language...Compiler & Runtime JBoss Application Server Applications, Messaging, Translation Java EE Application Server Ruby on Rails Applications Ruby Web

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.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

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.

Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.

PubMed

Dahruddin, Hadi; Hutama, Aditya; Busson, Frédéric; Sauri, Sopian; Hanner, Robert; Keith, Philippe; Hadiaty, Renny; Hubert, Nicolas

2017-03-01

Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. © 2016 John Wiley & Sons Ltd.

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.

A comparison of common programming languages used in bioinformatics.

PubMed

Fourment, Mathieu; Gillings, Michael R

2008-02-05

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

A comparison of common programming languages used in bioinformatics

PubMed Central

Fourment, Mathieu; Gillings, Michael R

2008-01-01

Background The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Results Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from Conclusion This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language. PMID:18251993

JEnsembl: a version-aware Java API to Ensembl data systems.

PubMed

Paterson, Trevor; Law, Andy

2012-11-01

The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

AST: World Coordinate Systems in Astronomy

NASA Astrophysics Data System (ADS)

Berry, David S.; Warren-Smith, Rodney F.

2014-04-01

The AST library provides a comprehensive range of facilities for attaching world coordinate systems to astronomical data, for retrieving and interpreting that information in a variety of formats, including FITS-WCS, and for generating graphical output based on it. Core projection algorithms are provided by WCSLIB (ascl:1108.003) and astrometry is provided by the PAL (ascl:1606.002) and SOFA (ascl:1403.026) libraries. AST bindings are available in Python (pyast), Java (JNIAST) and Perl (Starlink::AST). AST is used as the plotting and astrometry library in DS9 and GAIA, and is distributed separately and as part of the Starlink software collection.

GPC: General Polygon Clipper library

NASA Astrophysics Data System (ADS)

Murta, Alan

2015-12-01

The University of Manchester GPC library is a flexible and highly robust polygon set operations library for use with C, C#, Delphi, Java, Perl, Python, Haskell, Lua, VB.Net and other applications. It supports difference, intersection, exclusive-or and union clip operations, and polygons may be comprised of multiple disjoint contours. Contour vertices may be given in any order - clockwise or anticlockwise, and contours may be convex, concave or self-intersecting, and may be nested (i.e. polygons may have holes). Output may take the form of either polygon contours or tristrips, and hole and external contours are differentiated in the result.

The openEHR Java reference implementation project.

PubMed

Chen, Rong; Klein, Gunnar

2007-01-01

The openEHR foundation has developed an innovative design for interoperable and future-proof Electronic Health Record (EHR) systems based on a dual model approach with a stable reference information model complemented by archetypes for specific clinical purposes.A team from Sweden has implemented all the stable specifications in the Java programming language and donated the source code to the openEHR foundation. It was adopted as the openEHR Java Reference Implementation in March 2005 and released under open source licenses. This encourages early EHR implementation projects around the world and a number of groups have already started to use this code. The early Java implementation experience has also led to the publication of the openEHR Java Implementation Technology Specification. A number of design changes to the specifications and important minor corrections have been directly initiated by the implementation project over the last two years. The Java Implementation has been important for the validation and improvement of the openEHR design specifications and provides building blocks for future EHR systems.

Touch Interaction with 3D Geographical Visualization on Web: Selected Technological and User Issues

NASA Astrophysics Data System (ADS)

Herman, L.; Stachoň, Z.; Stuchlík, R.; Hladík, J.; Kubíček, P.

2016-10-01

The use of both 3D visualization and devices with touch displays is increasing. In this paper, we focused on the Web technologies for 3D visualization of spatial data and its interaction via touch screen gestures. At the first stage, we compared the support of touch interaction in selected JavaScript libraries on different hardware (desktop PCs with touch screens, tablets, and smartphones) and software platforms. Afterward, we realized simple empiric test (within-subject design, 6 participants, 2 simple tasks, LCD touch monitor Acer and digital terrain models as stimuli) focusing on the ability of users to solve simple spatial tasks via touch screens. An in-house testing web tool was developed and used based on JavaScript, PHP, and X3DOM languages and Hammer.js libraries. The correctness of answers, speed of users' performances, used gestures, and a simple gesture metric was recorded and analysed. Preliminary results revealed that the pan gesture is most frequently used by test participants and it is also supported by the majority of 3D libraries. Possible gesture metrics and future developments including the interpersonal differences are discussed in the conclusion.

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

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

PubMed

McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

2016-08-19

VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.

PubMed

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

2014-01-01

Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig's scalability over many computing nodes and illustrate its use with example scripts. Available under the open source MIT license at http://sourceforge.net/projects/seqpig/

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

NASA Astrophysics Data System (ADS)

Halder, P.; Chakraborty, A.; Deb Roy, P.; Das, H. S.

2014-09-01

In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Catalogue identifier: AETB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571570 No. of bytes in distributed program, including test data, etc.: 120226886 Distribution format: tar.gz Programming language: Java, Fortran95. Computer: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler; Developed on 2.40 GHz Intel Core i3. Operating system: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler. RAM: Ranging from a few Mbytes to several Gbytes, depending on the input parameters. Classification: 1.3. External routines: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] (3D visualization). Nature of problem: Optical properties of cosmic dust aggregates. Solution method: Java application based on Mackowski and Mischenko's Superposition T-Matrix code. Restrictions: The program is designed for single processor systems. Additional comments: The distribution file for this program is over 120 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Ranging from few minutes to several hours, depending on the input parameters. References: [1] http://www.jfree.org/index.html [2] https://java3d.java.net/

Java Performance for Scientific Applications on LLNL Computer Systems

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

Kapfer, C; Wissink, A

2002-05-10

Languages in use for high performance computing at the laboratory--Fortran (f77 and f90), C, and C++--have many years of development behind them and are generally considered the fastest available. However, Fortran and C do not readily extend to object-oriented programming models, limiting their capability for very complex simulation software. C++ facilitates object-oriented programming but is a very complex and error-prone language. Java offers a number of capabilities that these other languages do not. For instance it implements cleaner (i.e., easier to use and less prone to errors) object-oriented models than C++. It also offers networking and security as part ofmore » the language standard, and cross-platform executables that make it architecture neutral, to name a few. These features have made Java very popular for industrial computing applications. The aim of this paper is to explain the trade-offs in using Java for large-scale scientific applications at LLNL. Despite its advantages, the computational science community has been reluctant to write large-scale computationally intensive applications in Java due to concerns over its poor performance. However, considerable progress has been made over the last several years. The Java Grande Forum [1] has been promoting the use of Java for large-scale computing. Members have introduced efficient array libraries, developed fast just-in-time (JIT) compilers, and built links to existing packages used in high performance parallel computing.« less

JNDMS Task Authorization 2 Report

DTIC Science & Technology

2013-10-01

uses Barnyard to store alarms from all DREnet Snort sensors in a MySQL database. Barnyard is an open source tool designed to work with Snort to take...Technology ITI Information Technology Infrastructure J2EE Java 2 Enterprise Edition JAR Java Archive. This is an archive file format defined by Java ...standards. JDBC Java Database Connectivity JDW JNDMS Data Warehouse JNDMS Joint Network and Defence Management System JNDMS Joint Network Defence and

Streamlining the Process of Acquiring Secure Open Architecture Software Systems

DTIC Science & Technology

2013-10-08

Microsoft.NET, Enterprise Java Beans, GNU Lesser General Public License (LGPL) libraries, and data communication protocols like the Hypertext Transfer...NetBeans development environments),  customer relationship management (SugarCRM),  database management systems (PostgreSQL, MySQL ),  operating

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.

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…

Online spectral fit tool (OSFT) for analyzing reflectance spectra

NASA Astrophysics Data System (ADS)

Penttilä, A.; Kohout, T.; Muinonen, K.

2015-10-01

We present an algorithm and its implementation for fitting continuum and absorption bands to UV/VIS/NIR reflectance spectra. The implementation is done completely in JavaScript and HTML, and will run in any modern web browser without requiring external libraries to be installed.

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.

GC-MS analysis of clove (Syzygium aromaticum) bud essential oil from Java and Manado

NASA Astrophysics Data System (ADS)

Amelia, B.; Saepudin, E.; Cahyana, A. H.; Rahayu, D. U.; Sulistyoningrum, A. S.; Haib, J.

2017-07-01

The largest clove production contributors in Indonesia are mostly coming from Java and Manado. Different flavor among clove origins is caused by chemical constituents in clove oil. Unfortunately, scientific research and publications about flavor in clove from Indonesia's origin are still limited. The objective of this research is to determine significant differences of constituents in terms of flavor in clove oil originated from Java and Manado. The essential oils were isolated from cut clove bud samples by steam distillation method. The chemical constituents of clove bud oil were analyzed by using gas chromatography-mass spectrometry (GC-MS). Constituents were then identified by comparing the results of the chromatogram and reference retention time using Wiley mass spectra library (Wiley W9N11). Thirty-six and thirty-four chemical constituents were identified based on GC-MS from clove oil collected from Java and Manado, respectively. Major classes of compounds are sesquiterpenes, phenyl propanoid, oxygenated sesquiterpenes, and esters. Different compositions in major constituents were found between both origins. Clove Java contained eugenol (55.60 %), eugenyl acetate (20.54 %), caryophyllene (14.84 %), and α-humulene (2.75 %). While, in clove Manado, the composition were eugenol (74.64 %), caryophyllene (12.79 %), eugenyl acetate (8.70 %), and α-humulene (1.53 %). Moreover, minor constituents β-elemene (0.04 %), α-cadinene (0.05 %) and ledol (0.06 %) were existed only in clove Java, while clove Manado had some unique minor constituents which were not found in clove Java, i.e. β-gurjunene (0.04 %), γ-cadinene %), and humulene oxide (0.05 %). In conclusion, both clove oils from Java and Manado contained same major chemical constituents but different in their composition. In addition, some minor constituents existed only in specific origin.

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

PubMed

Beisken, Stephan; Earll, Mark; Portwood, David; Seymour, Mark; Steinbeck, Christoph

2014-04-01

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

Common Patterns with End-to-end Interoperability for Data Access

NASA Astrophysics Data System (ADS)

Gallagher, J.; Potter, N.; Jones, M. B.

2010-12-01

At first glance, using common storage formats and open standards should be enough to ensure interoperability between data servers and client applications, but that is often not the case. In the REAP (Realtime Environment for Analytical Processing; NSF #0619060) project we integrated access to data from OPeNDAP servers into the Kepler workflow system and found that, as in previous cases, we spent the bulk of our effort addressing the twin issues of data model compatibility and integration strategies. Implementing seamless data access between a remote data source and a client application (data sink) can be broken down into two kinds of issues. First, the solution must address any differences in the data models used by the data source (OPeNDAP) and the data sink (the Kepler workflow system). If these models match completely, there is little work to be done. However, that is rarely the case. To map OPeNDAP's data model to Kepler's, we used two techniques (ignoring trivial conversions): On-the-fly type mapping and out-of-band communication. Type conversion takes place both for data and metadata because Kepler requires a priori knowledge of some aspects (e.g., syntactic metadata) of the data to build a workflow. In addition, OPeNDAP's constraint expression syntax was used to send out-of-band information to restrict the data requested from the server, facilitating changes in the returned data's type. This technique provides a way for users to exert fine-grained control over the data request, a potentially useful technique, at the cost of requiring that users understand a little about the data source's processing capabilities. The second set of issues for end-to-end data access are integration strategies. OPeNDAP provides several different tools for bringing data into an application: C++, C and Java libraries that provide functions for newly written software; The netCDF library which enables existing applications to read from servers using an older interface; and simple file transfers. These options affect seamlessness in that they represent tradeoffs in new development (required for the first option) with cumbersome extra user actions (required by the last option). While the middle option, adding new functionality to an existing library (netCDF), is very appealing because practice has shown that it can be very effective over a wide range of clients, it's very hard to build these libraries because correctly writing a new implementation of an existing API that preserves the original's exact semantics can be a daunting task. In the example discussed here, we developed a new module for Kepler using OPeNDAP's Java API. This provided a way to leverage internal optimizations for data organization in Kepler and we felt that outweighed the additional cost of new development and the need for users to learn how to use a new Kepler module. While common storage formats and open standards play an important role in data access, our work with the Kepler workflow system reinforces the experience that matching the data models of the data server (source) and user client (sink) and choosing the most appropriate integration strategy are critical to achieving interoperability.

Usage of the Jess Engine, Rules and Ontology to Query a Relational Database

NASA Astrophysics Data System (ADS)

Bak, Jaroslaw; Jedrzejek, Czeslaw; Falkowski, Maciej

We present a prototypical implementation of a library tool, the Semantic Data Library (SDL), which integrates the Jess (Java Expert System Shell) engine, rules and ontology to query a relational database. The tool extends functionalities of previous OWL2Jess with SWRL implementations and takes full advantage of the Jess engine, by separating forward and backward reasoning. The optimization of integration of all these technologies is an advancement over previous tools. We discuss the complexity of the query algorithm. As a demonstration of capability of the SDL library, we execute queries using crime ontology which is being developed in the Polish PPBW project.

A Security-façade Library for Virtual-observatory Software

NASA Astrophysics Data System (ADS)

Rixon, G.

2009-09-01

The security-façade library implements, for Java, IVOA's security standards. It supports the authentication mechanisms for SOAP and REST web-services, the sign-on mechanisms (with MyProxy, AstroGrid Accounts protocol or local credential-caches), the delegation protocol, and RFC3820-enabled HTTPS for Apache Tomcat. Using the façade, a developer who is not a security specialist can easily add access control to a virtual-observatory service and call secured services from an application. The library has been an internal part of AstroGrid software for some time and it is now offered for use by other developers.

Parallel evolutionary computation in bioinformatics applications.

PubMed

Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

2013-05-01

A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

JavaScript Access to DICOM Network and Objects in Web Browser.

PubMed

Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

2017-10-01

Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

Modular VO oriented Java EE service deployer

NASA Astrophysics Data System (ADS)

Molinaro, Marco; Cepparo, Francesco; De Marco, Marco; Knapic, Cristina; Apollo, Pietro; Smareglia, Riccardo

2014-07-01

The International Virtual Observatory Alliance (IVOA) has produced many standards and recommendations whose aim is to generate an architecture that starts from astrophysical resources, in a general sense, and ends up in deployed consumable services (that are themselves astrophysical resources). Focusing on the Data Access Layer (DAL) system architecture, that these standards define, in the last years a web based application has been developed and maintained at INAF-OATs IA2 (Italian National institute for Astrophysics - Astronomical Observatory of Trieste, Italian center of Astronomical Archives) to try to deploy and manage multiple VO (Virtual Observatory) services in a uniform way: VO-Dance. However a set of criticalities have arisen since when the VO-Dance idea has been produced, plus some major changes underwent and are undergoing at the IVOA DAL layer (and related standards): this urged IA2 to identify a new solution for its own service layer. Keeping on the basic ideas from VO-Dance (simple service configuration, service instantiation at call time and modularity) while switching to different software technologies (e.g. dismissing Java Reflection in favour of Enterprise Java Bean, EJB, based solution), the new solution has been sketched out and tested for feasibility. Here we present the results originating from this test study. The main constraints for this new project come from various fields. A better homogenized solution rising from IVOA DAL standards: for example the new DALI (Data Access Layer Interface) specification that acts as a common interface system for previous and oncoming access protocols. The need for a modular system where each component is based upon a single VO specification allowing services to rely on common capabilities instead of homogenizing them inside service components directly. The search for a scalable system that takes advantage from distributed systems. The constraints find answer in the adopted solutions hereafter sketched. The development of the new system using Java Enterprise technologies can better benefit from existing libraries to build up the single tokens implementing the IVOA standards. Each component can be built from single standards and each deployed service (i.e. service components instantiations) can consume the other components' exposed methods and services without the need of homogenizing them in dedicated libraries. Scalability can be achieved in an easier way by deploying components or sets of services on a distributed environment and using JNDI (Java Naming and Directory Interface) and RMI (Remote Method Invocation) technologies. Single service configuration will not be significantly different from the VO-Dance solution given that Java class instantiation that benefited from Java Reflection will only be moved to Java EJB pooling (and not, e.g. embedded in bundles for subsequent deployment).

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.

DbMap: improving database interoperability issues in medical software using a simple, Java-Xml based solution.

PubMed Central

Karadimas, H.; Hemery, F.; Roland, P.; Lepage, E.

2000-01-01

In medical software development, the use of databases plays a central role. However, most of the databases have heterogeneous encoding and data models. To deal with these variations in the application code directly is error-prone and reduces the potential reuse of the produced software. Several approaches to overcome these limitations have been proposed in the medical database literature, which will be presented. We present a simple solution, based on a Java library, and a central Metadata description file in XML. This development approach presents several benefits in software design and development cycles, the main one being the simplicity in maintenance. PMID:11079915

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

LISA: a java API for performing simulations of trajectories for all types of balloons

NASA Astrophysics Data System (ADS)

Conessa, Huguette

2016-07-01

LISA (LIbrarie de Simulation pour les Aerostats) is a java API for performing simulations of trajectories for all types of balloons (Zero Pressure Balloons, Pressurized Balloons, Infrared Montgolfier), and for all phases of flight (ascent, ceiling, descent). This library has for goals to establish a reliable repository of Balloons flight physics models, to capitalize developments and control models used in different tools. It is already used for flight physics study software in CNES, to understand and reproduce the behavior of balloons, observed during real flights. It will be used operationally for the ground segment of the STRATEOLE2 mission. It was developed with quality rules of "critical software." It is based on fundamental generic concepts, linking the simulation state variables to interchangeable calculation models. Each LISA model defines how to calculate a consistent set of state variables combining validity checks. To perform a simulation for a type of balloon and a phase of flight, it is necessary to select or create a macro-model that is to say, a consistent set of models to choose from among those offered by LISA, defining the behavior of the environment and the balloon. The purpose of this presentation is to introduce the main concepts of LISA, and the new perspectives offered by this library.

Building Geospatial Web Services for Ecological Monitoring and Forecasting

NASA Astrophysics Data System (ADS)

Hiatt, S. H.; Hashimoto, H.; Melton, F. S.; Michaelis, A. R.; Milesi, C.; Nemani, R. R.; Wang, W.

2008-12-01

The Terrestrial Observation and Prediction System (TOPS) at NASA Ames Research Center is a modeling system that generates a suite of gridded data products in near real-time that are designed to enhance management decisions related to floods, droughts, forest fires, human health, as well as crop, range, and forest production. While these data products introduce great possibilities for assisting management decisions and informing further research, realization of their full potential is complicated by their shear volume and by the need for a necessary infrastructure for remotely browsing, visualizing, and analyzing the data. In order to address these difficulties we have built an OGC-compliant WMS and WCS server based on an open source software stack that provides standardized access to our archive of data. This server is built using the open source Java library GeoTools which achieves efficient I/O and image rendering through Java Advanced Imaging. We developed spatio-temporal raster management capabilities using the PostGrid raster indexation engine. We provide visualization and browsing capabilities through a customized Ajax web interface derived from the kaMap project. This interface allows resource managers to quickly assess ecosystem conditions and identify significant trends and anomalies from within their web browser without the need to download source data or install special software. Our standardized web services also expose TOPS data to a range of potential clients, from web mapping applications to virtual globes and desktop GIS packages. However, support for managing the temporal dimension of our data is currently limited in existing software systems. Future work will attempt to overcome this shortcoming by building time-series visualization and analysis tools that can be integrated with existing geospatial software.

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Service Incentive: Towards an SOA-Friendly Acquisition Process

DTIC Science & Technology

2010-11-01

cell) 17000 Commerce Parkway, Suite A Mt. Laurel, NJ 08054 arlene.minkiewicz@pricesystems.com 1. McGovern, J, et. al., Java Based Web Applications...Web Services”, Dec 2004, available at <https://www.sdn.sap.com/irj/ servlet /prt/portal/prtroot/docs/library/ uuid/512de490-0201-0010-ffb4

The Competitive Struggle.

ERIC Educational Resources Information Center

Barry, Jeff; Bilal, Dania; Penniman, W. David

1998-01-01

Presents results of a survey of 30 library systems vendors to examine how successfully they met the key challenges of 1997: integration, testing, and marketing a new generation of systems. Character-based systems, the Dublin Core, Java, and the Z39.50 standard are discussed. Profiles describing sales and product developments for each of the…

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

AIBench: a rapid application development framework for translational research in biomedicine.

PubMed

Glez-Peña, D; Reboiro-Jato, M; Maia, P; Rocha, M; Díaz, F; Fdez-Riverola, F

2010-05-01

Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allow for efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input-processing-output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

JEnsembl: a version-aware Java API to Ensembl data systems

PubMed Central

Paterson, Trevor; Law, Andy

2012-01-01

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact: jensembl-develop@lists.sf.net, andy.law@roslin.ed.ac.uk, trevor.paterson@roslin.ed.ac.uk PMID:22945789

Accelerating next generation sequencing data analysis with system level optimizations.

PubMed

Kathiresan, Nagarajan; Temanni, Ramzi; Almabrazi, Hakeem; Syed, Najeeb; Jithesh, Puthen V; Al-Ali, Rashid

2017-08-22

Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.

CruiseViewer: SIOExplorer Graphical Interface to Metadata and Archives.

NASA Astrophysics Data System (ADS)

Sutton, D. W.; Helly, J. J.; Miller, S. P.; Chase, A.; Clark, D.

2002-12-01

We are introducing "CruiseViewer" as a prototype graphical interface for the SIOExplorer digital library project, part of the overall NSF National Science Digital Library (NSDL) effort. When complete, CruiseViewer will provide access to nearly 800 cruises, as well as 100 years of documents and images from the archives of the Scripps Institution of Oceanography (SIO). The project emphasizes data object accessibility, a rich metadata format, efficient uploading methods and interoperability with other digital libraries. The primary function of CruiseViewer is to provide a human interface to the metadata database and to storage systems filled with archival data. The system schema is based on the concept of an "arbitrary digital object" (ADO). Arbitrary in that if the object can be stored on a computer system then SIOExplore can manage it. Common examples are a multibeam swath bathymetry file, a .pdf cruise report, or a tar file containing all the processing scripts used on a cruise. We require a metadata file for every ADO in an ascii "metadata interchange format" (MIF), which has proven to be highly useful for operability and extensibility. Bulk ADO storage is managed using the Storage Resource Broker, SRB, data handling middleware developed at the San Diego Supercomputer Center that centralizes management and access to distributed storage devices. MIF metadata are harvested from several sources and housed in a relational (Oracle) database. For CruiseViewer, cgi scripts resident on an Apache server are the primary communication and service request handling tools. Along with the CruiseViewer java application, users can query, access and download objects via a separate method that operates through standard web browsers, http://sioexplorer.ucsd.edu. Both provide the functionability to query and view object metadata, and select and download ADOs. For the CruiseViewer application Java 2D is used to add a geo-referencing feature that allows users to select basemap images and have vector shapes representing query results mapped over the basemap in the image panel. The two methods together address a wide range of user access needs and will allow for widespread use of SIOExplorer.

SnopViz, an interactive snow profile visualization tool

NASA Astrophysics Data System (ADS)

Fierz, Charles; Egger, Thomas; gerber, Matthias; Bavay, Mathias; Techel, Frank

2016-04-01

SnopViz is a visualization tool for both simulation outputs of the snow-cover model SNOWPACK and observed snow profiles. It has been designed to fulfil the needs of operational services (Swiss Avalanche Warning Service, Avalanche Canada) as well as offer the flexibility required to satisfy the specific needs of researchers. This JavaScript application runs on any modern browser and does not require an active Internet connection. The open source code is available for download from models.slf.ch where examples can also be run. Both the SnopViz library and the SnopViz User Interface will become a full replacement of the current research visualization tool SN_GUI for SNOWPACK. The SnopViz library is a stand-alone application that parses the provided input files, for example, a single snow profile (CAAML file format) or multiple snow profiles as output by SNOWPACK (PRO file format). A plugin architecture allows for handling JSON objects (JavaScript Object Notation) as well and plugins for other file formats may be added easily. The outputs are provided either as vector graphics (SVG) or JSON objects. The SnopViz User Interface (UI) is a browser based stand-alone interface. It runs in every modern browser, including IE, and allows user interaction with the graphs. SVG, the XML based standard for vector graphics, was chosen because of its easy interaction with JS and a good software support (Adobe Illustrator, Inkscape) to manipulate graphs outside SnopViz for publication purposes. SnopViz provides new visualization for SNOWPACK timeline output as well as time series input and output. The actual output format for SNOWPACK timelines was retained while time series are read from SMET files, a file format used in conjunction with the open source data handling code MeteoIO. Finally, SnopViz is able to render single snow profiles, either observed or modelled, that are provided as CAAML-file. This file format (caaml.org/Schemas/V5.0/Profiles/SnowProfileIACS) is an international standard to exchange snow profile data. It is supported by the International Association of Cryospheric Sciences (IACS) and was developed in collaboration with practitioners (Avalanche Canada).

JSME: a free molecule editor in JavaScript.

PubMed

Bienfait, Bruno; Ertl, Peter

2013-01-01

A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

Mining collections of compounds with Screening Assistant 2

PubMed Central

2012-01-01

Background High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. Results We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Conclusions Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/. PMID:23327565

Mining collections of compounds with Screening Assistant 2.

PubMed

Guilloux, Vincent Le; Arrault, Alban; Colliandre, Lionel; Bourg, Stéphane; Vayer, Philippe; Morin-Allory, Luc

2012-08-31

High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/.

LibKiSAO: a Java library for Querying KiSAO.

PubMed

Zhukova, Anna; Adams, Richard; Laibe, Camille; Le Novère, Nicolas

2012-09-24

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characteristics, parameters and inter-relationships. KiSAO enables the unambiguous identification of algorithms from simulation descriptions. Information about analogous methods having similar characteristics and about algorithm parameters incorporated into KiSAO is desirable for simulation tools. To retrieve this information programmatically an application programming interface (API) for KiSAO is needed. We developed libKiSAO, a Java library to enable querying of the KiSA Ontology. It implements methods to retrieve information about simulation algorithms stored in KiSAO, their characteristics and parameters, and methods to query the algorithm hierarchy and search for similar algorithms providing comparable results for the same simulation set-up. Using libKiSAO, simulation tools can make logical inferences based on this knowledge and choose the most appropriate algorithm to perform a simulation. LibKiSAO also enables simulation tools to handle a wider range of simulation descriptions by determining which of the available methods are similar and can be used instead of the one indicated in the simulation description if that one is not implemented. LibKiSAO enables Java applications to easily access information about simulation algorithms, their characteristics and parameters stored in the OWL-encoded Kinetic Simulation Algorithm Ontology. LibKiSAO can be used by simulation description editors and simulation tools to improve reproducibility of computational simulation tasks and facilitate model re-use.

A Visual Editor in Java for View

NASA Technical Reports Server (NTRS)

Stansifer, Ryan

2000-01-01

In this project we continued the development of a visual editor in the Java programming language to create screens on which to display real-time data. The data comes from the numerous systems monitoring the operation of the space shuttle while on the ground and in space, and from the many tests of subsystems. The data can be displayed on any computer platform running a Java-enabled World Wide Web (WWW) browser and connected to the Internet. Previously a special-purpose program bad been written to display data on emulations of character-based display screens used for many years at NASA. The goal now is to display bit-mapped screens created by a visual editor. We report here on the visual editor that creates the display screens. This project continues the work we bad done previously. Previously we had followed the design of the 'beanbox,' a prototype visual editor created by Sun Microsystems. We abandoned this approach and implemented a prototype using a more direct approach. In addition, our prototype is based on newly released Java 2 graphical user interface (GUI) libraries. The result has been a visually more appealing appearance and a more robust application.

Extending the Virtual Solar Observatory (VSO) to Incorporate Data Analysis Capabilities (III)

NASA Astrophysics Data System (ADS)

Csillaghy, A.; Etesi, L.; Dennis, B.; Zarro, D.; Schwartz, R.; Tolbert, K.

2008-12-01

We will present a progress report on our activities to extend the data analysis capabilities of the VSO. Our efforts to date have focused on three areas: 1. Extending the data retrieval capabilities by developing a centralized data processing server. The server is built with Java, IDL (Interactive Data Language), and the SSW (Solar SoftWare) package with all SSW-related instrument libraries and required calibration data. When a user requests VSO data that requires preprocessing, the data are transparently sent to the server, processed, and returned to the user's IDL session for viewing and analysis. It is possible to have any Java or IDL client connect to the server. An IDL prototype for preparing and calibrating SOHO/EIT data wll be demonstrated. 2. Improving the solar data search in SHOW SYNOP, a graphical user tool connected to VSO in IDL. We introduce the Java-IDL interface that allows a flexible dynamic, and extendable way of searching the VSO, where all the communication with VSO are managed dynamically by standard Java tools. 3. Improving image overlay capability to support coregistration of solar disk observations obtained from different orbital view angles, position angles, and distances - such as from the twin STEREO spacecraft.

Online Information 96. Proceedings of the International Online Information Meeting (20th, London, England, UK, December 3-5, 1996).

ERIC Educational Resources Information Center

Raitt, David I., Ed.; Jeapes, Ben, Ed.

This proceedings volume contains 68 papers. Subjects addressed include: access to information; the future of information managers/librarians; intelligent agents; changing roles of library users; disintermediation; Internet review sites; World Wide Web (WWW) search engines; Java; online searching; future of online education; integrated information…

Chapter 21: Programmatic Interfaces - STILTS

NASA Astrophysics Data System (ADS)

Fitzpatrick, M. J.

STILTS is the Starlink Tables Infrastructure Library Tool Set developed by Mark Taylor of the former Starlink Project. STILTS is a command-line tool (see the NVOSS_HOME/bin/stilts command) providing access to the same functionality driving the TOPCAT application and can be run using either the STILTS-specific jar file, or the more general TOPCAT jar file (both are available in the NVOSS_HOME/java/lib directory and are included in the default software environment classpath). The heart of both STILTS and TOPCAT is the STIL Java library. STIL is designed to efficiently handle the input, output and processing of very large tabular datasets and the STILTS task interface makes it an ideal tool for the scripting environment. Multiple formats are supported (including FITS Binary Tables, VOTable, CSV, SQL databases and ASCII, amongst others) and while some tools will generically handle all supported formats, others are specific to the VOTable format. Converting a VOTable to a more script-friendly format is the first thing most users will encounter, but there are many other useful tools as well.

ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2017-02-15

ImageJ-MATLAB is a lightweight Java library facilitating bi-directional interoperability between MATLAB and ImageJ. By defining a standard for translation between matrix and image data structures, researchers are empowered to select the best tool for their image-analysis tasks. Freely available extension to ImageJ2 ( http://imagej.net/Downloads ). Installation and use instructions available at http://imagej.net/MATLAB_Scripting. Tested with ImageJ 2.0.0-rc-54 , Java 1.8.0_66 and MATLAB R2015b. eliceiri@wisc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

GEODATA: Information System Based on Geospatial for Early Warning Tracking and Analysis Agricultural Plant Diseases in Central Java

NASA Astrophysics Data System (ADS)

Prasetyo, S. Y. J.; Agus, Y. H.; Dewi, C.; Simanjuntak, B. H.; Hartomo, K. D.

2017-03-01

The Government of Indonesia is currently faced with the problems of food, especially rice. It needs in large numbers that have to import from neighboring countries. Actually, the Indonesian government has the ability to produce rice to meet national needs but is still faced with the problem of pest attack rice annually increasing extent. One of the factors is that geographically Indonesia located on the migration path of world rice insect pests (called BPH or Brown Planthoppers) (Nilaparvata lugens Stal.) It leads endemic status annually. One proposed strategy to be applied is to use an early warning system based on a specific region of the main pest population. The proposed information system called GEODATA. GEODATA is Geospatial Outbreak of Disease Tracking and Analysis. The system works using a library ESSA (Exponential Smoothing - Spatial Autocorrelation) developed in previous studies in Satya Wacana Christian University. GEODATA built to meet the qualifications required surveillance device by BMKG (Indonesian Agency of Meteorology, Climatology and Geophysics’ Central Java Provinces), BPTPH (Indonesian Agency of Plant Protection and Horticulture) Central Java Provinces, BKP-KP District Boyolali, Central Java, (Indonesian Agency of Food Security and Agriculture Field Supervisor, District Boyolali, Central Java Provinces) and farmer groups. GIS GEODATA meets the needs of surveillance devices that include: (1) mapping of the disease, (2) analysis of the dynamics of the disease, and (3) prediction of attacks / disease outbreaks in a particular region. GIS GEODATA is currently under implementation in the laboratory field observations of plant pest in Central Java province, Indonesia.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

PubMed Central

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

2014-01-01

Summary: Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts. Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ Contact: andre.schumacher@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24149054

JANIS: NEA JAva-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, Nicolas; Bossant, Manuel; Cabellos, Oscar; Dupont, Emmeric; Díez, Carlos J.

2017-09-01

JANIS (JAva-based Nuclear Data Information System) software is developed by the OECD Nuclear Energy Agency (NEA) Data Bank to facilitate the visualization and manipulation of nuclear data, giving access to evaluated nuclear data libraries, such as ENDF, JEFF, JENDL, TENDL etc., and also to experimental nuclear data (EXFOR) and bibliographical references (CINDA). It is available as a standalone Java program, downloadable and distributed on DVD and also a web application available on the NEA website. One of the main new features in JANIS is the scripting capability via command line, which notably automatizes plots generation and permits automatically extracting data from the JANIS database. Recent NEA software developments rely on these JANIS features to access nuclear data, for example the Nuclear Data Sensitivity Tool (NDaST) makes use of covariance data in BOXER and COVERX formats, which are retrieved from the JANIS database. New features added in this version of the JANIS software are described along this paper with some examples.

SCEC-VDO: A New 3-Dimensional Visualization and Movie Making Software for Earth Science Data

NASA Astrophysics Data System (ADS)

Milner, K. R.; Sanskriti, F.; Yu, J.; Callaghan, S.; Maechling, P. J.; Jordan, T. H.

2016-12-01

Researchers and undergraduate interns at the Southern California Earthquake Center (SCEC) have created a new 3-dimensional (3D) visualization software tool called SCEC Virtual Display of Objects (SCEC-VDO). SCEC-VDO is written in Java and uses the Visualization Toolkit (VTK) backend to render 3D content. SCEC-VDO offers advantages over existing 3D visualization software for viewing georeferenced data beneath the Earth's surface. Many popular visualization packages, such as Google Earth, restrict the user to views of the Earth from above, obstructing views of geological features such as faults and earthquake hypocenters at depth. SCEC-VDO allows the user to view data both above and below the Earth's surface at any angle. It includes tools for viewing global earthquakes from the U.S. Geological Survey, faults from the SCEC Community Fault Model, and results from the latest SCEC models of earthquake hazards in California including UCERF3 and RSQSim. Its object-oriented plugin architecture allows for the easy integration of new regional and global datasets, regardless of the science domain. SCEC-VDO also features rich animation capabilities, allowing users to build a timeline with keyframes of camera position and displayed data. The software is built with the concept of statefulness, allowing for reproducibility and collaboration using an xml file. A prior version of SCEC-VDO, which began development in 2005 under the SCEC Undergraduate Studies in Earthquake Information Technology internship, used the now unsupported Java3D library. Replacing Java3D with the widely supported and actively developed VTK libraries not only ensures that SCEC-VDO can continue to function for years to come, but allows for the export of 3D scenes to web viewers and popular software such as Paraview. SCEC-VDO runs on all recent 64-bit Windows, Mac OS X, and Linux systems with Java 8 or later. More information, including downloads, tutorials, and example movies created fully within SCEC-VDO is available here: http://scecvdo.usc.edu

DNAism: exploring genomic datasets on the web with Horizon Charts.

PubMed

Rio Deiros, David; Gibbs, Richard A; Rogers, Jeffrey

2016-01-27

Computational biologists daily face the need to explore massive amounts of genomic data. New visualization techniques can help researchers navigate and understand these big data. Horizon Charts are a relatively new visualization method that, under the right circumstances, maximizes data density without losing graphical perception. Horizon Charts have been successfully applied to understand multi-metric time series data. We have adapted an existing JavaScript library (Cubism) that implements Horizon Charts for the time series domain so that it works effectively with genomic datasets. We call this new library DNAism. Horizon Charts can be an effective visual tool to explore complex and large genomic datasets. Researchers can use our library to leverage these techniques to extract additional insights from their own datasets.

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

Arion is a library and tool set that enables researchers to holistically define test system models. To define a complex system for testing an algorithm or control requires expertise across multiple domains. Simulating a complex system requires the integration of multiple simulators and test hardware, each with their own specification languages and concepts. This requires extensive set of knowledge and capabilities. Arion was developed to alleviate this challenge. Arion is a library of Java libraries that abstracts the concepts from supported simulators into a cohesive model language that allows someone to build models to their needed level of fidelity andmore » expertise. Arion is also a software tool that translates the users model back into the specification languages of the simulators and test hardware needed for execution.« less

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.

Applying a Service-Oriented Architecture to Operational Flight Program Development

DTIC Science & Technology

2007-09-01

using two Java 2 Enterprise Edition (J2EE) Web servers. The weapon models were accessed using a SUN Microsystems Java Web Services Development Pack...Oriented Architectures 22 CROSSTALK The Journal of Defense Software Engineering September 2007 tion, and Spring/ Hibernate to provide the data access...tion since a major coding effort was avoided. The majority of the effort was tweaking pre-existing Java source code and editing of eXtensible Markup

ReSEARCH: A Requirements Search Engine: Progress Report 2

DTIC Science & Technology

2008-09-01

and provides a convenient user interface for the search process. Ideally, the web application would be based on Tomcat, a free Java Servlet and JSP...Implementation issues Lucene Java is an Open Source project, available under the Apache License, which provides an accessible API for the development of...from the Apache Lucene website (Lucene- java Wiki , 2008). A search application developed with Lucene consists of the same two major com- ponents

Building an Ajax Application from Scratch

ERIC Educational Resources Information Center

Clark, Jason A.

2006-01-01

The author of this article suggests that to refresh Web pages and online library catalogs in a more pleasing way, Ajax, an acronym for Asynchronous JavaScript and XML, should be used. Ajax is the way to use Web technologies that work together to refresh sections of Web pages to allow almost instant responses to user input. This article describes…

Creating Engaging Online Learning Material with the JSAV JavaScript Algorithm Visualization Library

ERIC Educational Resources Information Center

Karavirta, Ville; Shaffer, Clifford A.

2016-01-01

Data Structures and Algorithms are a central part of Computer Science. Due to their abstract and dynamic nature, they are a difficult topic to learn for many students. To alleviate these learning difficulties, instructors have turned to algorithm visualizations (AV) and AV systems. Research has shown that especially engaging AVs can have an impact…

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

Kartsaklis, Christos; Civario, G

This paper discusses an ongoing progress regarding the development of a Java-based library for rapid kernel prototyping in NVIDIA PTX and PTX instruction scheduling. It is aimed at developers seeking total control of emitted PTX, highly parametric emission of, and tunable instruction reordering. It is primarily used for code development at ICHEC but is also hoped that NVIDIA GPU community will also find it beneficial.

Boninite-like intraplate magmas from Manihiki Plateau require ultra-depleted and enriched source components

PubMed Central

Golowin, Roman; Portnyagin, Maxim; Hoernle, Kaj; Hauff, Folkmar; Gurenko, Andrey; Garbe-Schönberg, Dieter; Werner, Reinhard; Turner, Simon

2017-01-01

The Ontong Java and Manihiki oceanic plateaus are believed to have formed through high-degree melting of a mantle plume head. Boninite-like, low-Ti basement rocks at Manihiki, however, imply a more complex magma genesis compared with Ontong Java basement lavas that can be generated by ∼30% melting of a primitive mantle source. Here we show that the trace element and isotope compositions of low-Ti Manihiki rocks can best be explained by re-melting of an ultra-depleted source (possibly a common mantle component in the Ontong Java and Manihiki plume sources) re-enriched by ≤1% of an ocean-island-basalt-like melt component. Unlike boninites formed via hydrous flux melting of refractory mantle at subduction zones, these boninite-like intraplate rocks formed through adiabatic decompression melting of refractory plume material that has been metasomatized by ocean-island-basalt-like melts. Our results suggest that caution is required before assuming all Archaean boninites were formed in association with subduction processes. PMID:28181497

Python scripting in the nengo simulator.

PubMed

Stewart, Terrence C; Tripp, Bryan; Eliasmith, Chris

2009-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models.

Python Scripting in the Nengo Simulator

PubMed Central

Stewart, Terrence C.; Tripp, Bryan; Eliasmith, Chris

2008-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models. PMID:19352442

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

PubMed

Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

2014-07-03

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

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.

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

Tatool: a Java-based open-source programming framework for psychological studies.

PubMed

von Bastian, Claudia C; Locher, André; Ruflin, Michael

2013-03-01

Tatool (Training and Testing Tool) was developed to assist researchers with programming training software, experiments, and questionnaires. Tatool is Java-based, and thus is a platform-independent and object-oriented framework. The architecture was designed to meet the requirements of experimental designs and provides a large number of predefined functions that are useful in psychological studies. Tatool comprises features crucial for training studies (e.g., configurable training schedules, adaptive training algorithms, and individual training statistics) and allows for running studies online via Java Web Start. The accompanying "Tatool Online" platform provides the possibility to manage studies and participants' data easily with a Web-based interface. Tatool is published open source under the GNU Lesser General Public License, and is available at www.tatool.ch.

JTSA: an open source framework for time series abstractions.

PubMed

Sacchi, Lucia; Capozzi, Davide; Bellazzi, Riccardo; Larizza, Cristiana

2015-10-01

The evaluation of the clinical status of a patient is frequently based on the temporal evolution of some parameters, making the detection of temporal patterns a priority in data analysis. Temporal abstraction (TA) is a methodology widely used in medical reasoning for summarizing and abstracting longitudinal data. This paper describes JTSA (Java Time Series Abstractor), a framework including a library of algorithms for time series preprocessing and abstraction and an engine to execute a workflow for temporal data processing. The JTSA framework is grounded on a comprehensive ontology that models temporal data processing both from the data storage and the abstraction computation perspective. The JTSA framework is designed to allow users to build their own analysis workflows by combining different algorithms. Thanks to the modular structure of a workflow, simple to highly complex patterns can be detected. The JTSA framework has been developed in Java 1.7 and is distributed under GPL as a jar file. JTSA provides: a collection of algorithms to perform temporal abstraction and preprocessing of time series, a framework for defining and executing data analysis workflows based on these algorithms, and a GUI for workflow prototyping and testing. The whole JTSA project relies on a formal model of the data types and of the algorithms included in the library. This model is the basis for the design and implementation of the software application. Taking into account this formalized structure, the user can easily extend the JTSA framework by adding new algorithms. Results are shown in the context of the EU project MOSAIC to extract relevant patterns from data coming related to the long term monitoring of diabetic patients. The proof that JTSA is a versatile tool to be adapted to different needs is given by its possible uses, both as a standalone tool for data summarization and as a module to be embedded into other architectures to select specific phenotypes based on TAs in a large dataset. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

SIOExplorer: Modern IT Methods and Tools for Digital Library Management

NASA Astrophysics Data System (ADS)

Sutton, D. W.; Helly, J.; Miller, S.; Chase, A.; Clarck, D.

2003-12-01

With more geoscience disciplines becoming data-driven it is increasingly important to utilize modern techniques for data, information and knowledge management. SIOExplorer is a new digital library project with 2 terabytes of oceanographic data collected over the last 50 years on 700 cruises by the Scripps Institution of Oceanography. It is built using a suite of information technology tools and methods that allow for an efficient and effective digital library management system. The library consists of a number of independent collections, each with corresponding metadata formats. The system architecture allows each collection to be built and uploaded based on a collection dependent metadata template file (MTF). This file is used to create the hierarchical structure of the collection, create metadata tables in a relational database, and to populate object metadata files and the collection as a whole. Collections are comprised of arbitrary digital objects stored at the San Diego Supercomputer Center (SDSC) High Performance Storage System (HPSS) and managed using the Storage Resource Broker (SRB), data handling middle ware developed at SDSC. SIOExplorer interoperates with other collections as a data provider through the Open Archives Initiative (OAI) protocol. The user services for SIOExplorer are accessed from CruiseViewer, a Java application served using Java Web Start from the SIOExplorer home page. CruiseViewer is an advanced tool for data discovery and access. It implements general keyword and interactive geospatial search methods for the collections. It uses a basemap to georeference search results on user selected basemaps such as global topography or crustal age. User services include metadata viewing, opening of selective mime type digital objects (such as images, documents and grid files), and downloading of objects (including the brokering of proprietary hold restrictions).

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

An Investigation into Digital Media: Characteristics of Learning Objects Which K-12 Teachers Determine Meet Their Instructional Needs

ERIC Educational Resources Information Center

Guthrie, Patricia Ann

2010-01-01

In recent years, learning objects have emerged as an instructional tool for teachers. Digital libraries and collections provide teachers with free or fee-base access to a variety of learning objects from photos and famous speeches to Flash animations and interactive Java Applets. Learning objects offer opportunities for students to interact with…

Quantifying Uncertainty in Expert Judgment: Initial Results

DTIC Science & Technology

2013-03-01

lines of source code were added in . ---------- C++ = 32%; JavaScript = 29%; XML = 15%; C = 7%; CSS = 7%; Java = 5%; Oth- er = 5% LOC = 927,266...much total effort in person years has been spent on this project? CMU/SEI-2013-TR-001 | 33 5 MySQL , the most popular Open Source SQL...as MySQL , Oracle, PostgreSQL, MS SQL Server, ODBC, or Interbase. Features include email reminders, iCal/vCal import/export, re- mote subscriptions

Verification Tools Secure Online Shopping, Banking

NASA Technical Reports Server (NTRS)

2010-01-01

Just like rover or rocket technology sent into space, the software that controls these technologies must be extensively tested to ensure reliability and effectiveness. Ames Research Center invented the open-source Java Pathfinder (JPF) toolset for the deep testing of Java-based programs. Fujitsu Labs of America Inc., based in Sunnyvale, California, improved the capabilities of the JPF Symbolic Pathfinder tool, establishing the tool as a means of thoroughly testing the functionality and security of Web-based Java applications such as those used for Internet shopping and banking.

A Simple and Customizable Web Interface to the Virtual Solar Observatory

NASA Astrophysics Data System (ADS)

Hughitt, V. Keith; Hourcle, J.; Suarez-Sola, I.; Davey, A.

2010-05-01

As the variety and number of solar data sources continue to increase at a rapid rate, the importance of providing methods to search through these sources becomes increasingly important. By taking advantage of the power of modern JavaScript libraries, a new version of the Virtual Solar Observatory's web interface aims to provide a significantly faster and simpler way to explore the multitude of data repositories available. Querying asynchroniously serves not only to eliminates bottlenecks resulting from slow or unresponsive data providers, but also allows for displaying of results as soon as they are returned. Implicit pagination and post-query filtering enables users to work with large result-sets, while a more modular and customizable UI provides a mechanism for customizing both the look-and-feel and behavior of the VSO web interface. Finally, the new web interface features a custom widget system capable of displaying additional tools and information along-side of the standard VSO search form. Interested users can also write their own widgets and submit them for future incorporation into VSO.

TIM, a ray-tracing program for METATOY research and its dissemination

NASA Astrophysics Data System (ADS)

Lambert, Dean; Hamilton, Alasdair C.; Constable, George; Snehanshu, Harsh; Talati, Sharvil; Courtial, Johannes

2012-03-01

TIM (The Interactive METATOY) is a ray-tracing program specifically tailored towards our research in METATOYs, which are optical components that appear to be able to create wave-optically forbidden light-ray fields. For this reason, TIM possesses features not found in other ray-tracing programs. TIM can either be used interactively or by modifying the openly available source code; in both cases, it can easily be run as an applet embedded in a web page. Here we describe the basic structure of TIM's source code and how to extend it, and we give examples of how we have used TIM in our own research. Program summaryProgram title: TIM Catalogue identifier: AEKY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 124 478 No. of bytes in distributed program, including test data, etc.: 4 120 052 Distribution format: tar.gz Programming language: Java Computer: Any computer capable of running the Java Virtual Machine (JVM) 1.6 Operating system: Any; developed under Mac OS X Version 10.6 RAM: Typically 145 MB (interactive version running under Mac OS X Version 10.6) Classification: 14, 18 External routines: JAMA [1] (source code included) Nature of problem: Visualisation of scenes that include scene objects that create wave-optically forbidden light-ray fields. Solution method: Ray tracing. Unusual features: Specifically designed to visualise wave-optically forbidden light-ray fields; can visualise ray trajectories; can visualise geometric optic transformations; can create anaglyphs (for viewing with coloured "3D glasses") and random-dot autostereograms of the scene; integrable into web pages. Running time: Problem-dependent; typically seconds for a simple scene.

Small Boat and Swarm Defense: A Gap Study

DTIC Science & Technology

2008-09-01

25 1. Java......................................................................................................25 2. The NetBeans ...Figure 12. Overview of Java program development (Zakhour 2006)...............................26 Figure 13. NetBeans IDE generating new “Hello World...Application (Zakhour 2006) ..27 Figure 14. Example source code generation using NetBeans for the “Hello World” application (Zakhour 2006

Dependency Tree Annotation Software

DTIC Science & Technology

2015-11-01

formats, and it provides numerous options for customizing how dependency trees are displayed. Built entirely in Java , it can run on a wide range of...tree can be saved as an image, .mxe (a mxGraph editing file), a .conll file, and several other file formats. DTE uses the open source Java version

ChEBI in 2016: Improved services and an expanding collection of metabolites

PubMed Central

Hastings, Janna; Owen, Gareth; Dekker, Adriano; Ennis, Marcus; Kale, Namrata; Muthukrishnan, Venkatesh; Turner, Steve; Swainston, Neil; Mendes, Pedro; Steinbeck, Christoph

2016-01-01

ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a ‘live’ website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. PMID:26467479

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.

ChemCalc: a building block for tomorrow's chemical infrastructure.

PubMed

Patiny, Luc; Borel, Alain

2013-05-24

Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data manipulation functionality that students and researchers need for chemical calculations. These services return their results as JSON (JavaScript Object Notation) objects, which facilitates their use for Web applications. The ChemCalc project http://www.chemcalc.org demonstrates this approach: we present three Web services related with mass spectrometry, namely isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. We also developed a complete Web application based on these three Web services, taking advantage of modern HTML5 and JavaScript libraries (ChemDoodle and jQuery).

Generic, Type-Safe and Object Oriented Computer Algebra Software

NASA Astrophysics Data System (ADS)

Kredel, Heinz; Jolly, Raphael

Advances in computer science, in particular object oriented programming, and software engineering have had little practical impact on computer algebra systems in the last 30 years. The software design of existing systems is still dominated by ad-hoc memory management, weakly typed algorithm libraries and proprietary domain specific interactive expression interpreters. We discuss a modular approach to computer algebra software: usage of state-of-the-art memory management and run-time systems (e.g. JVM) usage of strongly typed, generic, object oriented programming languages (e.g. Java) and usage of general purpose, dynamic interactive expression interpreters (e.g. Python) To illustrate the workability of this approach, we have implemented and studied computer algebra systems in Java and Scala. In this paper we report on the current state of this work by presenting new examples.

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.

JBioWH: an open-source Java framework for bioinformatics data integration

PubMed Central

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

JBioWH: an open-source Java framework for bioinformatics data integration.

PubMed

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

PubMed Central

2013-01-01

Background System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Results Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Conclusions Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr. PMID:23586463

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.

PubMed

Chen, Edward Y; Tan, Christopher M; Kou, Yan; Duan, Qiaonan; Wang, Zichen; Meirelles, Gabriela Vaz; Clark, Neil R; Ma'ayan, Avi

2013-04-15

System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

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 discuss the development of both these efforts and how they are beginning to influence the solar physics community.

NearFar: A computer program for nearside farside decomposition of heavy-ion elastic scattering amplitude

NASA Astrophysics Data System (ADS)

Cha, Moon Hoe

2007-02-01

The NearFar program is a package for carrying out an interactive nearside-farside decomposition of heavy-ion elastic scattering amplitude. The program is implemented in Java to perform numerical operations on the nearside and farside angular distributions. It contains a graphical display interface for the numerical results. A test run has been applied to the elastic O16+Si28 scattering at E=1503 MeV. Program summaryTitle of program: NearFar Catalogue identifier: ADYP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYP_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Computers: designed for any machine capable of running Java, developed on PC-Pentium-4 Operating systems under which the program has been tested: Microsoft Windows XP (Home Edition) Program language used: Java Number of bits in a word: 64 Memory required to execute with typical data: case dependent No. of lines in distributed program, including test data, etc.: 3484 Number of bytes distributed program, including test data, etc.: 142 051 Distribution format: tar.gz Other software required: A Java runtime interpreter, or the Java Development Kit, version 5.0 Nature of physical problem: Interactive nearside-farside decomposition of heavy-ion elastic scattering amplitude. Method of solution: The user must supply a external data file or PPSM parameters which calculates theoretical values of the quantities to be decomposed. Typical running time: Problem dependent. In a test run, it is about 35 s on a 2.40 GHz Intel P4-processor machine.

Enhancement of the Logistics Battle Command Model: Architecture Upgrades and Attrition Module Development

DTIC Science & Technology

2017-01-05

module. 15. SUBJECT TERMS Logistics, attrition, discrete event simulation, Simkit, LBC 16. SECURITY CLASSIFICATION OF: Unclassified 17. LIMITATION...stochastics, and discrete event model programmed in Java building largely on the Simkit library. The primary purpose of the LBC model is to support...equations makes them incompatible with the discrete event construct of LBC. Bullard further advances this methodology by developing a stochastic

Rule-Based Runtime Verification

NASA Technical Reports Server (NTRS)

Barringer, Howard; Goldberg, Allen; Havelund, Klaus; Sen, Koushik

2003-01-01

We present a rule-based framework for defining and implementing finite trace monitoring logics, including future and past time temporal logic, extended regular expressions, real-time logics, interval logics, forms of quantified temporal logics, and so on. Our logic, EAGLE, is implemented as a Java library and involves novel techniques for rule definition, manipulation and execution. Monitoring is done on a state-by-state basis, without storing the execution trace.

Internet Patient Records: new techniques

PubMed Central

Moehrs, Sascha; Anedda, Paolo; Tuveri, Massimiliano; Zanetti, Gianluigi

2001-01-01

Background The ease by which the Internet is able to distribute information to geographically-distant users on a wide variety of computers makes it an obvious candidate for a technological solution for electronic patient record systems. Indeed, second-generation Internet technologies such as the ones described in this article - XML (eXtensible Markup Language), XSL (eXtensible Style Language), DOM (Document Object Model), CSS (Cascading Style Sheet), JavaScript, and JavaBeans - may significantly reduce the complexity of the development of distributed healthcare systems. Objective The demonstration of an experimental Electronic Patient Record (EPR) system built from those technologies that can support viewing of medical imaging exams and graphically-rich clinical reporting tools, while conforming to the newly emerging XML standard for digital documents. In particular, we aim to promote rapid prototyping of new reports by clinical specialists. Methods We have built a prototype EPR client, InfoDOM, that runs in both the popular web browsers. In this second version it receives each EPR as an XML record served via the secure SSL (Secure Socket Layer) protocol. JavaBean software components manipulate the XML to store it and then to transform it into a variety of useful clinical views. First a web page summary for the patient is produced. From that web page other JavaBeans can be launched. In particular, we have developed a medical imaging exam Viewer and a clinical Reporter bean parameterized appropriately for the particular patient and exam in question. Both present particular views of the XML data. The Viewer reads image sequences from a patient-specified network URL on a PACS (Picture Archiving and Communications System) server and presents them in a user-controllable animated sequence, while the Reporter provides a configurable anatomical map of the site of the pathology, from which individual "reportlets" can be launched. The specification of these reportlets is achieved using standard HTML forms and thus may conceivably be authored by clinical specialists. A generic JavaScript library has been written that allows the seamless incorporation of such contributions into the InfoDOM client. In conjunction with another JavaBean, that library renders graphically-enhanced reporting tools that read and write content to and from the XML data-structure, ready for resubmission to the EPR server. Results We demonstrate the InfoDOM experimental EPR system that is currently being adapted for test-bed use in three hospitals in Cagliari, Italy. For this we are working with specialists in neurology, radiology, and epilepsy. Conclusions Early indications are that the rapid prototyping of reports afforded by our EPR system can assist communication between clinical specialists and our system developers. We are now experimenting with new technologies that may provide services to the kind of XML EPR client described here. PMID:11720950

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.

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.

Test-Case Generation using an Explicit State Model Checker Final Report

NASA Technical Reports Server (NTRS)

Heimdahl, Mats P. E.; Gao, Jimin

2003-01-01

In the project 'Test-Case Generation using an Explicit State Model Checker' we have extended an existing tools infrastructure for formal modeling to export Java code so that we can use the NASA Ames tool Java Pathfinder (JPF) for test case generation. We have completed a translator from our source language RSML(exp -e) to Java and conducted initial studies of how JPF can be used as a testing tool. In this final report, we provide a detailed description of the translation approach as implemented in our tools.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening.

PubMed

Karthikeyan, Muthukumarasamy; Pandit, Deepak; Vyas, Renu

2015-01-01

In this work we present ChemScreener, a Java-based application to perform virtual library generation combined with virtual screening in a platform-independent distributed computing environment. ChemScreener comprises a scaffold identifier, a distinct scaffold extractor, an interactive virtual library generator as well as a virtual screening module for subsequently selecting putative bioactive molecules. The virtual libraries are annotated with chemophore-, pharmacophore- and toxicophore-based information for compound prioritization. The hits selected can then be further processed using QSAR, docking and other in silico approaches which can all be interfaced within the ChemScreener framework. As a sample application, in this work scaffold selectivity, diversity, connectivity and promiscuity towards six important therapeutic classes have been studied. In order to illustrate the computational power of the application, 55 scaffolds extracted from 161 anti-psychotic compounds were enumerated to produce a virtual library comprising 118 million compounds (17 GB) and annotated with chemophore, pharmacophore and toxicophore based features in a single step which would be non-trivial to perform with many standard software tools today on libraries of this size.

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.

A Hybrid Constraint Representation and Reasoning Framework

NASA Technical Reports Server (NTRS)

Golden, Keith; Pang, Wan-Lin

2003-01-01

This paper introduces JNET, a novel constraint representation and reasoning framework that supports procedural constraints and constraint attachments, providing a flexible way of integrating the constraint reasoner with a run- time software environment. Attachments in JNET are constraints over arbitrary Java objects, which are defined using Java code, at runtime, with no changes to the JNET source code.

OpenGL in Multi-User Web-Based Applications

NASA Astrophysics Data System (ADS)

Szostek, K.; Piórkowski, A.

In this article construction and potential of OpenGL multi-user web-based application are presented. The most common technologies like: .NET ASP, Java and Mono were used with specific OpenGL libraries to visualize tree-dimensional medical data. The most important conclusion of this work is that server side applications can easily take advantage of fast GPU and produce efficient results of advanced computation just like the visualization.

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

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.

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

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.

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.

ESTminer: a Web interface for mining EST contig and cluster databases.

PubMed

Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

2005-03-01

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data.

PubMed

Pirooznia, Mehdi; Deng, Youping

2006-12-12

Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpose of this study is to create a GUI application that allows SVM users to perform SVM training, classification and prediction. The GUI provides user-friendly access to state-of-the-art SVM methods embodied in the LIBSVM implementation of Support Vector Machine. We implemented the java interface using standard swing libraries. We used a sample data from a breast cancer study for testing classification accuracy. We achieved 100% accuracy in classification among the BRCA1-BRCA2 samples with RBF kernel of SVM. We have developed a java GUI application that allows SVM users to perform SVM training, classification and prediction. We have demonstrated that support vector machines can accurately classify genes into functional categories based upon expression data from DNA microarray hybridization experiments. Among the different kernel functions that we examined, the SVM that uses a radial basis kernel function provides the best performance. The SVM Classifier is available at http://mfgn.usm.edu/ebl/svm/.

JavaScript DNA translator: DNA-aligned protein translations.

PubMed

Perry, William L

2002-12-01

There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

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/

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

PubMed

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

Authorship attribution of source code by using back propagation neural network based on particle swarm optimization

PubMed Central

Xu, Guoai; Li, Qi; Guo, Yanhui; Zhang, Miao

2017-01-01

Authorship attribution is to identify the most likely author of a given sample among a set of candidate known authors. It can be not only applied to discover the original author of plain text, such as novels, blogs, emails, posts etc., but also used to identify source code programmers. Authorship attribution of source code is required in diverse applications, ranging from malicious code tracking to solving authorship dispute or software plagiarism detection. This paper aims to propose a new method to identify the programmer of Java source code samples with a higher accuracy. To this end, it first introduces back propagation (BP) neural network based on particle swarm optimization (PSO) into authorship attribution of source code. It begins by computing a set of defined feature metrics, including lexical and layout metrics, structure and syntax metrics, totally 19 dimensions. Then these metrics are input to neural network for supervised learning, the weights of which are output by PSO and BP hybrid algorithm. The effectiveness of the proposed method is evaluated on a collected dataset with 3,022 Java files belong to 40 authors. Experiment results show that the proposed method achieves 91.060% accuracy. And a comparison with previous work on authorship attribution of source code for Java language illustrates that this proposed method outperforms others overall, also with an acceptable overhead. PMID:29095934

IJ-OpenCV: Combining ImageJ and OpenCV for processing images in biomedicine.

PubMed

Domínguez, César; Heras, Jónathan; Pascual, Vico

2017-05-01

The effective processing of biomedical images usually requires the interoperability of diverse software tools that have different aims but are complementary. The goal of this work is to develop a bridge to connect two of those tools: ImageJ, a program for image analysis in life sciences, and OpenCV, a computer vision and machine learning library. Based on a thorough analysis of ImageJ and OpenCV, we detected the features of these systems that could be enhanced, and developed a library to combine both tools, taking advantage of the strengths of each system. The library was implemented on top of the SciJava converter framework. We also provide a methodology to use this library. We have developed the publicly available library IJ-OpenCV that can be employed to create applications combining features from both ImageJ and OpenCV. From the perspective of ImageJ developers, they can use IJ-OpenCV to easily create plugins that use any functionality provided by the OpenCV library and explore different alternatives. From the perspective of OpenCV developers, this library provides a link to the ImageJ graphical user interface and all its features to handle regions of interest. The IJ-OpenCV library bridges the gap between ImageJ and OpenCV, allowing the connection and the cooperation of these two systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metadata management for high content screening in OMERO

PubMed Central

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

2016-01-01

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org. PMID:26476368

Metadata management for high content screening in OMERO.

PubMed

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

2016-03-01

High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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.

Placing User-Generated Content on the Map with Confidence

DTIC Science & Technology

2014-11-03

Terms Theory,Algorithms Keywords Geographic information retrieval, Geolocation 1. INTRODUCTION We describe a method that places on the map short text...we collected using twitter4j, a Java library for the Twitter API . After filtering, there were 44,289 documents in the Twitter test set We evaluate how...Baldwin. Text-based twitter user geolocation prediction. J. Artif. Intell. Res.(JAIR), 49:451–500, 2014. [4] C. Hauff, B. Thomee, and M. Trevisiol

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

Utah Virtual Lab: JAVA interactivity for teaching science and statistics on line.

PubMed

Malloy, T E; Jensen, G C

2001-05-01

The Utah on-line Virtual Lab is a JAVA program run dynamically off a database. It is embedded in StatCenter (www.psych.utah.edu/learn/statsampler.html), an on-line collection of tools and text for teaching and learning statistics. Instructors author a statistical virtual reality that simulates theories and data in a specific research focus area by defining independent, predictor, and dependent variables and the relations among them. Students work in an on-line virtual environment to discover the principles of this simulated reality: They go to a library, read theoretical overviews and scientific puzzles, and then go to a lab, design a study, collect and analyze data, and write a report. Each student's design and data analysis decisions are computer-graded and recorded in a database; the written research report can be read by the instructor or by other students in peer groups simulating scientific conventions.

Writing an Electronic Astronomy Book with Interactive Curricular Material

NASA Astrophysics Data System (ADS)

Thompson, Kristen L.; Belloni, Mario; Christian, Wolfgang

2015-01-01

With the rise of tablets, the past few years have seen an increase in the demand for quality electronic textbooks. Unfortunately, most of the current offerings do not exploit the accessibility and interactivity that electronic books can deliver. In this poster, we discuss how we are merging our curriculum development projects (Physlets, Easy Java/JavaScript Simulations, and Open Source Physics) with the EPUB electronic book format to develop an interactive textbook for use in a one-semester introductory astronomy course. The book, Astronomy: An Interactive Introduction, combines the narrative, equations, and images of a traditional astronomy text with new JavaScript simulations.

ProMC: Input-output data format for HEP applications using varint encoding

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; May, E.; Strand, K.; Van Gemmeren, P.

2014-10-01

A new data format for Monte Carlo (MC) events, or any structural data, including experimental data, is discussed. The format is designed to store data in a compact binary form using variable-size integer encoding as implemented in the Google's Protocol Buffers package. This approach is implemented in the PROMC library which produces smaller file sizes for MC records compared to the existing input-output libraries used in high-energy physics (HEP). Other important features of the proposed format are a separation of abstract data layouts from concrete programming implementations, self-description and random access. Data stored in PROMC files can be written, read and manipulated in a number of programming languages, such C++, JAVA, FORTRAN and PYTHON.

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

Bastian, Mark; Trigueros, Jose V.

Phoenix is a Java Virtual Machine (JVM) based library for performing mathematical and astrodynamics calculations. It consists of two primary sub-modules, phoenix-math and phoenix-astrodynamics. The mathematics package has a variety of mathematical classes for performing 3D transformations, geometric reasoning, and numerical analysis. The astrodynamics package has various classes and methods for computing locations, attitudes, accesses, and other values useful for general satellite modeling and simulation. Methods for computing celestial locations, such as the location of the Sun and Moon, are also included. Phoenix is meant to be used as a library within the context of a larger application. For example,more » it could be used for a web service, desktop client, or to compute simple values in a scripting environment.« less

PAVE: program for assembling and viewing ESTs.

PubMed

Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

2009-08-26

New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

TOPCAT -- Tool for OPerations on Catalogues And Tables

NASA Astrophysics Data System (ADS)

Taylor, Mark

TOPCAT is an interactive graphical viewer and editor for tabular data. It has been designed for use with astronomical tables such as object catalogues, but is not restricted to astronomical applications. It understands a number of different astronomically important formats, and more formats can be added. It is designed to cope well with large tables; a million rows by a hundred columns should not present a problem even with modest memory and CPU resources. It offers a variety of ways to view and analyse the data, including a browser for the cell data themselves, viewers for information about table and column metadata, tools for joining tables using flexible matching algorithms, and visualisation facilities including histograms, 2- and 3-dimensional scatter plots, and density maps. Using a powerful and extensible Java-based expression language new columns can be defined and row subsets selected for separate analysis. Selecting a row can be configured to trigger an action, for instance displaying an image of the catalogue object in an external viewer. Table data and metadata can be edited and the resulting modified table can be written out in a wide range of output formats. A number of options are provided for loading data from external sources, including Virtual Observatory (VO) services, thus providing a gateway to many remote archives of astronomical data. It can also interoperate with other desktop tools using the SAMP protocol. TOPCAT is written in pure Java and is available under the GNU General Public Licence. Its underlying table processing facilities are provided by STIL, the Starlink Tables Infrastructure Library.

Student Research Projects

NASA Technical Reports Server (NTRS)

Yeske, Lanny A.

1998-01-01

Numerous FY1998 student research projects were sponsored by the Mississippi State University Center for Air Sea Technology. This technical note describes these projects which include research on: (1) Graphical User Interfaces, (2) Master Environmental Library, (3) Database Management Systems, (4) Naval Interactive Data Analysis System, (5) Relocatable Modeling Environment, (6) Tidal Models, (7) Book Inventories, (8) System Analysis, (9) World Wide Web Development, (10) Virtual Data Warehouse, (11) Enterprise Information Explorer, (12) Equipment Inventories, (13) COADS, and (14) JavaScript Technology.

Processable Data Making in the Remote Server Sent by Android Phone as a GIS Data Collecting Tool

NASA Astrophysics Data System (ADS)

Karaagac, Abdullah; Bostancı, Bulent

2016-04-01

Mobile technologies are improving and getting cheaper everyday. Not only smart phones are improved much but also new types of mobile applications and sensors come with the smart phone together. Maps and navigation applications one of the most popular types of applications on these types. Most of these applications uses location services including GNSS, Wi Fi, cellular data and beacon services. Although these coordinate precision not very high, it is appropriate for many applications to utilize. Android is a mobile operating system based on Linux Kernel. It is compatible for varies mobile devices like smart phones, tablets, smart TV's, wearable technologies etc. Android has large capability for application development by using the open source libraries and device sensors like gyroscope, GNSS etc. Android Studio is the most popular integrated development environment (IDE) for Android devices, mainly developing by Google. It had been announced on May 16, 2013 at Google I/O conference. Android Studio is built upon Gradle architecture which is written in Java language. SQLite is a relational database operating system which has so common usage for mobile devices. It developed by using C programming library. It is mostly used via embedding into a software or application. It supports many operating systems including Android. Remote servers can be in several forms from high complexity to simplicity. For this project we will use a open source quad core board computer named Raspberry Pi 2. This device includes 900 MHz ARMv7 compatible quad core CPU, VideoCore IV GPU and 1 GB RAM. Although Raspberry Pi 2's main operating system is Raspbian, we use Debian which are both Linux based operating systems. Raspberry is compatible for many programming language, however some languages are optimized for this device. These are Python, Java, C, C++, Ruby, Perl and Squeak Smalltalk. In this paper, a mobile application will be developed to send coordinate and string data to a SQL database embedded to a remote server. The application will run on Android Operating System running mobile phone. The application will get the location information from the GNSS and cellular data. The user will enter the other information individually. These information will send by clicking a button to remote server which runs SQLite. All these informations will be convertible to any type of measure like type of coordinates could be converted from WGS 84 to ITRF.

Library/Information Science Education, Placement, and Salaries. Guide to Employment Sources in the Library and Information Professions; Placements and Salaries 2000: Plenty of Jobs, Salaries Flat; Accredited Master's Programs in Library and Information Studies; Library Scholarship Sources; Library Scholarship and Award Recipients, 2001.

ERIC Educational Resources Information Center

Davis, Darlena; Terrell, Tom; Gregory, Vicki L.

2002-01-01

Includes five articles that report on employment sources in the library and information professions; placements and salaries, which indicate plenty of jobs and salaries that are flat; accredited master's programs in library and information studies; library scholarship sources; and library scholarship and award recipients. (LRW)

An open source Java web application to build self-contained Web GIS sites

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Ahmed, A.; Chassignet, E.; Zavala-Hidalgo, J.

2014-12-01

This work describes OWGIS, an open source Java web application that creates Web GIS sites by automatically writing HTML and JavaScript code. OWGIS is configured by XML files that define which layers (geographic datasets) will be displayed on the websites. This project uses several Open Geospatial Consortium standards to request data from typical map servers, such as GeoServer, and is also able to request data from ncWMS servers. The latter allows for the displaying of 4D data stored using the NetCDF file format (widely used for storing environmental model datasets). Some of the features available on the sites built with OWGIS are: multiple languages, animations, vertical profiles and vertical transects, color palettes, color ranges, and the ability to download data. OWGIS main users are scientists, such as oceanographers or climate scientists, who store their data in NetCDF files and want to analyze, visualize, share, or compare their data using a website.

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.

Web-based network analysis and visualization using CellMaps

PubMed Central

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-01-01

Summary: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. Availability and Implementation: The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps. The client is implemented in JavaScript and the server in C and Java. Contact: jdopazo@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27296979

Web-based network analysis and visualization using CellMaps.

PubMed

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-10-01

: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps The client is implemented in JavaScript and the server in C and Java. jdopazo@cipf.es Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Chemozart: a web-based 3D molecular structure editor and visualizer platform.

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user-friendly interface is composed. More than 30 packages are used to compose this application which adds enough flexibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (application programming interface). JavaScript libraries which allow creation of web pages containing interactive three-dimensional molecular structures has also been made available. The application has been released under Apache 2 License and is available from the project website https://chemozart.com.

The Importance of Artificial Intelligence for Naval Intelligence Training Simulations

DTIC Science & Technology

2006-09-01

experimental investigation described later. B. SYSTEM ARCHITECTURE The game-based simulator was created using NetBeans , which is an open source integrated...development environment (IDE) written entirely in Java using the NetBeans Platform. NetBeans is based upon the Java language which contains the...involved within the simulation are conducted in a GUI built within the NetBeans IDE. The opening display allows the user to setup the simulation

Employment Sources on the Internet; Placements and Salaries 2001: Salaries Rebound, Women Break Out; Accredited Master's Programs in Library and Information Studies; Library Scholarship Sources; Library Scholarship and Award Recipients, 2002.

ERIC Educational Resources Information Center

Barr, Catherine; Terrell, Tom

2003-01-01

These five articles report on library and information science employment sources on the Internet; librarians' placement and salary trends, including library school graduates, gender differences, and minorities; a list of accredited Mater's programs; a list of library scholarship sources; and a list of library scholarship and award recipients. (LRW)

A component-based problem list subsystem for the HOLON testbed. Health Object Library Online.

PubMed Central

Law, V.; Goldberg, H. S.; Jones, P.; Safran, C.

1998-01-01

One of the deliverables of the HOLON (Health Object Library Online) project is the specification of a reference architecture for clinical information systems that facilitates the development of a variety of discrete, reusable software components. One of the challenges facing the HOLON consortium is determining what kinds of components can be made available in a library for developers of clinical information systems. To further explore the use of component architectures in the development of reusable clinical subsystems, we have incorporated ongoing work in the development of enterprise terminology services into a Problem List subsystem for the HOLON testbed. We have successfully implemented a set of components using CORBA (Common Object Request Broker Architecture) and Java distributed object technologies that provide a functional problem list application and UMLS-based "Problem Picker." Through this development, we have overcome a variety of obstacles characteristic of rapidly emerging technologies, and have identified architectural issues necessary to scale these components for use and reuse within an enterprise clinical information system. PMID:9929252

A component-based problem list subsystem for the HOLON testbed. Health Object Library Online.

PubMed

Law, V; Goldberg, H S; Jones, P; Safran, C

1998-01-01

One of the deliverables of the HOLON (Health Object Library Online) project is the specification of a reference architecture for clinical information systems that facilitates the development of a variety of discrete, reusable software components. One of the challenges facing the HOLON consortium is determining what kinds of components can be made available in a library for developers of clinical information systems. To further explore the use of component architectures in the development of reusable clinical subsystems, we have incorporated ongoing work in the development of enterprise terminology services into a Problem List subsystem for the HOLON testbed. We have successfully implemented a set of components using CORBA (Common Object Request Broker Architecture) and Java distributed object technologies that provide a functional problem list application and UMLS-based "Problem Picker." Through this development, we have overcome a variety of obstacles characteristic of rapidly emerging technologies, and have identified architectural issues necessary to scale these components for use and reuse within an enterprise clinical information system.

Modeling intelligent agent beliefs in a card game scenario

NASA Astrophysics Data System (ADS)

Gołuński, Marcel; Tomanek, Roman; WÄ siewicz, Piotr

In this paper we explore the problem of intelligent agent beliefs. We model agent beliefs using multimodal logics of belief, KD45(m) system implemented as a directed graph depicting Kripke semantics, precisely. We present a card game engine application which allows multiple agents to connect to a given game session and play the card game. As an example simplified version of popular Saboteur card game is used. Implementation was done in Java language using following libraries and applications: Apache Mina, LWJGL.

Direct volumetric rendering based on point primitives in OpenGL.

PubMed

da Rosa, André Luiz Miranda; de Almeida Souza, Ilana; Yuuji Hira, Adilson; Zuffo, Marcelo Knörich

2006-01-01

The aim of this project is to present a renderization by software algorithm of acquired volumetric data. The algorithm was implemented in Java language and the LWJGL graphical library was used, allowing the volume renderization by software and thus preventing the necessity to acquire specific graphical boards for the 3D reconstruction. The considered algorithm creates a model in OpenGL, through point primitives, where each voxel becomes a point with the color values related to this pixel position in the corresponding images.

Programming with Intervals

NASA Astrophysics Data System (ADS)

Matsakis, Nicholas D.; Gross, Thomas R.

Intervals are a new, higher-level primitive for parallel programming with which programmers directly construct the program schedule. Programs using intervals can be statically analyzed to ensure that they do not deadlock or contain data races. In this paper, we demonstrate the flexibility of intervals by showing how to use them to emulate common parallel control-flow constructs like barriers and signals, as well as higher-level patterns such as bounded-buffer producer-consumer. We have implemented intervals as a publicly available library for Java and Scala.

Compressing Test and Evaluation by Using Flow Data for Scalable Network Traffic Analysis

DTIC Science & Technology

2014-10-01

test events, quality of service and other key metrics of military systems and networks are evaluated. Network data captured in standard flow formats...mentioned here. The Ozone Widget Framework (Next Century, n.d.) has proven to be very useful. Also, an extensive, clean, and optimized JavaScript ...library for visualizing many types of data can be found in D3–Data Driven Documents (Bostock, 2013). Quality of Service from Flow Two essential metrics of

Proactive Response to Potential Material Shortages Arising from Environmental Restrictions Using Automatic Discovery and Extraction of Information from Technical Documents

DTIC Science & Technology

2012-12-21

material data and other key information in a UIMA environment. In the course of this project, the tools and methods developed were used to extract and...Architecture ( UIMA ) library from the Apache Software Foundation. Using this architecture, a given document is run through several “annotators” to...material taxonomy developed for the XSB, Inc. Coherent View™ database. In order to integrate this technology into the Java-based UIMA annotation

"gnparser": a powerful parser for scientific names based on Parsing Expression Grammar.

PubMed

Mozzherin, Dmitry Y; Myltsev, Alexander A; Patterson, David J

2017-05-26

Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role. We refer to this as 'parsing' the name. Parsing categorizes name's elements into those that are stable and those that are prone to change. Names are matched first by combining them according to their stable elements. Matches are then refined by examining their varying elements. This two stage process dramatically improves the number and quality of matches. It is especially useful for the automatic data exchange within the context of "Big Data" in biology. We introduce Global Names Parser (gnparser). It is a Java tool written in Scala language (a language for Java Virtual Machine) to parse scientific names. It is based on a Parsing Expression Grammar. The parser can be applied to scientific names of any complexity. It assigns a semantic meaning (such as genus name, species epithet, rank, year of publication, authorship, annotations, etc.) to all elements of a name. It is able to work with nested structures as in the names of hybrids. gnparser performs with ≈99% accuracy and processes 30 million name-strings/hour per CPU thread. The gnparser library is compatible with Scala, Java, R, Jython, and JRuby. The parser can be used as a command line application, as a socket server, a web-app or as a RESTful HTTP-service. It is released under an Open source MIT license. Global Names Parser (gnparser) is a fast, high precision tool for biodiversity informaticians and biologists working with large numbers of scientific names. It can replace expensive and error-prone manual parsing and standardization of scientific names in many situations, and can quickly enhance the interoperability of distributed biological information.

SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript.

PubMed

Bakhtiari, M

2012-06-01

Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems. The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation. The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers. HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox). © 2012 American Association of Physicists in Medicine.

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.

Specification and Error Pattern Based Program Monitoring

NASA Technical Reports Server (NTRS)

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

2001-01-01

We briefly present Java PathExplorer (JPAX), a tool developed at NASA Ames for monitoring the execution of Java programs. JPAX can be used not only during program testing to reveal subtle errors, but also can be applied during operation to survey safety critical systems. The tool facilitates automated instrumentation of a program in order to properly observe its execution. The instrumentation can be either at the bytecode level or at the source level when the source code is available. JPaX is an instance of a more general project, called PathExplorer (PAX), which is a basis for experiments rather than a fixed system, capable of monitoring various programming languages and experimenting with other logics and analysis techniques

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 contained in the Digital Elevation Model (DEM). There is finally a set of tools making up the operational chain to automatically run, monitor and publish SNOWPACK simulations for operational avalanche warning purposes. This tool chain has been developed with the aim of offering very low maintenance operation and very fast deployment and to easily adapt to other avalanche services.

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

SMS Security System on Mobile Devices Using Tiny Encryption Algorithm

NASA Astrophysics Data System (ADS)

Novelan, M. S.; Husein, A. M.; Harahap, M.; Aisyah, S.

2018-04-01

The development of telecommunications technology is so rapid has given such great benefits. With the telecommunication technology, distance and time no longer be a significant obstacle. One of the results of telecommunications technology that is well known is the Short Message Service. In this study developed an application on the mobile phone to modify the SMS message into ciphertext so that the information content of the SMS is not known by others. SMS delivery system for encrypting messages into ciphertext using a key that is entered by the sender then sends to the destination number. SMS reception system to decrypt it to others via SMS without the fear of information from these messages will be known by others. The method used in the system encrypt and decrypt the message is the algorithm Tiny Encryption Algorithm and implemented using the Java programming language. JDK 1.7 as the Java programming language ciphertext into plaintext using the key entered by the receiver and displays the original message to the recipient. This application can be used by someone who wants to send a confidential information and the Java compiler. Eclipse, a Java SDK and the Android SDK as a Java source code editor.

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.

Propel: Tools and Methods for Practical Source Code Model Checking

NASA Technical Reports Server (NTRS)

Mansouri-Samani, Massoud; Mehlitz, Peter; Markosian, Lawrence; OMalley, Owen; Martin, Dale; Moore, Lantz; Penix, John; Visser, Willem

2003-01-01

The work reported here is an overview and snapshot of a project to develop practical model checking tools for in-the-loop verification of NASA s mission-critical, multithreaded programs in Java and C++. Our strategy is to develop and evaluate both a design concept that enables the application of model checking technology to C++ and Java, and a model checking toolset for C++ and Java. The design concept and the associated model checking toolset is called Propel. It builds upon the Java PathFinder (JPF) tool, an explicit state model checker for Java applications developed by the Automated Software Engineering group at NASA Ames Research Center. The design concept that we are developing is Design for Verification (D4V). This is an adaption of existing best design practices that has the desired side-effect of enhancing verifiability by improving modularity and decreasing accidental complexity. D4V, we believe, enhances the applicability of a variety of V&V approaches; we are developing the concept in the context of model checking. The model checking toolset, Propel, is based on extending JPF to handle C++. Our principal tasks in developing the toolset are to build a translator from C++ to Java, productize JPF, and evaluate the toolset in the context of D4V. Through all these tasks we are testing Propel capabilities on customer applications.

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.

SVGMap: configurable image browser for experimental data.

PubMed

Rafael-Palou, Xavier; Schroeder, Michael P; Lopez-Bigas, Nuria

2012-01-01

Spatial data visualization is very useful to represent biological data and quickly interpret the results. For instance, to show the expression pattern of a gene in different tissues of a fly, an intuitive approach is to draw the fly with the corresponding tissues and color the expression of the gene in each of them. However, the creation of these visual representations may be a burdensome task. Here we present SVGMap, a java application that automatizes the generation of high-quality graphics for singular data items (e.g. genes) and biological conditions. SVGMap contains a browser that allows the user to navigate the different images created and can be used as a web-based results publishing tool. SVGMap is freely available as precompiled java package as well as source code at http://bg.upf.edu/svgmap. It requires Java 6 and any recent web browser with JavaScript enabled. The software can be run on Linux, Mac OS X and Windows systems. nuria.lopez@upf.edu

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

PubMed

Rosen, Jebediah; Handy, Kyle; Gillan, André; Smith, Rob

2017-11-06

Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.

Owgis 2.0: Open Source Java Application that Builds Web GIS Interfaces for Desktop Andmobile Devices

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Chassignet, E.; Zavala-Hidalgo, J.; Pandav, H.; Velissariou, P.; Meyer-Baese, A.

2016-12-01

OWGIS is an open source Java and JavaScript application that builds easily configurable Web GIS sites for desktop and mobile devices. The current version of OWGIS generates mobile interfaces based on HTML5 technology and can be used to create mobile applications. The style of the generated websites can be modified using COMPASS, a well known CSS Authoring Framework. In addition, OWGIS uses several Open Geospatial Consortium standards to request datafrom the most common map servers, such as GeoServer. It is also able to request data from ncWMS servers, allowing the websites to display 4D data from NetCDF files. This application is configured by XML files that define which layers, geographic datasets, are displayed on the Web GIS sites. Among other features, OWGIS allows for animations; streamlines from vector data; virtual globe display; vertical profiles and vertical transects; different color palettes; the ability to download data; and display text in multiple languages. OWGIS users are mainly scientists in the oceanography, meteorology and climate fields.

MEMOPS: data modelling and automatic code generation.

PubMed

Fogh, Rasmus H; Boucher, Wayne; Ionides, John M C; Vranken, Wim F; Stevens, Tim J; Laue, Ernest D

2010-03-25

In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces--APIs--currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology.

A quantitative analysis of household energy consumption in rural west Java: with particular emphasis on socio-economic influences

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

Hadi, S.S.

1982-01-01

A survey was conducted to estimate per capita, per household, and total energy consumption by region, by level of development, and by fuel source in rural West Java. Socio-economic conditions were also measured by using parameters that included income, family size, husband education, wife education, biomass fuelstock, level of village development, and land size. These data are tabulated and used to develop a model that can predict probabilities of fuel use, consumption, and variety.

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

Building and Vegetation Rasterization for the Three-dimensional Wind Field (3DWF) Model

DTIC Science & Technology

2010-12-01

Maps API. By design, JavaScript limits access to local resources. This is done to protect against the execution of malicious code. However, ActiveX ...to only use these types of objects ( ActiveX or XPCOM) from a trusted source in order to minimize the exposure of a computer system to malware...Microsoft ActiveX . There is also a need to restructure and rethink the implementation of the JavaScript code. It would be desirable to save the digitized

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.

PubMed

Van Landeghem, Sofie; Van Parys, Thomas; Dubois, Marieke; Inzé, Dirk; Van de Peer, Yves

2016-01-05

Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time. In this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator. Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.

Using a Java Dynamic Tree to manage the terminology in a suite of medical applications.

PubMed

Yang, K; Evens, M W; Trace, D A

2008-01-01

Now that the National Library of Medicine has made SNOMED-CT widely available, we are trying to manage the terminology of a whole suite of medical applications and map our terminology into that in SNOMED. This paper describes the design and implementation of the Java Dynamic Tree that provides structure to our medical terminology and explains how it functions as the core of our system. The tree was designed to reflect the stages in a patient interview, so it contains components for identifying the patient and the provider, a large set of chief complaints, review of systems, physical examination, several history modules, medications, laboratory tests, imaging, and special procedures. The tree is mirrored in a commercial DBMS, which also stores multi-encounter patient data, disorder patterns for our Bayesian diagnostic system, and the data and rules for other expert systems. The DBMS facilitates the import and export of large terminology files. Our Java Dynamic Tree allows the health care provider to view the entire terminology along with the structure that supports it, as well as the mechanism for the generation of progress notes and other documents, in terms of a single hierarchical structure. Changes in terminology can be propagated through the system under the control of the expert. The import/ export facility has been a major help by replacing our original terminology by the terminology in SNOMED-CT.

Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit.

PubMed

Jiang, Chen; Jin, Xi; Dong, Ying; Chen, Ming

2016-06-27

Kekule.js is an open-source, object-oriented JavaScript toolkit for chemoinformatics. It provides methods for many common tasks in molecular informatics, including chemical data input/output (I/O), two- and three-dimensional (2D/3D) rendering of chemical structure, stereo identification, ring perception, structure comparison, and substructure search. Encapsulated widgets to display and edit chemical structures directly in web context are also supplied. Developed with web standards, the toolkit is ideal for building chemoinformatics applications over the Internet. Moreover, it is highly platform-independent and can also be used in desktop or mobile environments. Some initial applications, such as plugins for inputting chemical structures on the web and uses in chemistry education, have been developed based on the toolkit.

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.

EUMIS - an open portal framework for interoperable marine environmental services

NASA Astrophysics Data System (ADS)

Hamre, T.; Sandven, S.; Leadbetter, A.; Gouriou, V.; Dunne, D.; Grant, M.; Treguer, M.; Torget, Ø.

2012-04-01

NETMAR (Open service network for marine environmental data) is an FP7 project that aims to develop a pilot European Marine Information System (EUMIS) for searching, downloading and integrating satellite, in situ and model data from ocean and coastal areas. EUMIS will use a semantic framework coupled with ontologies for identifying and accessing distributed data, such as near-real time, forecast and historical data. Four pilots have been defined to clarify the needs for satellite, in situ and model based products and services in selected user communities. The pilots are: · Pilot 1: Arctic Sea Ice Monitoring and Forecasting · Pilot 2: Oil spill drift forecast and shoreline cleanup assessment services in France · Pilot 3: Ocean colour - Marine Ecosystem, Research and Monitoring · Pilot 4: International Coastal Atlas Network (ICAN) for coastal zone management NETMAR is developing a set of data delivery services for the targeted user communities by means of standard web-GIS and OPeNDAP protocols. Processing services and adaptive service chaining services will also be developed, to enable users to generate new products suited to their needs. Both data retrieved from online repositories as well as the products generated dynamically can be accessed and visualised in the EUMIS portal. For this purpose, a GIS Viewer, a Service Chaining Editor and a Ontology Browser/Discovery Client have been developed and integrated in EUMIS. The EUMIS portal is developed using a portal framework that is compliant with the JSR-168 (Java Portlet Specification 1.0) and JSR-286 (Java Portlet Specification, 2.0) standards. These standards defines the interface (contract) and lifecycle management for a portal system component, a portlet, which can be implemented in a number of programming languages, not only Java. The GIS Viewer is developed using a combination of Java, JavaScript and JSF (e.g. MapFaces). The Service chaining editor is implemented in JavaScript (using different libraries like jQuery and WireIt), and the Ontology Browser/Discovery Client by means of Adobe Flex. In addition to the portlets developed in the project, we have also used several of the pre-built portlets that come with the Liferay Community Edition portal framework, notably the wiki, forum and RSS feed portlets. The presentation will focus on the developed system components and show some examples of products and services from the defined pilots.

Polyglot Programming in Applications Used for Genetic Data Analysis

PubMed Central

Nowak, Robert M.

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

Polyglot programming in applications used for genetic data analysis.

PubMed

Nowak, Robert M

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

XMM-Newton Mobile Web Application

NASA Astrophysics Data System (ADS)

Ibarra, A.; Kennedy, M.; Rodríguez, P.; Hernández, C.; Saxton, R.; Gabriel, C.

2013-10-01

We present the first XMM-Newton web mobile application, coded using new web technologies such as HTML5, the Query mobile framework, and D3 JavaScript data-driven library. This new web mobile application focuses on re-formatted contents extracted directly from the XMM-Newton web, optimizing the contents for mobile devices. The main goals of this development were to reach all kind of handheld devices and operating systems, while minimizing software maintenance. The application therefore has been developed as a web mobile implementation rather than a more costly native application. New functionality will be added regularly.

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

Nested generalized linear mixed model with ordinal response: Simulation and application on poverty data in Java Island

NASA Astrophysics Data System (ADS)

Widyaningsih, Yekti; Saefuddin, Asep; Notodiputro, Khairil A.; Wigena, Aji H.

2012-05-01

The objective of this research is to build a nested generalized linear mixed model using an ordinal response variable with some covariates. There are three main jobs in this paper, i.e. parameters estimation procedure, simulation, and implementation of the model for the real data. At the part of parameters estimation procedure, concepts of threshold, nested random effect, and computational algorithm are described. The simulations data are built for 3 conditions to know the effect of different parameter values of random effect distributions. The last job is the implementation of the model for the data about poverty in 9 districts of Java Island. The districts are Kuningan, Karawang, and Majalengka chose randomly in West Java; Temanggung, Boyolali, and Cilacap from Central Java; and Blitar, Ngawi, and Jember from East Java. The covariates in this model are province, number of bad nutrition cases, number of farmer families, and number of health personnel. In this modeling, all covariates are grouped as ordinal scale. Unit observation in this research is sub-district (kecamatan) nested in district, and districts (kabupaten) are nested in province. For the result of simulation, ARB (Absolute Relative Bias) and RRMSE (Relative Root of mean square errors) scale is used. They show that prov parameters have the highest bias, but more stable RRMSE in all conditions. The simulation design needs to be improved by adding other condition, such as higher correlation between covariates. Furthermore, as the result of the model implementation for the data, only number of farmer family and number of medical personnel have significant contributions to the level of poverty in Central Java and East Java province, and only district 2 (Karawang) of province 1 (West Java) has different random effect from the others. The source of the data is PODES (Potensi Desa) 2008 from BPS (Badan Pusat Statistik).

HMMER web server: 2018 update.

PubMed

Potter, Simon C; Luciani, Aurélien; Eddy, Sean R; Park, Youngmi; Lopez, Rodrigo; Finn, Robert D

2018-06-14

The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite (http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has been expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into third-party websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

The July 17, 2006 Java Tsunami: Tsunami Modeling and the Probable Causes of the Extreme Run-up

NASA Astrophysics Data System (ADS)

Kongko, W.; Schlurmann, T.

2009-04-01

On 17 July 2006, an Earthquake magnitude Mw 7.8 off the south coast of west Java, Indonesia generated tsunami that affected over 300 km of south Java coastline and killed more than 600 people. Observed tsunami heights and field measurement of run-up distributions were uniformly scattered approximately 5 to 7 m along a 200 km coastal stretch; remarkably, a locally focused tsunami run-up height exceeding 20 m at Nusakambangan Island has been observed. Within the framework of the German Indonesia Tsunami Early Warning System (GITEWS) Project, a high-resolution near-shore bathymetrical survey equipped by multi-beam echo-sounder has been recently conducted. Additional geodata have been collected using Intermap Technologies STAR-4 airborne interferometric SAR data acquisition system on a 5 m ground sample distance basis in order to establish a most-sophisticated Digital Terrain Model (DTM). This paper describes the outcome of tsunami modelling approaches using high resolution data of bathymetry and topography being part of a general case study in Cilacap, Indonesia, and medium resolution data for other area along coastline of south Java Island. By means of two different seismic deformation models to mimic the tsunami source generation, a numerical code based on the 2D nonlinear shallow water equations is used to simulate probable tsunami run-up scenarios. Several model tests are done and virtual points in offshore, near-shore, coastline, as well as tsunami run-up on the coast are collected. For the purpose of validation, the model results are compared with field observations and sea level data observed at several tide gauges stations. The performance of numerical simulations and correlations with observed field data are highlighted, and probable causes for the extreme wave heights and run-ups are outlined. References Ammon, C.J., Kanamori, K., Lay, T., and Velasco, A., 2006. The July 2006 Java Tsunami Earthquake, Geophysical Research Letters, 33(L24308). Fritz, H.M., Kongko, W., Moore, A., McAdoo, B., Goff, J., Harbitz, C., Uslu, B., Kalligeris, N., Suteja, D., Kalsum, K., Titov, V., Gusman, A., Latief, H., Santoso, E., Sujoko, S., Djulkarnaen, D., Sunendar, H., and Synolakis, C., 2007. Extreme Run-up from the 17 July 2006 Java Tsunami. Geophysical Research Letters, 34(L12602). Fujii, Y., and Satake, K., 2006. Source of the July 2006 Java Tsunami Estimated from Tide Gauge Records. Geophysical Research Letters, 33(L23417). Intermap Federal Services Inc., 2007. Digital Terrain Model Cilacap, version 1. Project of GITEWS, DLR Germany. Kongko, W., and Leschka, S., 2008. Nearshore Bathymetry Measurements in Indonesia: Part 1. Cilacap, Technical Report, DHI-WASY GmbH Syke Germany. Kongko, W., Suranto, Chaeroni, Aprijanto, Zikra, and SUjantoko, 2006, Rapid Survey on Tsunami Jawa 17 July 2006, http://nctr.pmel.noaa.gov/java20060717/tsunami-java170706_e.pdf Lavigne, F., Gomes, C., Giffo, M., Wassmer, P., Hoebreck, C., Mardiatno, D., Prioyono, J., and Paris R., 2007. Field Observation of the 17 July 2006 Tsunami in Java. Natural Hazards and Earth Systems Sciences, 7: 177-183.

Sources for Selecting School Library Resource Materials.

ERIC Educational Resources Information Center

Friderichsen, Blanche

A Department of Education publication on an integrated program for Alberta school libraries, this document recommends the use of specific material selection sources designed to aid schools in developing their library collections. Materials are listed in the following sections: (1) Sources for Selecting School Library Resource Materials; (2)…

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.

Modular Chemical Descriptor Language (MCDL): Stereochemical modules

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

Gakh, Andrei A; Burnett, Michael N; Trepalin, Sergei V.

2011-01-01

In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDLmore » processing module software packages. Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.« less

A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.

PubMed

Tregouet, D A; Garelle, V

2007-04-15

THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.

Next Generation Transport Phenomenology Model

NASA Technical Reports Server (NTRS)

Strickland, Douglas J.; Knight, Harold; Evans, J. Scott

2004-01-01

This report describes the progress made in Quarter 3 of Contract Year 3 on the development of Aeronomy Phenomenology Modeling Tool (APMT), an open-source, component-based, client-server architecture for distributed modeling, analysis, and simulation activities focused on electron and photon transport for general atmospheres. In the past quarter, column emission rate computations were implemented in Java, preexisting Fortran programs for computing synthetic spectra were embedded into APMT through Java wrappers, and work began on a web-based user interface for setting input parameters and running the photoelectron and auroral electron transport models.

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.

Web-based encyclopedia on physical effects

NASA Astrophysics Data System (ADS)

Papliatseyeu, Andrey; Repich, Maryna; Ilyushonak, Boris; Hurbo, Aliaksandr; Makarava, Katerina; Lutkovski, Vladimir M.

2004-07-01

Web-based learning applications open new horizons for educators. In this work we present the computer encyclopedia designed to overcome drawbacks of traditional paper information sources such as awkward search, low update rate, limited copies count and high cost. Moreover, we intended to improve access and search functions in comparison with some Internet sources in order to make it more convenient. The system is developed using modern Java technologies (Jave Servlets, Java Server Pages) and contains systemized information about most important and explored physical effects. It also may be used in other fields of science. The system is accessible via Intranet/Internet networks by means of any up-to-date Internet browser. It may be used for general learning purposes and as a study guide or tutorial for performing laboratory works.

Library/Information Science Education, Placement, and Salaries.

ERIC Educational Resources Information Center

Davis, Darlena; Gregory, Vicki L.; Wohlmuth, Sonia Ramirez

2001-01-01

Includes five articles: a guide to employment sources in the library and information professions, including the Internet, library joblines, specialized associations, state agencies, and overseas exchange programs; placements and salaries in 1999; accredited master's programs in library and information studies; library scholarship sources; and…

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…

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

McKisson, John

The source code for the Java Data Acquisition suite provides interfaces to the JLab built USB FPGA ADC across a LAN network. Each jDaq node provides ListMode data from JLab built detector systems and readouts.

X-Windows PVT Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

The X-Windows Process Validation Table (PVT) Widget Class ( Class is used here in the object-oriented-programming sense of the word) was devised to simplify the task of implementing network registration services for Information Sharing Protocol (ISP) graphical-user-interface (GUI) computer programs. Heretofore, ISP PVT programming tasks have required many method calls to identify, query, and interpret the connections and messages exchanged between a client and a PVT server. Normally, programmers have utilized direct access to UNIX socket libraries to implement the PVT protocol queries, necessitating the use of many lines of source code to perform frequent tasks. Now, the X-Windows PVT Widget Class encapsulates ISP client server network registration management tasks within the framework of an X Windows widget. Use of the widget framework enables an X Windows GUI program to interact with PVT services in an abstract way and in the same manner as that of other graphical widgets, making it easier to program PVT clients. Wrapping the PVT services inside the widget framework enables a programmer to treat a PVT server interface as though it were a GUI. Moreover, an alternate subclass could implement another service in a widget of the same type. This program was written by Matthew R. Barry of United Space Alliance for Johnson Space Center. For further information, contact the Johnson Technology Transfer Office at (281) 483-3809. MSC-23582 Shuttle Data Center File- Processing Tool in Java A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

Astronomical Image Processing with Hadoop

NASA Astrophysics Data System (ADS)

Wiley, K.; Connolly, A.; Krughoff, S.; Gardner, J.; Balazinska, M.; Howe, B.; Kwon, Y.; Bu, Y.

2011-07-01

In the coming decade astronomical surveys of the sky will generate tens of terabytes of images and detect hundreds of millions of sources every night. With a requirement that these images be analyzed in real time to identify moving sources such as potentially hazardous asteroids or transient objects such as supernovae, these data streams present many computational challenges. In the commercial world, new techniques that utilize cloud computing have been developed to handle massive data streams. In this paper we describe how cloud computing, and in particular the map-reduce paradigm, can be used in astronomical data processing. We will focus on our experience implementing a scalable image-processing pipeline for the SDSS database using Hadoop (http://hadoop.apache.org). This multi-terabyte imaging dataset approximates future surveys such as those which will be conducted with the LSST. Our pipeline performs image coaddition in which multiple partially overlapping images are registered, integrated and stitched into a single overarching image. We will first present our initial implementation, then describe several critical optimizations that have enabled us to achieve high performance, and finally describe how we are incorporating a large in-house existing image processing library into our Hadoop system. The optimizations involve prefiltering of the input to remove irrelevant images from consideration, grouping individual FITS files into larger, more efficient indexed files, and a hybrid system in which a relational database is used to determine the input images relevant to the task. The incorporation of an existing image processing library, written in C++, presented difficult challenges since Hadoop is programmed primarily in Java. We will describe how we achieved this integration and the sophisticated image processing routines that were made feasible as a result. We will end by briefly describing the longer term goals of our work, namely detection and classification of transient objects and automated object classification.

D Virtual CH Interactive Information Systems for a Smart Web Browsing Experience for Desktop Pcs and Mobile Devices

NASA Astrophysics Data System (ADS)

Scianna, A.; La Guardia, M.

2018-05-01

Recently, the diffusion of knowledge on Cultural Heritage (CH) has become an element of primary importance for its valorization. At the same time, the diffusion of surveys based on UAV Unmanned Aerial Vehicles (UAV) technologies and new methods of photogrammetric reconstruction have opened new possibilities for 3D CH representation. Furthermore the recent development of faster and more stable internet connections leads people to increase the use of mobile devices. In the light of all this, the importance of the development of Virtual Reality (VR) environments applied to CH is strategic for the diffusion of knowledge in a smart solution. In particular, the present work shows how, starting from a basic survey and the further photogrammetric reconstruction of a cultural good, is possible to built a 3D CH interactive information system useful for desktop and mobile devices. For this experimentation the Arab-Norman church of the Trinity of Delia (in Castelvetrano-Sicily-Italy) has been adopted as case study. The survey operations have been carried out considering different rapid methods of acquisition (UAV camera, SLR camera and smartphone camera). The web platform to publish the 3D information has been built using HTML5 markup language and WebGL JavaScript libraries (Three.js libraries). This work presents the construction of a 3D navigation system for a web-browsing of a virtual CH environment, with the integration of first person controls and 3D popup links. This contribution adds a further step to enrich the possibilities of open-source technologies applied to the world of CH valorization on web.

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

Automated Source-Code-Based Testing of Object-Oriented Software

NASA Astrophysics Data System (ADS)

Gerlich, Ralf; Gerlich, Rainer; Dietrich, Carsten

2014-08-01

With the advent of languages such as C++ and Java in mission- and safety-critical space on-board software, new challenges for testing and specifically automated testing arise. In this paper we discuss some of these challenges, consequences and solutions based on an experiment in automated source- code-based testing for C++.

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.

Bioaccumulation of Copper (Cu) and Chromium (Cr) on export comodity vanamei shrimp from Karawang, West Java

NASA Astrophysics Data System (ADS)

Rahman, A.; Takarina, N. D.; Siswantining, T.; Pin, T. G.; Soedjiarti, T.

2018-05-01

Karawang is one of regencies in West Java which has great potential for vannamei culture. The farm here was modern farm and using Citarum River as water source. Human activities like household and industry around the river cause its quality decrease and give negative impact to shrimp farm. This research was aimed to investigate the bioaccumulation of copper (Cu) and chromium (Cr) on vannamei shrimp from Karawang, West Java. Amount of shrimp’s meat and carapace were used for heavy metal measurement using Atomic Absorption Specthrophotometry. Result showed that contents of copper both in meat and carapace were higher than content of chromium. Moreover, the content of both metals was higher on carapace compared to meat. Since the content of meat were below threshold, so it is safe for consumption. There is no significant difference content of both metals in carapace.

Rupture evolution of the 2006 Java tsunami earthquake and the possible role of splay faults

NASA Astrophysics Data System (ADS)

Fan, Wenyuan; Bassett, Dan; Jiang, Junle; Shearer, Peter M.; Ji, Chen

2017-11-01

The 2006 Mw 7.8 Java earthquake was a tsunami earthquake, exhibiting frequency-dependent seismic radiation along strike. High-frequency global back-projection results suggest two distinct rupture stages. The first stage lasted ∼65 s with a rupture speed of ∼1.2 km/s, while the second stage lasted from ∼65 to 150 s with a rupture speed of ∼2.7 km/s. High-frequency radiators resolved with back-projection during the second stage spatially correlate with splay fault traces mapped from residual free-air gravity anomalies. These splay faults also colocate with a major tsunami source associated with the earthquake inferred from tsunami first-crest back-propagation simulation. These correlations suggest that the splay faults may have been reactivated during the Java earthquake, as has been proposed for other tsunamigenic earthquakes, such as the 1944 Mw 8.1 Tonankai earthquake in the Nankai Trough.

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 location of a proposed subducting seamount. This correlation is less clear along the southern Sumatran segment. One longer duration event is located within the high slip area of the Mw=8.4 2007 rupture, while another is located in the weakly coupled region of the 1935 Mw=7.7 rupture area.

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.

Point Analysis in Java applied to histological images of the perforant pathway: a user's account.

PubMed

Scorcioni, Ruggero; Wright, Susan N; Patrick Card, J; Ascoli, Giorgio A; Barrionuevo, Germán

2008-01-01

The freeware Java tool Point Analysis in Java (PAJ), created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (x2 objective) comprised the entire perforant pathway, while the high magnification set (x100 objective) allowed the identification of individual fibers. A preliminary stereological study revealed a striking linear relationship between the fiber count at high magnification and the optical density at low magnification. PAJ enabled fast analysis for down-sampled data sets and a friendly interface with automated plot drawings. Noted strengths included the multi-platform support as well as the free availability of the source code, conducive to a broad user base and maximum flexibility for ad hoc requirements. PAJ has great potential to extend its usability by (a) improving its graphical user interface, (b) increasing its input size limit, (c) improving response time for large data sets, and (d) potentially being integrated with other Java graphical tools such as ImageJ.

JaxoDraw: A graphical user interface for drawing Feynman diagrams

NASA Astrophysics Data System (ADS)

Binosi, D.; Theußl, L.

2004-08-01

JaxoDraw is a Feynman graph plotting tool written in Java. It has a complete graphical user interface that allows all actions to be carried out via mouse click-and-drag operations in a WYSIWYG fashion. Graphs may be exported to postscript/EPS format and can be saved in XML files to be used for later sessions. One of JaxoDraw's main features is the possibility to create ? code that may be used to generate graphics output, thus combining the powers of ? with those of a modern day drawing program. With JaxoDraw it becomes possible to draw even complicated Feynman diagrams with just a few mouse clicks, without the knowledge of any programming language. Program summaryTitle of program: JaxoDraw Catalogue identifier: ADUA Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUA Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar gzip file Operating system: Any Java-enabled platform, tested on Linux, Windows ME, XP, Mac OS X Programming language used: Java License: GPL Nature of problem: Existing methods for drawing Feynman diagrams usually require some 'hard-coding' in one or the other programming or scripting language. It is not very convenient and often time consuming, to generate relatively simple diagrams. Method of solution: A program is provided that allows for the interactive drawing of Feynman diagrams with a graphical user interface. The program is easy to learn and use, produces high quality output in several formats and runs on any operating system where a Java Runtime Environment is available. Number of bytes in distributed program, including test data: 2 117 863 Number of lines in distributed program, including test data: 60 000 Restrictions: Certain operations (like internal latex compilation, Postscript preview) require the execution of external commands that might not work on untested operating systems. Typical running time: As an interactive program, the running time depends on the complexity of the diagram to be drawn.

S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data.

PubMed

López-Fernández, Hugo; Araújo, José E; Jorge, Susana; Glez-Peña, Daniel; Reboiro-Jato, Miguel; Santos, Hugo M; Fdez-Riverola, Florentino; Capelo, José L

2018-03-01

2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Pedagogy and Primary Sources: Outcomes of the Library of Congress' Professional Development Program, Teaching with Primary Sources at Loyola

ERIC Educational Resources Information Center

Fry, Michelle L.

2010-01-01

Until recently, few K-12 teachers outside of social studies have integrated primary sources in classroom instruction. Integrating primary sources in educational practice does require an uncommon pedagogical understanding. Addressing this K-12 educator need is the Library of Congress. Recently, the Library implemented a national educator…

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

PubMed

Robinson, Oscar; Dylus, David; Dessimoz, Christophe

2016-08-01

Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.

PubMed

Smelter, Andrey; Astra, Morgan; Moseley, Hunter N B

2017-03-17

The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis. To aid in the use of this public resource, we have developed a package called nmrstarlib in the popular open-source programming language Python. The nmrstarlib's implementation is very efficient, both in design and execution. The library has facilities for reading and writing both NMR-STAR version 2.1 and 3.1 formatted files, parsing them into usable Python dictionary- and list-based data structures, making access and manipulation of the experimental data very natural within Python programs (i.e. "saveframe" and "loop" records represented as individual Python dictionary data structures). Another major advantage of this design is that data stored in original NMR-STAR can be easily converted into its equivalent JavaScript Object Notation (JSON) format, a lightweight data interchange format, facilitating data access and manipulation using Python and any other programming language that implements a JSON parser/generator (i.e., all popular programming languages). We have also developed tools to visualize assigned chemical shift values and to convert between NMR-STAR and JSONized NMR-STAR formatted files. Full API Reference Documentation, User Guide and Tutorial with code examples are also available. We have tested this new library on all current BMRB entries: 100% of all entries are parsed without any errors for both NMR-STAR version 2.1 and version 3.1 formatted files. We also compared our software to three currently available Python libraries for parsing NMR-STAR formatted files: PyStarLib, NMRPyStar, and PyNMRSTAR. The nmrstarlib package is a simple, fast, and efficient library for accessing data from the BMRB. The library provides an intuitive dictionary-based interface with which Python programs can read, edit, and write NMR-STAR formatted files and their equivalent JSONized NMR-STAR files. The nmrstarlib package can be used as a library for accessing and manipulating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STAR file format into its equivalent JSON file format and vice versa, and to visualize chemical shift values. Furthermore, the nmrstarlib implementation provides a guide for effectively JSONizing other older scientific formats, improving the FAIRness of data in these formats.

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

Beginning a few thousand years ago, global climate and environmental change have become more and more affected by human activities. Hence, quantifying the 'human component' becomes increasingly important in order to predict future developments. Indonesia and the surrounding oceans are key in this respect, because it is in the region (i) that receives the highest inputs of water, sediment and associated dissolved and particulate substances and (ii) that suffers from anthropogenically modified landscapes and coastal zones. As opposing the global trend, land-based human activities have increased the sediment input into the ocean from Indonesia since pre-human times. Nevertheless, there are strong gradients in land use/cover and resulting river fluxes within Indonesia as, for example, between Java and Kalimantan. Major goal of this study is to identify the contribution of human activities in river catchments (i.e. land use/cover change, hydrological alterations) to gradients in carbon and nitrogen deposition in sediments of the Java Sea between densely populated Java and sparsely populated Kalimantan during the Late Holocene. We hypothesized that the riverine input of C and N increased during the late Holocene and increased more off Java than off Kalimantan. Sediment cores (80 to 130 cm long) off major river mouths from Java (2 cores off Bengawan Solo) and Kalimantan (1 core off Pembuang, 1 core off Jelai) were dated and analysed for Corg, Ntot, carbonate and stable isotope composition (δ13Corg, δ15N) in 3 cm intervals. Sedimentation rates off the Kalimantan rivers with 0.05-0.11 cm yr-1 were higher than off the Bengawan Solo, the largest river catchment on Java (<0.04 cm yr-1). Ntot contents in all sediment cores were low with ~0.07% and varied little over time. A higher Corg content, molar C/N ratio and variability over the past 5000 years in all parameters in the core closer to the river mouth off the Bengawan Solo than the one further offshore indicates that 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.

ODI - Portal, Pipeline, and Archive (ODI-PPA): a web-based astronomical compute archive, visualization, and analysis service

NASA Astrophysics Data System (ADS)

Gopu, Arvind; Hayashi, Soichi; Young, Michael D.; Harbeck, Daniel R.; Boroson, Todd; Liu, Wilson; Kotulla, Ralf; Shaw, Richard; Henschel, Robert; Rajagopal, Jayadev; Stobie, Elizabeth; Knezek, Patricia; Martin, R. Pierre; Archbold, Kevin

2014-07-01

The One Degree Imager-Portal, Pipeline, and Archive (ODI-PPA) is a web science gateway that provides astronomers a modern web interface that acts as a single point of access to their data, and rich computational and visualization capabilities. Its goal is to support scientists in handling complex data sets, and to enhance WIYN Observatory's scientific productivity beyond data acquisition on its 3.5m telescope. ODI-PPA is designed, with periodic user feedback, to be a compute archive that has built-in frameworks including: (1) Collections that allow an astronomer to create logical collations of data products intended for publication, further research, instructional purposes, or to execute data processing tasks (2) Image Explorer and Source Explorer, which together enable real-time interactive visual analysis of massive astronomical data products within an HTML5 capable web browser, and overlaid standard catalog and Source Extractor-generated source markers (3) Workflow framework which enables rapid integration of data processing pipelines on an associated compute cluster and users to request such pipelines to be executed on their data via custom user interfaces. ODI-PPA is made up of several light-weight services connected by a message bus; the web portal built using Twitter/Bootstrap, AngularJS and jQuery JavaScript libraries, and backend services written in PHP (using the Zend framework) and Python; it leverages supercomputing and storage resources at Indiana University. ODI-PPA is designed to be reconfigurable for use in other science domains with large and complex datasets, including an ongoing offshoot project for electron microscopy data.

Lowering the Barrier to Cross-Disciplinary Scientific Data Access via a Brokering Service Built Around a Unified Data Model

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Wilson, A.

2012-12-01

The steps many scientific data users go through to use data (after discovering it) can be rather tedious, even when dealing with datasets within their own discipline. Accessing data across domains often seems intractable. We present here, LaTiS, an Open Source brokering solution that bridges the gap between the source data and the user's code by defining a unified data model plus a plugin framework for "adapters" to read data from their native source, "filters" to perform server side data processing, and "writers" to output any number of desired formats or streaming protocols. A great deal of work is being done in the informatics community to promote multi-disciplinary science with a focus on search and discovery based on metadata - information about the data. The goal of LaTiS is to go that last step to provide a uniform interface to read the dataset into computer programs and other applications once it has been identified. The LaTiS solution for integrating a wide variety of data models is to return to mathematical fundamentals. The LaTiS data model emphasizes functional relationships between variables. For example, a time series of temperature measurements can be thought of as a function that maps a time to a temperature. With just three constructs: "Scalar" for a single variable, "Tuple" for a collection of variables, and "Function" to represent a set of independent and dependent variables, the LaTiS data model can represent most scientific datasets at a low level that enables uniform data access. Higher level abstractions can be built on top of the basic model to add more meaningful semantics for specific user communities. LaTiS defines its data model in terms of the Unified Modeling Language (UML). It also defines a very thin Java Interface that can be implemented by numerous existing data interfaces (e.g. NetCDF-Java) such that client code can access any dataset via the Java API, independent of the underlying data access mechanism. LaTiS also provides a reference implementation of the data model and server framework (with a RESTful service interface) in the Scala programming language. Scala can be thought of as the next generation of Java. It runs on the Java Virtual Machine and can directly use Java code. Scala improves upon Java's object-oriented capabilities and adds support for functional programming paradigms which are particularly well suited for scientific data analysis. The Scala implementation of LaTiS can be thought of as a Domain Specific Language (DSL) which presents an API that better matches the semantics of the problems scientific data users are trying to solve. Instead of working with bytes, ints, or arrays, the data user can directly work with data as "time series" or "spectra". LaTiS provides many layers of abstraction with which users can interact to support a wide variety of data access and analysis needs.

XML schemas for common bioinformatic data types and their application in workflow systems.

PubMed

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed.

PubMed

Moore, D F; Harwood, V J; Ferguson, D M; Lukasik, J; Hannah, P; Getrich, M; Brownell, M

2005-01-01

The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sources of faecal bacterial pollution in an urban southern California watershed was determined using blinded proficiency samples. Antibiotic resistance patterns and HindIII ribotypes of Escherichia coli (n = 997), and antibiotic resistance patterns of Enterococcus spp. (n = 3657) were used to construct libraries from sewage samples and from faeces of seagulls, dogs, cats, horses and humans within the watershed. The three libraries were analysed to determine the accuracy of host source prediction. The internal accuracy of the libraries (average rate of correct classification, ARCC) with six source categories was 44% for E. coli ARA, 69% for E. coli ribotyping and 48% for Enterococcus ARA. Each library's predictive ability towards isolates that were not part of the library was determined using a blinded proficiency panel of 97 E. coli and 99 Enterococcus isolates. Twenty-eight per cent (by ARA) and 27% (by ribotyping) of the E. coli proficiency isolates were assigned to the correct source category. Sixteen per cent were assigned to the same source category by both methods, and 6% were assigned to the correct category. Addition of 2480 E. coli isolates to the ARA library did not improve the ARCC or proficiency accuracy. In contrast, 45% of Enterococcus proficiency isolates were correctly identified by ARA. None of the methods performed well enough on the proficiency panel to be judged ready for application to environmental samples. Most microbial source tracking (MST) studies published have demonstrated library accuracy solely by the internal ARCC measurement. Low rates of correct classification for E. coli proficiency isolates compared with the ARCCs of the libraries indicate that testing of bacteria from samples that are not represented in the library, such as blinded proficiency samples, is necessary to accurately measure predictive ability. The library-based MST methods used in this study may not be suited for determination of the source(s) of faecal pollution in large, urban watersheds.

P and S velocity structure of the crust and the upper mantle beneath central Java from local tomography inversion

NASA Astrophysics Data System (ADS)

Koulakov, I.; Bohm, M.; Asch, G.; Lühr, B.-G.; Manzanares, A.; Brotopuspito, K. S.; Fauzi, Pak; Purbawinata, M. A.; Puspito, N. T.; Ratdomopurbo, A.; Kopp, H.; Rabbel, W.; Shevkunova, E.

2007-08-01

Here we present the results of local source tomographic inversion beneath central Java. The data set was collected by a temporary seismic network. More than 100 stations were operated for almost half a year. About 13,000 P and S arrival times from 292 events were used to obtain three-dimensional (3-D) Vp, Vs, and Vp/Vs models of the crust and the mantle wedge beneath central Java. Source location and determination of the 3-D velocity models were performed simultaneously based on a new iterative tomographic algorithm, LOTOS-06. Final event locations clearly image the shape of the subduction zone beneath central Java. The dipping angle of the slab increases gradually from almost horizontal to about 70°. A double seismic zone is observed in the slab between 80 and 150 km depth. The most striking feature of the resulting P and S models is a pronounced low-velocity anomaly in the crust, just north of the volcanic arc (Merapi-Lawu anomaly (MLA)). An algorithm for estimation of the amplitude value, which is presented in the paper, shows that the difference between the fore arc and MLA velocities at a depth of 10 km reaches 30% and 36% in P and S models, respectively. The value of the Vp/Vs ratio inside the MLA is more than 1.9. This shows a probable high content of fluids and partial melts within the crust. In the upper mantle we observe an inclined low-velocity anomaly which links the cluster of seismicity at 100 km depth with MLA. This anomaly might reflect ascending paths of fluids released from the slab. The reliability of all these patterns was tested thoroughly.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.

PubMed

de Andrade, Roberto R S; Vaslin, Maite F S

2014-03-07

Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

PubMed Central

2014-01-01

Background Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. Methods In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. Results The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. Conclusions SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. Availability and implementation SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/. PMID:24607237

The Systems Function. SPEC Kit 29.

ERIC Educational Resources Information Center

Association of Research Libraries, Washington, DC. Office of Management Studies.

This kit on the systems functions in Association of Research Libraries (ARL) member institutions contains 10 source documents from ARL libraries and a summary of data from a 1976 survey on the organization, staffing, and operation of library systems functions. Source documents include: (1) "Library Systems Office Annual Report, 1974-75"…

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

PubMed

Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin

2014-07-01

The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu. © The Author 2014. Published by Oxford University Press.

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

PubMed

Bunk, Boyke; Kucklick, Martin; Jonas, Rochus; Münch, Richard; Schobert, Max; Jahn, Dieter; Hiller, Karsten

2006-12-01

MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

Uncertainty visualisation in the Model Web

NASA Astrophysics Data System (ADS)

Gerharz, L. E.; Autermann, C.; Hopmann, H.; Stasch, C.; Pebesma, E.

2012-04-01

Visualisation of geospatial data as maps is a common way to communicate spatially distributed information. If temporal and furthermore uncertainty information are included in the data, efficient visualisation methods are required. For uncertain spatial and spatio-temporal data, numerous visualisation methods have been developed and proposed, but only few tools for visualisation of data in a standardised way exist. Furthermore, usually they are realised as thick clients, and lack functionality of handling data coming from web services as it is envisaged in the Model Web. We present an interactive web tool for visualisation of uncertain spatio-temporal data developed in the UncertWeb project. The client is based on the OpenLayers JavaScript library. OpenLayers provides standard map windows and navigation tools, i.e. pan, zoom in/out, to allow interactive control for the user. Further interactive methods are implemented using jStat, a JavaScript library for statistics plots developed in UncertWeb, and flot. To integrate the uncertainty information into existing standards for geospatial data, the Uncertainty Markup Language (UncertML) was applied in combination with OGC Observations&Measurements 2.0 and JavaScript Object Notation (JSON) encodings for vector and NetCDF for raster data. The client offers methods to visualise uncertain vector and raster data with temporal information. Uncertainty information considered for the tool are probabilistic and quantified attribute uncertainties which can be provided as realisations or samples, full probability distributions functions and statistics. Visualisation is supported for uncertain continuous and categorical data. In the client, the visualisation is realised using a combination of different methods. Based on previously conducted usability studies, a differentiation between expert (in statistics or mapping) and non-expert users has been indicated as useful. Therefore, two different modes are realised together in the tool: (i) adjacent maps showing data and uncertainty separately, and (ii) multidimensional mapping providing different visualisation methods in combination to explore the spatial, temporal and uncertainty distribution of the data. Adjacent maps allow a simpler visualisation by separating value and uncertainty maps for non-experts and a first overview. The multidimensional approach allows a more complex exploration of the data for experts by browsing through the different dimensions. It offers the visualisation of maps, statistic plots and time series in different windows and sliders to interactively move through time, space and uncertainty (thresholds).

[Central online quality assurance in radiology: an IT solution exemplified by the German Breast Cancer Screening Program].

PubMed

Czwoydzinski, J; Girnus, R; Sommer, A; Heindel, W; Lenzen, H

2011-09-01

Physical-technical quality assurance is one of the essential tasks of the National Reference Centers in the German Breast Cancer Screening Program. For this purpose the mammography units are required to transfer the measured values of the constancy tests on a daily basis and all phantom images created for this purpose on a weekly basis to the reference centers. This is a serious logistical challenge. To meet these requirements, we developed an innovative software tool. By the end of 2005, we had already developed web-based software (MammoControl) allowing the transmission of constancy test results via entry forms. For automatic analysis and transmission of the phantom images, we then introduced an extension (MammoControl DIANA). This was based on Java, Java Web Start, the NetBeans Rich Client Platform, the Pixelmed Java DICOM Toolkit and the ImageJ library. MammoControl DIANA was designed to run locally in the mammography units. This allows automated on-site image analysis. Both results and compressed images can then be transmitted to the reference center. We developed analysis modules for the daily and monthly consistency tests and additionally for a homogeneity test. The software we developed facilitates the immediate availability of measurement results, phantom images, and DICOM header data in all reference centers. This allows both targeted guidance and short response time in the case of errors. We achieved a consistent IT-based evaluation with standardized tools for the entire screening program in Germany. © Georg Thieme Verlag KG Stuttgart · New York.

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…

jSquid: a Java applet for graphical on-line network exploration.

PubMed

Klammer, Martin; Roopra, Sanjit; Sonnhammer, Erik L L

2008-06-15

jSquid is a graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user. jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly. erik.sonnhammer@sbc.su.se Supplementary data are available at Bioinformatics online.

Information Sources on U. S. Radio Regulations in the Law Library.

ERIC Educational Resources Information Center

Lockwood, James D.

An annotated bibliography gives the radio regulations in the U.S., using sources available in the University of Michigan Law Library as well as the University of Michigan Libraries. Information is applicable to other law, university and public libraries. Relevant material on television regulations is included. Listings cover federal agencies, card…

BioC implementations in Go, Perl, Python and Ruby

PubMed Central

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W. John; Comeau, Donald C.

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ PMID:24961236

Integrated web system of geospatial data services for climate research

NASA Astrophysics Data System (ADS)

Okladnikov, Igor; Gordov, Evgeny; Titov, Alexander

2016-04-01

Georeferenced datasets are currently actively used for modeling, interpretation and forecasting of climatic and ecosystem changes on different spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their huge size (up to tens terabytes for a single dataset) a special software supporting studies in the climate and environmental change areas is required. An approach for integrated analysis of georefernced climatological data sets based on combination of web and GIS technologies in the framework of spatial data infrastructure paradigm is presented. According to this approach a dedicated data-processing web system for integrated analysis of heterogeneous georeferenced climatological and meteorological data is being developed. It is based on Open Geospatial Consortium (OGC) standards and involves many modern solutions such as object-oriented programming model, modular composition, and JavaScript libraries based on GeoExt library, ExtJS Framework and OpenLayers software. This work is supported by the Ministry of Education and Science of the Russian Federation, Agreement #14.613.21.0037.

Multimedia explorer: image database, image proxy-server and search-engine.

PubMed Central

Frankewitsch, T.; Prokosch, U.

1999-01-01

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval. PMID:10566463

Multimedia explorer: image database, image proxy-server and search-engine.

PubMed

Frankewitsch, T; Prokosch, U

1999-01-01

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval.

Multiple geophysical observations indicate possible splay fault activation during the 2006 Java Tsunami earthquake

NASA Astrophysics Data System (ADS)

Fan, W.; Bassett, D.; Denolle, M.; Shearer, P. M.; Ji, C.; Jiang, J.

2017-12-01

The 2006 Mw 7.8 Java earthquake was a tsunami earthquake, exhibiting frequency-dependent seismic radiation along strike. High-frequency global back-projection results suggest two distinct rupture stages. The first stage lasted 65 s with a rupture speed of 1.2 km/s, while the second stage lasted from 65 to 150 s with a rupture speed of 2.7 km/s. In addition, P-wave high-frequency radiated energy and fall-off rates indicate a rupture transition at 60 s. High-frequency radiators resolved with back-projection during the second stage spatially correlate with splay fault traces mapped from residual free-air gravity anomalies. These splay faults also collocate with a major tsunami source associated with the earthquake inferred from tsunami first-crest back-propagation simulation. These correlations suggest that the splay faults may have been reactivated during the Java earthquake, as has been proposed for other tsunamigenic earthquakes, such as the 1944 Mw 8.1 Tonankai earthquake in the Nankai Trough.

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.

JAVA Stereo Display Toolkit

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

This toolkit provides a common interface for displaying graphical user interface (GUI) components in stereo using either specialized stereo display hardware (e.g., liquid crystal shutter or polarized glasses) or anaglyph display (red/blue glasses) on standard workstation displays. An application using this toolkit will work without modification in either environment, allowing stereo software to reach a wider audience without sacrificing high-quality display on dedicated hardware. The toolkit is written in Java for use with the Swing GUI Toolkit and has cross-platform compatibility. It hooks into the graphics system, allowing any standard Swing component to be displayed in stereo. It uses the OpenGL graphics library to control the stereo hardware and to perform the rendering. It also supports anaglyph and special stereo hardware using the same API (application-program interface), and has the ability to simulate color stereo in anaglyph mode by combining the red band of the left image with the green/blue bands of the right image. This is a low-level toolkit that accomplishes simply the display of components (including the JadeDisplay image display component). It does not include higher-level functions such as disparity adjustment, 3D cursor, or overlays all of which can be built using this toolkit.

Interface COMSOL-PHREEQC (iCP), an efficient numerical framework for the solution of coupled multiphysics and geochemistry

NASA Astrophysics Data System (ADS)

Nardi, Albert; Idiart, Andrés; Trinchero, Paolo; de Vries, Luis Manuel; Molinero, Jorge

2014-08-01

This paper presents the development, verification and application of an efficient interface, denoted as iCP, which couples two standalone simulation programs: the general purpose Finite Element framework COMSOL Multiphysics® and the geochemical simulator PHREEQC. The main goal of the interface is to maximize the synergies between the aforementioned codes, providing a numerical platform that can efficiently simulate a wide number of multiphysics problems coupled with geochemistry. iCP is written in Java and uses the IPhreeqc C++ dynamic library and the COMSOL Java-API. Given the large computational requirements of the aforementioned coupled models, special emphasis has been placed on numerical robustness and efficiency. To this end, the geochemical reactions are solved in parallel by balancing the computational load over multiple threads. First, a benchmark exercise is used to test the reliability of iCP regarding flow and reactive transport. Then, a large scale thermo-hydro-chemical (THC) problem is solved to show the code capabilities. The results of the verification exercise are successfully compared with those obtained using PHREEQC and the application case demonstrates the scalability of a large scale model, at least up to 32 threads.

A semi-automated tool for treatment plan-quality evaluation and clinical trial quality assurance

NASA Astrophysics Data System (ADS)

Wang, Jiazhou; Chen, Wenzhou; Studenski, Matthew; Cui, Yunfeng; Lee, Andrew J.; Xiao, Ying

2013-07-01

The goal of this work is to develop a plan-quality evaluation program for clinical routine and multi-institutional clinical trials so that the overall evaluation efficiency is improved. In multi-institutional clinical trials evaluating the plan quality is a time-consuming and labor-intensive process. In this note, we present a semi-automated plan-quality evaluation program which combines MIMVista, Java/MATLAB, and extensible markup language (XML). More specifically, MIMVista is used for data visualization; Java and its powerful function library are implemented for calculating dosimetry parameters; and to improve the clarity of the index definitions, XML is applied. The accuracy and the efficiency of the program were evaluated by comparing the results of the program with the manually recorded results in two RTOG trials. A slight difference of about 0.2% in volume or 0.6 Gy in dose between the semi-automated program and manual recording was observed. According to the criteria of indices, there are minimal differences between the two methods. The evaluation time is reduced from 10-20 min to 2 min by applying the semi-automated plan-quality evaluation program.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

PubMed

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E; Troein, Carl; Millar, Andrew J; Goryanin, Igor; Gilmore, Stephen

2013-03-01

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI's use of standard data formats. All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.

The 2006 Java Earthquake revealed by the broadband seismograph network in Indonesia

NASA Astrophysics Data System (ADS)

Nakano, M.; Kumagai, H.; Miyakawa, K.; Yamashina, T.; Inoue, H.; Ishida, M.; Aoi, S.; Morikawa, N.; Harjadi, P.

2006-12-01

On May 27, 2006, local time, a moderate-size earthquake (Mw=6.4) occurred in central Java. This earthquake caused severe damages near Yogyakarta City, and killed more than 5700 people. To estimate the source mechanism and location of this earthquake, we performed a waveform inversion of the broadband seismograms recorded by a nationwide seismic network in Indonesia (Realtime-JISNET). Realtime-JISNET is a part of the broadband seismograph network developed by an international cooperation among Indonesia, Germany, China, and Japan, aiming at improving the capabilities to monitor seismic activity and tsunami generation in Indonesia. 12 stations in Realitme-JISNET were in operation when the earthquake occurred. We used the three-component seismograms from the two closest stations, which were located about 100 and 300 km from the source. In our analysis, we assumed pure double couple as the source mechanism, thus reducing the number of free parameters in the waveform inversion. Therefore we could stably estimate the source mechanism using the signals observed by a small number of seismic stations. We carried out a grid search with respect to strike, dip, and rake angles to investigate fault orientation and slip direction. We determined source-time functions of the moment-tensor components in the frequency domain for each set of strike, dip, and rake angles. We also conducted a spatial grid search to find the best-fit source location. The best-fit source was approximately 12 km SSE of Yogyakarta at a depth of 10 km below sea level, immediately below the area of extensive damage. The focal mechanism indicates that this earthquake was caused by compressive stress in the NS direction and strike-slip motion was dominant. The moment magnitude (Mw) was 6.4. We estimated the seismic intensity in the areas of severe damage using the source paramters and an empirical attenuation relation for averaged peak ground velocity (PGV) of horizontal seismic motion. We then calculated the instrumental modified Mercalli intensity (Imm) from the estimated PGV values. Our result indicates that strong ground motion with Imm of 7 or more occurred within 10 km of the earthquake fault, although the actual seismic intensity can be affected by shallow structural heterogeneity. We therefore conclude that the severe damages of the Java earthquake are attributed to the strong ground motion, which was primarily caused by the source located immediately below the populated areas.

libChEBI: an API for accessing the ChEBI database.

PubMed

Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

2016-01-01

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

Using THEMIS and TES to conduct a mineral analysis on Olympus Mons

NASA Astrophysics Data System (ADS)

Chase, Nicole Danielle

2016-10-01

Olympus Mons is the largest shield volcano in our known solar system. In previous studies, the composition of the basaltic lava flows on Olympus Mons was shown to be similar to the composition of those lava flows of Earth's shield volcanoes. It has been suggested that basalt located near volcanoes contained bacteria living below the surface of the Earth. In this pilot study, the effect of Olympus Mons' aspect (i.e. north- vs. south-facing slope) on its mineral composition was examined. Imagery from Thermal Emission Imaging System (THEMIS), onboard the Mars Odyssey spacecraft, were used because Olympus Mons' size and surface roughness hinder rover exploration. After removing transmission errors and performing an atmospheric correction, the THEMIS images were ready to be analyzed via a mineral spectral library. Using Arizona State University's Thermal Emission Spectrometer (TES) derived mineral spectral library, the images were classified in ENVI. These classifications were verified using ASU's GIS tool, Java Mission-planning and Analysis for Remote Sensing (JMARS) and TES. Results show differences in the mineral composition and in the geological features on Olympus Mons' surface. The mineral vanadinite was shown to be prevalent on the sampled southern portions of Olympus Mons, but was sparse on the sampled northern portions. Previous studies suggested that the mineral ilmenite, which this study found in high concentrations on the sampled northern portions of Olympus Mons, might serve as a food source for iron-oxidizing and iron-scavenging bacteria. Future research should focus on better understanding the concentrations of vanadinite and ilmenite on Olympus Mons to see if these minerals have a role in the potential presence of bacteria on Olympus Mons.

THEMIS analysis of Olympus Mons' mineralogical makeup

NASA Astrophysics Data System (ADS)

Chase, N. D.

2016-12-01

Olympus Mons is the largest shield volcano in our known solar system. In previous studies, the composition of the basaltic lava flows on Olympus Mons was shown to be similar to the composition of those lava flows of Earth's shield volcanoes. It has been suggested that basalt located near volcanoes contained bacteria living below the surface of the Earth. In this pilot study, the effect of Olympus Mons' aspect (i.e. north- vs. south-facing slope) on its mineral composition was examined. Imagery from Thermal Emission Imaging System (THEMIS), onboard the 2001 Mars Odyssey spacecraft, were used because Olympus Mons' size and surface roughness hinder rover exploration. After removing transmission errors and performing an atmospheric correction, the THEMIS images were ready to be analyzed via a mineral spectral library. Using Arizona State University's Thermal Emission Spectrometer (TES) derived mineral spectral library, the images were classified in ENVI. These classifications were verified using ASU's GIS tool, Java Mission-planning and Analysis for Remote Sensing (JMARS) and TES. Results show a significant amount of silicates located throughout the sampled areas of Olympus Mons. The results also show differences in the mineral composition and in the geological features on Olympus Mons' surface. The minerals vanadinite and halloysite were shown to be prevalent on the sampled southern portions of Olympus Mons, but were sparse on the sampled northern portions. Previous studies suggested that the mineral ilmenite, which this study found in high concentrations on the sampled northern portions of Olympus Mons, might serve as a food source for iron-oxidizing and iron-scavenging bacteria. Future research should focus on better understanding these concentrations on Olympus Mons to see if these minerals play a role in the potential bacterial presence on Olympus Mons.

Phased Migration to Koha: Our Library's Experience

ERIC Educational Resources Information Center

Kohn, Karen; McCloy, Eric

2010-01-01

Landman Library is two-thirds of the way through a three-stage process of migrating to the Koha open-source integrated library system (http://koha-community.org). We are an academic library with roughly 143,000 volumes, six professional librarians, and three support staff. The migration to open source was driven by the desire to access our own…

Evaluating One-Shot Library Sessions: Impact on the Quality and Diversity of Student Source Use

ERIC Educational Resources Information Center

Howard, Kristina; Nicholas, Thomas; Hayes, Tish; Appelt, Christopher W.

2014-01-01

This article examines the presumption that library research workshops will increase the quality, quantity and diversity of sources students use. This study compares bibliographies of research papers written by freshman composition students who received a library research session to those of students who did not receive any library instruction. Our…

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.

Programmatic access to data and information at the IRIS DMC via web services

NASA Astrophysics Data System (ADS)

Weertman, B. R.; Trabant, C.; Karstens, R.; Suleiman, Y. Y.; Ahern, T. K.; Casey, R.; Benson, R. B.

2011-12-01

The IRIS Data Management Center (DMC) has developed a suite of web services that provide access to the DMC's time series holdings, their related metadata and earthquake catalogs. In addition, services are available to perform simple, on-demand time series processing at the DMC prior to being shipped to the user. The primary goal is to provide programmatic access to data and processing services in a manner usable by and useful to the research community. The web services are relatively simple to understand and use and will form the foundation on which future DMC access tools will be built. Based on standard Web technologies they can be accessed programmatically with a wide range of programming languages (e.g. Perl, Python, Java), command line utilities such as wget and curl or with any web browser. We anticipate these services being used for everything from simple command line access, used in shell scripts and higher programming languages to being integrated within complex data processing software. In addition to improving access to our data by the seismological community the web services will also make our data more accessible to other disciplines. The web services available from the DMC include ws-bulkdataselect for the retrieval of large volumes of miniSEED data, ws-timeseries for the retrieval of individual segments of time series data in a variety of formats (miniSEED, SAC, ASCII, audio WAVE, and PNG plots) with optional signal processing, ws-station for station metadata in StationXML format, ws-resp for the retrieval of instrument response in RESP format, ws-sacpz for the retrieval of sensor response in the SAC poles and zeros convention and ws-event for the retrieval of earthquake catalogs. To make the services even easier to use, the DMC is developing a library that allows Java programmers to seamlessly retrieve and integrate DMC information into their own programs. The library will handle all aspects of dealing with the services and will parse the returned data. By using this library a developer will not need to learn the details of the service interfaces or understand the data formats returned. This library will be used to build the software bridge needed to request data and information from within MATLAB°. We also provide several client scripts written in Perl for the retrieval of waveform data, metadata and earthquake catalogs using command line programs. For more information on the DMC's web services please visit http://www.iris.edu/ws/

A Guide for Finding Biographical Sources.

ERIC Educational Resources Information Center

Huang, Samuel T., Comp.

Intended to assist library users in finding biographical sources in various disciplines, this compilation lists selective biographical sources which are available in the Northern Illinois University Libraries. The compilation is divided into four major areas: indexes to biographies, sources of information on living persons, sources of information…

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 Benthic Event Detector (BED). The BED records 50Hz samples of orientation and acceleration when it moves. These data are converted to the CF-NetCDF format and then loaded into a STOQS database. Using the Spatial-3D view a user may interact with a virtual playback of BED motions, giving new insight into submarine canyon sediment density flows.

Developing a Conceptual Architecture for a Generalized Agent-based Modeling Environment (GAME)

DTIC Science & Technology

2008-03-01

4. REPAST (Java, Python , C#, Open Source) ........28 5. MASON: Multi-Agent Modeling Language (Swarm Extension... Python , C#, Open Source) Repast (Recursive Porous Agent Simulation Toolkit) was designed for building agent-based models and simulations in the...Repast makes it easy for inexperienced users to build models by including a built-in simple model and provide interfaces through which menus and Python

Automated Report Generation for Research Data Repositories: From i2b2 to PDF.

PubMed

Thiemann, Volker S; Xu, Tingyan; Röhrig, Rainer; Majeed, Raphael W

2017-01-01

We developed an automated toolchain to generate reports of i2b2 data. It is based on free open source software and runs on a Java Application Server. It is sucessfully used in an ED registry project. The solution is highly configurable and portable to other projects based on i2b2 or compatible factual data sources.

Charting a Course through CORAL: Texas A&M University Libraries' Experience Implementing an Open-Source Electronic Resources Management System

ERIC Educational Resources Information Center

Hartnett, Eric; Beh, Eugenia; Resnick, Taryn; Ugaz, Ana; Tabacaru, Simona

2013-01-01

In 2010, after two previous unsuccessful attempts at electronic resources management system (ERMS) implementation, Texas A&M University (TAMU) Libraries set out once again to find an ERMS that would fit its needs. After surveying the field, TAMU Libraries selected the University of Notre Dame Hesburgh Libraries-developed, open-source ERMS,…

Realistic Library Research Methods: Bibliographic Sources Annotated.

ERIC Educational Resources Information Center

Kushon, Susan G.; Wells, Bernice

This guide gives an overview of basic library research methods with emphasis upon developing an understanding of library organization and professional services. Commonly used bibliographic techniques are described for various published and unpublished, print and nonprint materials. Standard reference sources (bibliographies, encyclopedias, annual…

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 OpenORB provides a Java implementation of the OMG Corba 2.4.2 specification (openorb.sourceforge.net) 1/16

Dr TIM: Ray-tracer TIM, with additional specialist scientific capabilities

NASA Astrophysics Data System (ADS)

Oxburgh, Stephen; Tyc, Tomáš; Courtial, Johannes

2014-03-01

We describe several extensions to TIM, a raytracing program for ray-optics research. These include relativistic raytracing; simulation of the external appearance of Eaton lenses, Luneburg lenses and generalised focusing gradient-index lens (GGRIN) lenses, which are types of perfect imaging devices; raytracing through interfaces between spaces with different optical metrics; and refraction with generalised confocal lenslet arrays, which are particularly versatile METATOYs. Catalogue identifier: AEKY_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKY_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licencing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 106905 No. of bytes in distributed program, including test data, etc.: 6327715 Distribution format: tar.gz Programming language: Java. Computer: Any computer capable of running the Java Virtual Machine (JVM) 1.6. Operating system: Any, developed under Mac OS X Version 10.6 and 10.8.3. RAM: Typically 130 MB (interactive version running under Mac OS X Version 10.8.3) Classification: 14, 18. Catalogue identifier of previous version: AEKY_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183(2012)711 External routines: JAMA [1] (source code included) Does the new version supersede the previous version?: Yes Nature of problem: Visualisation of scenes that include scene objects that create wave-optically forbidden light-ray fields. Solution method: Ray tracing. Reasons for new version: Significant extension of the capabilities (see Summary of revisions), as demanded by our research. Summary of revisions: Added capabilities include the simulation of different types of camera moving at relativistic speeds relative to the scene; visualisation of the external appearance of generalised focusing gradient-index (GGRIN) lenses, including Maxwell fisheye, Eaton and Luneburg lenses; calculation of refraction at the interface between spaces with different optical metrics; and handling of generalised confocal lenslet arrays (gCLAs), a new type of METATOY. Unusual features: Specifically designed to visualise wave-optically forbidden light-ray fields; can visualise ray trajectories and geometric optic transformations; can simulate photos taken with different types of camera moving at relativistic speeds, interfaces between spaces with different optical metrics, the view through METATOYs and generalised focusing gradient-index lenses; can create anaglyphs (for viewing with coloured “3D glasses”), HDMI-1.4a standard 3D images, and random-dot autostereograms of the scene; integrable into web pages. Running time: Problem-dependent; typically seconds for a simple scene. References: [1] JAMA: A Java Matrix Package, http://math.nist.gov/javanumerics/jama/

SU-F-T-47: MRI T2 Exclusive Based Planning Using the Endocavitary/interstitial Gynecological Benidorm Applicator: A Proposed TPS Library and Preplan Efficient Methodology

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

Richart, J; Otal, A; Rodriguez, S

Purpose: ABS and GEC-ESTRO have recommended MRI T2 for image guided brachytherapy. Recently, a new applicator (Benidorm Template, TB) has been developed in our Department (Rodriguez et al 2015). TB is fully MRI compatible because the Titanium needles and it allows the use of intrauterine tandem. Currently, TPS applicators library are not currently available for non-rigid applicators in case of interstitial component as the TB.The purpose of this work is to present the development of a library for the TB, together with its use on a pre-planning technique. Both new goals allow a very efficient and exclusive T2 MRI basedmore » planning clinical TB implementation. Methods: The developed library has been implemented in Oncentra Brachytherapy TPS, version 4.3.0 (Elekta) and now is being implemented on Sagiplan v 2.0 TPS (Eckert&Ziegler BEBIG). To model the TB, free and open software named FreeCAD and MeshLab have been used. The reconstruction process is based on three inserted A-vitamin pellets together with the data provided by the free length. The implemented preplanning procedure is as follow: 1) A MRI T2 acquisition is performed with the template in place just with the vaginal cylinder (no uterine tube nor needles). 2) The CTV is drawn and the required needles are selected using a developed Java based application and 3) A post-implant MRI T2 is performed. Results: This library procedure has been successfully applied by now in 25 patients. In this work the use of the developed library will be illustrated with clinical examples. The preplanning procedure has been applied by now in 6 patients, having significant advantages: needle depth estimation, needle positions and number are optimized a priori, time saving, etc Conclusion: TB library and pre-plan techniques are feasible and very efficient and their use will be illustrated in this work.« less

Scale-Independent Relational Query Processing

DTIC Science & Technology

2013-10-04

source options are also available, including Postgresql, MySQL , and SQLite. These mod- ern relational databases are generally very complex software systems...and Their Application to Data Stream Management. IGI Global, 2010. [68] George Reese. Database Programming with JDBC and Java , Second Edition. Ed. by

XML Files

MedlinePlus

... this page, please enable JavaScript. MedlinePlus produces XML data sets that you are welcome to download and use. If you have questions about the MedlinePlus XML files, please contact us . For additional sources of MedlinePlus data in XML format, visit our Web service page, ...

A step-by-step solution for embedding user-controlled cines into educational Web pages.

PubMed

Cornfeld, Daniel

2008-03-01

The objective of this article is to introduce a simple method for embedding user-controlled cines into a Web page using a simple JavaScript. Step-by-step instructions are included and the source code is made available. This technique allows the creation of portable Web pages that allow the user to scroll through cases as if seated at a PACS workstation. A simple JavaScript allows scrollable image stacks to be included on Web pages. With this technique, you can quickly and easily incorporate entire stacks of CT or MR images into online teaching files. This technique has the potential for use in case presentations, online didactics, teaching archives, and resident testing.

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.

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

ERIC Educational Resources Information Center

Fagan, Jody Condit; Keach, Jennifer A.

2010-01-01

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

The Bioperl Toolkit: Perl Modules for the Life Sciences

PubMed Central

Stajich, Jason E.; Block, David; Boulez, Kris; Brenner, Steven E.; Chervitz, Stephen A.; Dagdigian, Chris; Fuellen, Georg; Gilbert, James G.R.; Korf, Ian; Lapp, Hilmar; Lehväslaiho, Heikki; Matsalla, Chad; Mungall, Chris J.; Osborne, Brian I.; Pocock, Matthew R.; Schattner, Peter; Senger, Martin; Stein, Lincoln D.; Stupka, Elia; Wilkinson, Mark D.; Birney, Ewan

2002-01-01

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort. [Supplemental material is available online at www.genome.org. Bioperl is available as open-source software free of charge and is licensed under the Perl Artistic License (http://www.perl.com/pub/a/language/misc/Artistic.html). It is available for download at http://www.bioperl.org. Support inquiries should be addressed to bioperl-l@bioperl.org.] PMID:12368254

Scanning electron microscope measurement of width and shape of 10nm patterned lines using a JMONSEL-modeled library.

PubMed

Villarrubia, J S; Vladár, A E; Ming, B; Kline, R J; Sunday, D F; Chawla, J S; List, S

2015-07-01

The width and shape of 10nm to 12 nm wide lithographically patterned SiO2 lines were measured in the scanning electron microscope by fitting the measured intensity vs. position to a physics-based model in which the lines' widths and shapes are parameters. The approximately 32 nm pitch sample was patterned at Intel using a state-of-the-art pitch quartering process. Their narrow widths and asymmetrical shapes are representative of near-future generation transistor gates. These pose a challenge: the narrowness because electrons landing near one edge may scatter out of the other, so that the intensity profile at each edge becomes width-dependent, and the asymmetry because the shape requires more parameters to describe and measure. Modeling was performed by JMONSEL (Java Monte Carlo Simulation of Secondary Electrons), which produces a predicted yield vs. position for a given sample shape and composition. The simulator produces a library of predicted profiles for varying sample geometry. Shape parameter values are adjusted until interpolation of the library with those values best matches the measured image. Profiles thereby determined agreed with those determined by transmission electron microscopy and critical dimension small-angle x-ray scattering to better than 1 nm. Published by Elsevier B.V.

Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries.

PubMed

Horlacher, Oliver; Lisacek, Frederique; Müller, Markus

2016-03-04

Experimental improvements in post-translational modification (PTM) detection by tandem mass spectrometry (MS/MS) has allowed the identification of vast numbers of PTMs. Open modification searches (OMSs) of MS/MS data, which do not require prior knowledge of the modifications present in the sample, further increased the diversity of detected PTMs. Despite much effort, there is still a lack of functional annotation of PTMs. One possibility to narrow the annotation gap is to mine MS/MS data deposited in public repositories and to correlate the PTM presence with biological meta-information attached to the data. Since the data volume can be quite substantial and contain tens of millions of MS/MS spectra, the data mining tools must be able to cope with big data. Here, we present two tools, Liberator and MzMod, which are built using the MzJava class library and the Apache Spark large scale computing framework. Liberator builds large MS/MS spectrum libraries, and MzMod searches them in an OMS mode. We applied these tools to a recently published set of 25 million spectra from 30 human tissues and present tissue specific PTMs. We also compared the results to the ones obtained with the OMS tool MODa and the search engine X!Tandem.

Semantic framework for mapping object-oriented model to semantic web languages

PubMed Central

Ježek, Petr; Mouček, Roman

2015-01-01

The article deals with and discusses two main approaches in building semantic structures for electrophysiological metadata. It is the use of conventional data structures, repositories, and programming languages on one hand and the use of formal representations of ontologies, known from knowledge representation, such as description logics or semantic web languages on the other hand. Although knowledge engineering offers languages supporting richer semantic means of expression and technological advanced approaches, conventional data structures and repositories are still popular among developers, administrators and users because of their simplicity, overall intelligibility, and lower demands on technical equipment. The choice of conventional data resources and repositories, however, raises the question of how and where to add semantics that cannot be naturally expressed using them. As one of the possible solutions, this semantics can be added into the structures of the programming language that accesses and processes the underlying data. To support this idea we introduced a software prototype that enables its users to add semantically richer expressions into a Java object-oriented code. This approach does not burden users with additional demands on programming environment since reflective Java annotations were used as an entry for these expressions. Moreover, additional semantics need not to be written by the programmer directly to the code, but it can be collected from non-programmers using a graphic user interface. The mapping that allows the transformation of the semantically enriched Java code into the Semantic Web language OWL was proposed and implemented in a library named the Semantic Framework. This approach was validated by the integration of the Semantic Framework in the EEG/ERP Portal and by the subsequent registration of the EEG/ERP Portal in the Neuroscience Information Framework. PMID:25762923

Architecture for biomedical multimedia information delivery on the World Wide Web

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

1997-10-01

Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

Semantic framework for mapping object-oriented model to semantic web languages.

PubMed

Ježek, Petr; Mouček, Roman

2015-01-01

The article deals with and discusses two main approaches in building semantic structures for electrophysiological metadata. It is the use of conventional data structures, repositories, and programming languages on one hand and the use of formal representations of ontologies, known from knowledge representation, such as description logics or semantic web languages on the other hand. Although knowledge engineering offers languages supporting richer semantic means of expression and technological advanced approaches, conventional data structures and repositories are still popular among developers, administrators and users because of their simplicity, overall intelligibility, and lower demands on technical equipment. The choice of conventional data resources and repositories, however, raises the question of how and where to add semantics that cannot be naturally expressed using them. As one of the possible solutions, this semantics can be added into the structures of the programming language that accesses and processes the underlying data. To support this idea we introduced a software prototype that enables its users to add semantically richer expressions into a Java object-oriented code. This approach does not burden users with additional demands on programming environment since reflective Java annotations were used as an entry for these expressions. Moreover, additional semantics need not to be written by the programmer directly to the code, but it can be collected from non-programmers using a graphic user interface. The mapping that allows the transformation of the semantically enriched Java code into the Semantic Web language OWL was proposed and implemented in a library named the Semantic Framework. This approach was validated by the integration of the Semantic Framework in the EEG/ERP Portal and by the subsequent registration of the EEG/ERP Portal in the Neuroscience Information Framework.

Academic Libraries, Information Sources, and Shared Decision Making.

ERIC Educational Resources Information Center

McClure, Charles R.

1980-01-01

Analyzes the relationship of academic librarians' contact with information sources and their involvement in library decision making. Findings suggest that individuals rich in information sources are most closely linked to the decision-making process. (RAA)

Tracing crustal contamination along the Java segment of the Sunda Arc, Indonesia

NASA Astrophysics Data System (ADS)

Jolis, E. M.; Troll, V.; Deegan, F.; Blythe, L.; Harris, C.; Freda, C.; Hilton, D.; Chadwick, J.; Van Helden, M.

2012-04-01

Arc magmas typically display chemical and petrographic characteristics indicative of crustal input. Crustal contamination can take place either in the mantle source region or as magma traverses the upper crust (e.g. [1]). While source contamination is generally considered the dominant process (e.g. [2]), late-stage crustal contamination has been recognised at volcanic arcs too (e.g. [3]). In light of this, we aim to test the extent of upper crustal versus source contamination along the Java segment of the Sunda arc, which, due its variable upper crustal structure, is an exemplary natural laboratory. We present a detailed geochemical study of 7 volcanoes along a traverse from Anak-Krakatau in the Sunda strait through Java and Bali, to characterise the impact of the overlying crust on arc magma composition. Using rock and mineral elemental geochemistry, radiogenic (Sr, Nd and Pb) and, stable (O) isotopes, we show a correlation between upper crustal composition and the degree of upper crustal contamination. We find an increase in 87Sr/86Sr and δ18O values, and a decrease in 143Nd/144Nd values from Krakatau towards Merapi, indicating substantial crustal input from the thick continental basement present. Volcanoes to the east of Merapi and the Progo-Muria fault transition zone, where the upper crust is thinner, in turn, show considerably less crustal input in their isotopic signatures, indicating a stronger influence of the mantle source. Our new data represent a systematic and high-resolution arc-wide sampling effort that allows us to distinguish the effects of the upper crust on the compositional spectrum of individual volcanic systems along the Sunda arc. [1] Davidson, J.P, Hora, J.M, Garrison, J.M & Dungan, M.A 2005. Crustal Forensics in Arc Magmas. J. Geotherm. Res. 140, 157-170; [2] Debaille, V., Doucelance, R., Weis, D., & Schiano, P. 2005. Geochim. Cosmochim. Acta, 70,723-741; [3] Gasparon, M., Hilton, D.R., & Varne, R. 1994. Earth Planet. Sci. Lett., 126, 15-22.

Tracing the Source of Borneo's Cempaka Diamond Deposit

NASA Astrophysics Data System (ADS)

White, L. T.; Graham, I.; Armstrong, R. A.; Hall, R.

2014-12-01

Several gem quality diamond deposits are found in paleo-alluvial deposits across Borneo. The source of the diamonds and their origin are enigmatic. They could have formed in Borneo and be derived from local sources, or they could be related to diamond deposits in NW Australia, and carried with the Southwest Borneo Block after it rifted from Australia in the Late Jurassic. We collected U-Pb isotopic data from detrital zircons from the Cempaka alluvial diamond deposit in southeast Borneo. Two thirds of the zircons that were dated crystallized between 75 Ma and 110 Ma. The other third are Triassic or older (223 Ma, 314-319 Ma, 353-367 Ma, 402-414 Ma, 474 Ma, 521 Ma, 549 Ma, 1135-1176 Ma, 1535 Ma, 2716 Ma). All of the Cretaceous zircons are angular, euhedral grains with minor evidence of mechanical abrasion. Considering their age and morphology they were likely derived from the nearby Schwaner Granites. The Triassic and older grains are rounded to semi-rounded and were likely derived from Australia before Borneo rifted from Gondwana. Some of the zircons have ages that resemble those of the Merlin and Argyle diamond deposits of Australia. The diamonds themselves have delicate resorption features and overgrowths that would potentially be destroyed with prolonged transport. Geochemical data collected from the diamonds implies they were associated with lamproite intrusions. Deep seismic lines and zircons from igneous rocks suggest SE Borneo, the East Java Sea and East Java are largely underlain by thick lithosphere rifted from NW Australia. Based on several lines of evidence, we propose that diamond-bearing lamproites intruded before rifting of SW Borneo from Australia, or after collision with Sundaland of SW Borneo and the East Java-West Sulawesi Blocks during the Cretaceous. Exposure of the source after the Late Cretaceous led to diamond accumulation in river systems that flowed from the Schwaner Mountains.

ALMA Observing Strategies

NASA Astrophysics Data System (ADS)

Biggs, Andy

2018-03-01

The ALMA Observing Tool (OT) is a Java-based tool used to prepare ALMA observations. In this talk, I highlight the particular features relevant to setting up single dish observations when these are needed to observe sources where the largest angular scale requires the addition of the total power antennas.

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

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.

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

PubMed Central

Awad, Ihab AB; Rees, Christian A; Hernandez-Boussard, Tina; Ball, Catherine A; Sherlock, Gavin

2004-01-01

Background Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. Results We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. Conclusion Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context. PMID:15488149

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.

PubMed

Expósito, Roberto R; Veiga, Jorge; González-Domínguez, Jorge; Touriño, Juan

2017-09-01

This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool. Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es . rreye@udc.es. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A comparison study of 2006 Java earthquake and other Tsunami earthquakes

NASA Astrophysics Data System (ADS)

Ji, C.; Shao, G.

2006-12-01

We revise the slip processes of July 17 2006 Java earthquakes by combined inverting teleseismic body wave, long period surface waves, as well as the broadband records at Christmas island (XMIS), which is 220 km away from the hypocenter and so far the closest observation for a Tsunami earthquake. Comparing with the previous studies, our approach considers the amplitude variations of surface waves with source depths as well as the contribution of ScS phase, which usually has amplitudes compatible with that of direct S phase for such low angle thrust earthquakes. The fault dip angles are also refined using the Love waves observed along fault strike direction. Our results indicate that the 2006 event initiated at a depth around 12 km and unilaterally rupture southeast for 150 sec with a speed of 1.0 km/sec. The revised fault dip is only about 6 degrees, smaller than the Harvard CMT (10.5 degrees) but consistent with that of 1994 Java earthquake. The smaller fault dip results in a larger moment magnitude (Mw=7.9) for a PREM earth, though it is dependent on the velocity structure used. After verified with 3D SEM forward simulation, we compare the inverted result with the revised slip models of 1994 Java and 1992 Nicaragua earthquakes derived using the same wavelet based finite fault inversion methodology.

A Counterexample Guided Abstraction Refinement Framework for Verifying Concurrent C Programs

DTIC Science & Technology

2005-05-24

source code are routinely executed. The source code is written in languages ranging from C/C++/Java to ML/ Ocaml . These languages differ not only in...from the difficulty to model computer programs—due to the complexity of programming languages as compared to hardware description languages —to...intermediate specification language lying between high-level Statechart- like formalisms and transition systems. Actions are encoded as changes in

WebScope: A New Tool for Fusion Data Analysis and Visualization

NASA Astrophysics Data System (ADS)

Yang, Fei; Dang, Ningning; Xiao, Bingjia

2010-04-01

A visualization tool was developed through a web browser based on Java applets embedded into HTML pages, in order to provide a world access to the EAST experimental data. It can display data from various trees in different servers in a single panel. With WebScope, it is easier to make a comparison between different data sources and perform a simple calculation over different data sources.

Hand Gesture Data Collection Procedure Using a Myo Armband for Machine Learning

DTIC Science & Technology

2015-09-01

instructions, searching existing data sources , gathering and maintaining the data needed, and completing and reviewing the collection information...data using a Myo armband. The source code for this work is included as an Appendix. 15. SUBJECT TERMS Myo, Machine Learning, Classifier, Data...development in multiple platfonns (e.g., Windows, iOS, Android , etc.) and many languages (e.g. , Java, C++, C#, Lua, etc.). For the data collection

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, continued convergence caused contractional deformation and thrusting in Java. The slab then broke in front of the plateau. The trench stepped back to the south by about 150 km and subduction resumed behind the plateau, causing a hole to develop in the subducting slab. As the hole passed beneath the arc, and fluid flux declined, normal calc-alkaline volcanism ceased. With the mantle wedge melt component ‘switched off' K-rich melts, produced from a deeper mantle component that remained undiluted, dominated arc volcanism. As the hole got deeper K-rich volcanism ceased. Normal, calc-alkaline, arc activity resumed when the untorn slab following the hole was subducted.

Biographer: web-based editing and rendering of SBGN compliant biochemical networks.

PubMed

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-06-01

The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-independent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL

Feature Positioning on Google Street View Panoramas

NASA Astrophysics Data System (ADS)

Tsai, V. J. D.; Chang, C.-T.

2012-07-01

Location-based services (LBS) on web-based maps and images have come into real-time since Google launched its Street View imaging services in 2007. This research employs Google Maps API and Web Service, GAE for JAVA, AJAX, Proj4js, CSS and HTML in developing an internet platform for accessing the orientation parameters of Google Street View (GSV) panoramas in order to determine the three dimensional position of interest features that appear on two overlapping panoramas by geometric intersection. A pair of GSV panoramas was examined using known points located on the Library Building of National Chung Hsing University (NCHU) with the root-mean-squared errors of ±0.522m, ±1.230m, and ±5.779m for intersection and ±0.142m, ±1.558m, and ±5.733m for resection in X, Y, and h (elevation), respectively. Potential error sources in GSV positioning were analyzed and illustrated that the errors in Google provided GSV positional parameters dominate the errors in geometric intersection. The developed system is suitable for data collection in establishing LBS applications integrated with Google Maps and Google Earth in traffic sign and infrastructure inventory by adding automatic extraction and matching techniques for points of interest (POI) from GSV panoramas.

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

PubMed

Mitternacht, Simon

2016-01-01

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

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.

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.

Implementation of BT, SP, LU, and FT of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

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

2000-01-01

A number of Java features make it an attractive but a debatable choice for High Performance Computing. We have implemented benchmarks working on single structured grid BT,SP,LU and FT in Java. The performance and scalability of the Java code shows that a significant improvement in Java compiler technology and in Java thread implementation are necessary for Java to compete with Fortran in HPC applications.

LibHalfSpace: A C++ object-oriented library to study deformation and stress in elastic half-spaces

NASA Astrophysics Data System (ADS)

Ferrari, Claudio; Bonafede, Maurizio; Belardinelli, Maria Elina

2016-11-01

The study of deformation processes in elastic half-spaces is widely employed for many purposes (e.g. didactic, scientific investigation of real processes, inversion of geodetic data, etc.). We present a coherent programming interface containing a set of tools designed to make easier and faster the study of processes in an elastic half-space. LibHalfSpace is presented in the form of an object-oriented library. A set of well known and frequently used source models (Mogi source, penny shaped horizontal crack, inflating spheroid, Okada rectangular dislocation, etc.) are implemented to describe the potential usage and the versatility of the library. The common interface given to library tools enables us to switch easily among the effects produced by different deformation sources that can be monitored at the free surface. Furthermore, the library also offers an interface which simplifies the creation of new source models exploiting the features of object-oriented programming (OOP). These source models can be built as distributions of rectangular boundary elements. In order to better explain how new models can be deployed some examples are included in the library.

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.

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.

Accuracy of telephone reference service in health sciences libraries.

PubMed Central

Paskoff, B M

1991-01-01

Six factual queries were unobtrusively telephoned to fifty-one U.S. academic health sciences and hospital libraries. The majority of the queries (63.4%) were answered accurately. Referrals to another library or information source were made for 25.2% of the queries. Eleven answers (3.6%) were inaccurate, and no answer was provided for 7.8% of the queries. There was a correlation between the number of accurate answers provided and the presence of at least one staff member with a master's degree in library and information science. The correlation between employing a librarian certified by the Medical Library Association (MLA) and providing accurate answers was significant. The majority of referrals were to specific sources. If these "helpful referrals" are counted with accurate answers as correct responses, they total 76.8% of the answers. In a follow-up survey, five libraries stated that they did not provide accurate answers because they did not own an appropriate source. Staff-related problems were given as reasons for other than accurate answers by two of the libraries, while eight indicated that library policy prevented them from providing answers to the public. PMID:2039904

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

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

Acoustic Metadata Management and Transparent Access to Networked Oceanographic Data Sets

DTIC Science & Technology

2013-09-30

connectivity (ODBC) compliant data source for which drivers are available (e.g. MySQL , Oracle database, Postgres) can now be imported. Implementation...the possibility of speeding data transmission through compression (implemented) or the potential to use alternative data formats such as Java script

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

An open-source Java-based Toolbox for environmental model evaluation: The MOUSE Software Application

USDA-ARS?s Scientific Manuscript database

A consequence of environmental model complexity is that the task of understanding how environmental models work and identifying their sensitivities/uncertainties, etc. becomes progressively more difficult. Comprehensive numerical and visual evaluation tools have been developed such as the Monte Carl...

Public Relations in Special Libraries.

ERIC Educational Resources Information Center

Rutkowski, Hollace Ann; And Others

1991-01-01

This theme issue includes 11 articles on public relations (PR) in special libraries. Highlights include PR at the Special Libraries Association (SLA); sources for marketing research for libraries; developing a library image; sample PR releases; brand strategies for libraries; case studies; publicizing a consortium; and a bibliography of pertinent…

Digital Preservation in Open-Source Digital Library Software

ERIC Educational Resources Information Center

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

2012-01-01

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

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…

GarlicESTdb: an online database and mining tool for garlic EST sequences.

PubMed

Kim, Dae-Won; Jung, Tae-Sung; Nam, Seong-Hyeuk; Kwon, Hyuk-Ryul; Kim, Aeri; Chae, Sung-Hwa; Choi, Sang-Haeng; Kim, Dong-Wook; Kim, Ryong Nam; Park, Hong-Seog

2009-05-18

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at http://garlicdb.kribb.re.kr. GarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.

Research on Ajax and Hibernate technology in the development of E-shop system

NASA Astrophysics Data System (ADS)

Yin, Luo

2011-12-01

Hibernate is a object relational mapping framework of open source code, which conducts light-weighted object encapsulation of JDBC to let Java programmers use the concept of object-oriented programming to manipulate database at will. The appearence of the concept of Ajax (asynchronous JavaScript and XML technology) begins the time prelude of page partial refresh so that developers can develop web application programs with stronger interaction. The paper illustrates the concrete application of Ajax and Hibernate to the development of E-shop in details and adopts them to design to divide the entire program code into relatively independent parts which can cooperate with one another as well. In this way, it is easier for the entire program to maintain and expand.

Analysis of Ten Reverse Engineering Tools

NASA Astrophysics Data System (ADS)

Koskinen, Jussi; Lehmonen, Tero

Reverse engineering tools can be used in satisfying the information needs of software maintainers. Especially in case of maintaining large-scale legacy systems tool support is essential. Reverse engineering tools provide various kinds of capabilities to provide the needed information to the tool user. In this paper we analyze the provided capabilities in terms of four aspects: provided data structures, visualization mechanisms, information request specification mechanisms, and navigation features. We provide a compact analysis of ten representative reverse engineering tools for supporting C, C++ or Java: Eclipse Java Development Tools, Wind River Workbench (for C and C++), Understand (for C++), Imagix 4D, Creole, Javadoc, Javasrc, Source Navigator, Doxygen, and HyperSoft. The results of the study supplement the earlier findings in this important area.

JLIFE: THE JEFFERSON LAB INTERACTIVE FRONT END FOR THE OPTICAL PROPAGATION CODE

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

Watson, Anne M.; Shinn, Michelle D.

2013-08-01

We present details on a graphical interface for the open source software program Optical Propagation Code, or OPC. This interface, written in Java, allows a user with no knowledge of OPC to create an optical system, with lenses, mirrors, apertures, etc. and the appropriate drifts between them. The Java code creates the appropriate Perl script that serves as the input for OPC. The mode profile is then output at each optical element. The display can be either an intensity profile along the x axis, or as an isometric 3D plot which can be tilted and rotated. These profiles can bemore » saved. Examples of the input and output will be presented.« less

CMEMS (Copernicus Marine Environment Monitoring Service) In Situ Thematic Assembly Centre: A service for operational Oceanography

NASA Astrophysics Data System (ADS)

Manzano Muñoz, Fernando; Pouliquen, Sylvie; Petit de la Villeon, Loic; Carval, Thierry; Loubrieu, Thomas; Wedhe, Henning; Sjur Ringheim, Lid; Hammarklint, Thomas; Tamm, Susanne; De Alfonso, Marta; Perivoliotis, Leonidas; Chalkiopoulos, Antonis; Marinova, Veselka; Tintore, Joaquin; Troupin, Charles

2016-04-01

Copernicus, previously known as GMES (Global Monitoring for Environment and Security), is the European Programme for the establishment of a European capacity for Earth Observation and Monitoring. Copernicus aims to provide a sustainable service for Ocean Monitoring and Forecasting validated and commissioned by users. From May 2015, the Copernicus Marine Environment Monitoring Service (CMEMS) is working on an operational mode through a contract with services engagement (result is regular data provision). Within CMEMS, the In Situ Thematic Assembly Centre (INSTAC) distributed service integrates in situ data from different sources for operational oceanography needs. CMEMS INSTAC is collecting and carrying out quality control in a homogeneous manner on data from providers outside Copernicus (national and international networks), to fit the needs of internal and external users. CMEMS INSTAC has been organized in 7 regional Dissemination Units (DUs) to rely on the EuroGOOS ROOSes. Each DU aggregates data and metadata provided by a series of Production Units (PUs) acting as an interface for providers. Homogeneity and standardization are key features to ensure coherent and efficient service. All DUs provide data in the OceanSITES NetCDF format 1.2 (based on NetCDF 3.6), which is CF compliant, relies on SeaDataNet vocabularies and is able to handle profile and time-series measurements. All the products, both near real-time (NRT) and multi-year (REP), are available online for every CMEMS registered user through an FTP service. On top of the FTP service, INSTAC products are available through Oceanotron, an open-source data server dedicated to marine observations dissemination. It provides services such as aggregation on spatio-temporal coordinates and observed parameters, and subsetting on observed parameters and metadata. The accuracy of the data is checked on various levels. Quality control procedures are applied for the validity of the data and correctness tests for the metadata of each NetCDF file. The quality control procedures for the data include different routines for NRT and REP products. Key Performance Indicators (KPI) for monitoring purposes are also used in Copernicus. They allow a periodic monitoring of the availability, quantity and quality of the INSTAC data integrated in the NRT products. Statistical reports are generated on quarterly and yearly basis to provide more visibility on the coverage in space and time of the INSTAC NRT and REP products, as well as information on their quality. These reports are generated using Java and Python procedures developed within the INSTAC group. One of the most critical tasks for the DUs is to generate NetCDF files compliant with the agreed format. Many tools and programming libraries have been developed for that purpose, for instance Unidata Java Library. These tools provide NetCDF data management capabilities including creation, reading and modification. Some DUs have also developed regional data portals which offer useful information for the users including data charts, platforms availability through interactive maps, KPI and statistical figures and direct access to the FTP service. The proposed presentation will detail Copernicus in situ data service and the monitoring tools that have been developed by the INSTAC group.

Square2 - A Web Application for Data Monitoring in Epidemiological and Clinical Studies

PubMed

Schmidt, Carsten Oliver; Krabbe, Christine; Schössow, Janka; Albers, Martin; Radke, Dörte; Henke, Jörg

2017-01-01

Valid scientific inferences from epidemiological and clinical studies require high data quality. Data generating departments therefore aim to detect data irregularities as early as possible in order to guide quality management processes. In addition, after the completion of data collections the obtained data quality must be evaluated. This can be challenging in complex studies due to a wide scope of examinations, numerous study variables, multiple examiners, devices, and examination centers. This paper describes a Java EE web application used to monitor and evaluate data quality in institutions with complex and multiple studies, named Square 2 . It uses the Java libraries Apache MyFaces 2, extended by BootsFaces for layout and style. RServe and REngine manage calls to R server processes. All study data and metadata are stored in PostgreSQL. R is the statistics backend and LaTeX is used for the generation of print ready PDF reports. A GUI manages the entire workflow. Square 2 covers all steps in the data monitoring workflow, including the setup of studies and their structure, the handling of metadata for data monitoring purposes, selection of variables, upload of data, statistical analyses, and the generation as well as inspection of quality reports. To take into account data protection issues, Square 2 comprises an extensive user rights and roles concept.

Java-Library for the Access, Storage and Editing of Calibration Metadata of Optical Sensors

NASA Astrophysics Data System (ADS)

Firlej, M.; Kresse, W.

2016-06-01

The standardization of the calibration of optical sensors in photogrammetry and remote sensing has been discussed for more than a decade. Projects of the German DGPF and the European EuroSDR led to the abstract International Technical Specification ISO/TS 19159-1:2014 "Calibration and validation of remote sensing imagery sensors and data - Part 1: Optical sensors". This article presents the first software interface for a read- and write-access to all metadata elements standardized in the ISO/TS 19159-1. This interface is based on an xml-schema that was automatically derived by ShapeChange from the UML-model of the Specification. The software interface serves two cases. First, the more than 300 standardized metadata elements are stored individually according to the xml-schema. Secondly, the camera manufacturers are using many administrative data that are not a part of the ISO/TS 19159-1. The new software interface provides a mechanism for input, storage, editing, and output of both types of data. Finally, an output channel towards a usual calibration protocol is provided. The interface is written in Java. The article also addresses observations made when analysing the ISO/TS 19159-1 and compiles a list of proposals for maturing the document, i.e. for an updated version of the Specification.

Transformation Systems at NASA Ames

NASA Technical Reports Server (NTRS)

Buntine, Wray; Fischer, Bernd; Havelund, Klaus; Lowry, Michael; Pressburger, TOm; Roach, Steve; Robinson, Peter; VanBaalen, Jeffrey

1999-01-01

In this paper, we describe the experiences of the Automated Software Engineering Group at the NASA Ames Research Center in the development and application of three different transformation systems. The systems span the entire technology range, from deductive synthesis, to logic-based transformation, to almost compiler-like source-to-source transformation. These systems also span a range of NASA applications, including solving solar system geometry problems, generating data analysis software, and analyzing multi-threaded Java code.

BioC implementations in Go, Perl, Python and Ruby.

PubMed

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W John; Comeau, Donald C

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Marketing: A Bibliography of Marketing Reference Sources. The University of Rhode Island University Library.

ERIC Educational Resources Information Center

Masten, Lisa

This annotated bibliography provides a selected list of marketing reference sources for undergraduate and graduate business students interested in marketing and related topics. All sources listed are available in the Reference Department at the University Library at the University of Rhode Island Kingston campus. Most sources, with the exception…

Beacon- and Schema-Based Method for Recognizing Algorithms from Students' Source Code

ERIC Educational Resources Information Center

Taherkhani, Ahmad; Malmi, Lauri

2013-01-01

In this paper, we present a method for recognizing algorithms from students programming submissions coded in Java. The method is based on the concept of "programming schemas" and "beacons". Schemas are high-level programming knowledge with detailed knowledge abstracted out, and beacons are statements that imply specific…

Cellular Consequences of Telomere Shortening in Histologically Normal Breast Tissues

DTIC Science & Technology

2013-09-01

using the open source, JAVA -based image analysis software package ImageJ (http://rsb.info.nih.gov/ij/) and a custom designed plugin (“Telometer...Tabulated data were stored in a MySQL (http://www.mysql.com) database and viewed through Microsoft Access (Microsoft Corp.). Statistical Analysis For

Integrating model behavior, optimization, and sensitivity/uncertainty analysis: overview and application of the MOUSE software toolbox

USDA-ARS?s Scientific Manuscript database

This paper provides an overview of the Model Optimization, Uncertainty, and SEnsitivity Analysis (MOUSE) software application, an open-source, Java-based toolbox of visual and numerical analysis components for the evaluation of environmental models. MOUSE is based on the OPTAS model calibration syst...

An Earthquake Information Service with Free and Open Source Tools

NASA Astrophysics Data System (ADS)

Schroeder, M.; Stender, V.; Jüngling, S.

2015-12-01

At the GFZ German Research Centre for Geosciences in Potsdam, the working group Earthquakes and Volcano Physics examines the spatiotemporal behavior of earthquakes. In this context also the hazards of volcanic eruptions and tsunamis are explored. The aim is to collect related information after the occurrence of such extreme event and make them available for science and partly to the public as quickly as possible. However, the overall objective of this research is to reduce the geological risks that emanate from such natural hazards. In order to meet the stated objectives and to get a quick overview about the seismicity of a particular region and to compare the situation to historical events, a comprehensive visualization was desired. Based on the web-accessible data from the famous GFZ GEOFON network a user-friendly web mapping application was realized. Further, this web service integrates historical and current earthquake information from the USGS earthquake database, and more historical events from various other catalogues like Pacheco, International Seismological Centre (ISC) and more. This compilation of sources is unique in Earth sciences. Additionally, information about historical and current occurrences of volcanic eruptions and tsunamis are also retrievable. Another special feature in the application is the containment of times via a time shifting tool. Users can interactively vary the visualization by moving the time slider. Furthermore, the application was realized by using the newest JavaScript libraries which enables the application to run in all sizes of displays and devices. Our contribution will present the making of, the architecture behind, and few examples of the look and feel of this application.

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.

PubMed

Weaver, Steven; Shank, Stephen D; Spielman, Stephanie J; Li, Michael; Muse, Spencer V; Kosakovsky Pond, Sergei L

2018-01-02

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally-executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey. org, and the underlying codebase is available from https://github.com/veg/datamonkey-js. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

Automatic optimisation of gamma dose rate sensor networks: The DETECT Optimisation Tool

NASA Astrophysics Data System (ADS)

Helle, K. B.; Müller, T. O.; Astrup, P.; Dyve, J. E.

2014-05-01

Fast delivery of comprehensive information on the radiological situation is essential for decision-making in nuclear emergencies. Most national radiological agencies in Europe employ gamma dose rate sensor networks to monitor radioactive pollution of the atmosphere. Sensor locations were often chosen using regular grids or according to administrative constraints. Nowadays, however, the choice can be based on more realistic risk assessment, as it is possible to simulate potential radioactive plumes. To support sensor planning, we developed the DETECT Optimisation Tool (DOT) within the scope of the EU FP 7 project DETECT. It evaluates the gamma dose rates that a proposed set of sensors might measure in an emergency and uses this information to optimise the sensor locations. The gamma dose rates are taken from a comprehensive library of simulations of atmospheric radioactive plumes from 64 source locations. These simulations cover the whole European Union, so the DOT allows evaluation and optimisation of sensor networks for all EU countries, as well as evaluation of fencing sensors around possible sources. Users can choose from seven cost functions to evaluate the capability of a given monitoring network for early detection of radioactive plumes or for the creation of dose maps. The DOT is implemented as a stand-alone easy-to-use JAVA-based application with a graphical user interface and an R backend. Users can run evaluations and optimisations, and display, store and download the results. The DOT runs on a server and can be accessed via common web browsers; it can also be installed locally.

Library Employment Sources on the Internet

ERIC Educational Resources Information Center

Barr, Catherine

2012-01-01

This article presents a list of online resources for library job seekers. This includes general sites/portals like American Library Association (ALA): Education & Careers and Canadian Library Association: Library Careers. It also includes sites by sector, employment agencies/commercial services, listservs and networking sites.

Using Pamphlets With Disadvantaged Adults. Public Library Training Institutes Library Service Guide Number Three.

ERIC Educational Resources Information Center

Schmidt, Susan K.

Pamphlets are a useful way of presenting alternative sources of information to disadvantaged adults. Pamphlets are easy to handle and to read, inexpensive, and provide current information of various topics of interest. This brief guide lists sources of free or inexpensive pamphlets and describes various methods for their display in the library,…

Fac-Back-OPAC: An Open Source Interface to Your Library System

ERIC Educational Resources Information Center

Beccaria, Mike; Scott, Dan

2007-01-01

The new Fac-Back-OPAC (a faceted backup OPAC) is built on code that was originally developed by Casey Durfee in February 2007. It represents the convergence of two prominent trends in library tools: the decoupling of discovery tools from the traditional integrated library system (ILS) and the use of readily available open source components to…

The Humanities: A Selective Guide to Information Sources. Fifth Edition. Library and Information Science Text Series.

ERIC Educational Resources Information Center

Blazek, Ron; Aversa, Elizabeth

This book provides a guide to humanities information sources for teachers and students in schools of library and information science, reference librarians, collection development officers in libraries, humanities scholars, and others who have information needs in the broad discipline. This fifth edition represents a more comprehensive and updated…

Atlas - a data warehouse for integrative bioinformatics.

PubMed

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

2005-02-21

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Atlas – a data warehouse for integrative bioinformatics

PubMed Central

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

2005-01-01

Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

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.

Google vs. the Library (Part III): Assessing the Quality of Sources Found by Undergraduates

ERIC Educational Resources Information Center

Georgas, Helen

2015-01-01

This study assesses and compares the quality of sources found by undergraduate students when doing research using both Google and a library (federated) search tool. Thirty undergraduates were asked to find four sources (one book, two articles, and one additional source of their choosing) related to a selected research topic. Students used both…

Airlift Operation Modeling Using Discrete Event Simulation (DES)

DTIC Science & Technology

2009-12-01

Java ......................................................................................................20 2. Simkit...JRE Java Runtime Environment JVM Java Virtual Machine lbs Pounds LAM Load Allocation Mode LRM Landing Spot Reassignment Mode LEGO Listener Event...SOFTWARE DEVELOPMENT ENVIRONMENT The following are the software tools and development environment used for constructing the models. 1. Java Java

Investigation of different coastal processes in Indonesian waters using SeaWiFS data

NASA Astrophysics Data System (ADS)

Hendiarti, Nani; Siegel, Herbert; Ohde, Thomas

2004-01-01

SeaWiFS data were applied to investigate coastal processes in Indonesian waters around the most populated island of Java. Coastal processes due to wind forcing were studied the first time using SeaWiFS-derived chlorophyll and TSM concentrations in combination with AVHRR-derived SST in the period from September 1997 to December 2001. Upwelling events were studied along the southern coast of Java during the southeast monsoon (June to September). Satellite-derived chlorophyll concentrations higher than 0.8 mg/ m3 and sea-surface temperatures lower than 28°C are indications of upwelling. Upwelling events influence the distribution and growth of phytoplankton and provide by that good feeding condition for zooplankton, larvae, juvenile and adult of pelagic fish. Coastal discharge into the western Java Sea contains organic and inorganic materials originating from different sources. Diffuse impacts, particularly from fish farms and aquaculture, as well as coastal erosion influence large coastal areas during the rainy season (December to March), and to a lesser extent during the dry season. Strong Citarum river discharge was observed during the transition phase from the rainy to the dry season (March and April), when the maximum amount of transported material reaches the sea. The river plume is evident from chlorophyll concentrations higher than 2.5 mg/ m3, and suspended particulate matter concentrations of more than 8 mg/dm3. The Sunda Strait is seasonally influenced by water transport from the Java Sea and from the Indian Ocean. The satellite data show that water transport from the Java Sea occurs during the pre-dominantly easterly winds period (June to September). This is characterized by warm water (SST higher than 29.5°C) and chlorophyll concentrations higher than 0.5 mg/ m3. This water transport influences the fish abundance in the Sunda Strait. High fish catches coincide with the presence of Java Sea water, while the surface currents lead to the migration of pelagic fish. Conversely, during the dominant westerly winds period, oceanic waters from the Indian Ocean with low chlorophyll concentrations influence the Sunda Strait water.

Medicus Deus: a review of factors affecting hospital library services to patients between 1790–1950

PubMed Central

Perryman, Carol

2006-01-01

Question: What are some of the historical societal, medical, and public health trends leading to today's provision of hospital library services to patients? Data Sources: Literature from the archives of the Bulletin of the Medical Library Association and other library sources, medical journals, primary historical documents, and texts from the history of medicine form the core of this review. Study Selection: The period of review extends from about 1790 through 1950 and focuses solely on trends in the United States. Of primary concern are explicitly documented examples that appear to illustrate the patient-physician relationship and those between librarians and their patient-patrons during the earliest years of the profession's development. Data Extraction: An historical timeline was created to allow the identification of major trends that may have affected library services. Multiple literature searches were conducted using library, medical, and health anthropology resources. When possible, primary sources were preferred over reviews. Main Results: Juxtapositioning historical events allows the reader to obtain an overview of the roots of consumer health services in medical libraries and to consider their potential legacy in today's health care libraries. Conclusion: This review article highlights early developments in hospital library service to patients. Further research is needed to verify a preliminary conclusion that in some medical library settings, services to the general public are shaped by the broader health care environment as it has evolved. PMID:16888658

Sources of Research on Ranganathan.

ERIC Educational Resources Information Center

Satija, Mohinder Partap

1987-01-01

Identifies and describes major sources of information on the life and work of Ranganathan, the leader of the Indian library movement and a major contributor to the fields of library and information science. (CLB)

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

Friedman-Hill, Ernest

Java Expert Shell System - Jess - is a rule engine and scripting environment written entirely in Sun's Java language, Jess was orginially inspired by the CLIPS expert system shell, but has grown int a complete, distinct JAVA-influenced environment of its own. Using Jess, you can build Java applets and applications that have the capacity to "reason" using knowledge you supply in the form of declarative rules. Jess is surprisingly fast, and for some problems is faster than CLIPS, in that many Jess scripts are valid CLIPS scripts and vice-versa. Like CLIPS, Jess uses the Rete algorithm to process rules,more » a very efficient mechanism for solving the difficult many-to-many matching problem. Jess adds many features to CLIPS, including backwards chaining and the ability to manipulate and directly reason about Java objects. Jess is also a powerful Java scripting environment, from which you can create Java objects and call Java methods without compiling any Java Code.« less

Petrographic and major elements results as indicator of the geothermal potential in Java

NASA Astrophysics Data System (ADS)

Indarto, S.; Setiawan, I.; Kausar, A.; Permana, dan H.

2018-02-01

Geothermal manifestations existed in West Java (Cilayu, Papandayan Mountain, Telagabodas, Karaha, Tampomas Mountain), Central Java (Slamet Mountain, Dieng) and East Java (Argopuro Mountain) show a difference in their mineral and geochemical compositions. The petrographic analysis of volcanic rocks from Garut (West Java) are basalt, andesite basaltic and andesite. However, based on SiO2 vs K2O value, those volcanic rocks have wide ranges of fractionated magma resulting basalt - basaltic andesite to dacitic in composition rather than those of Slamet Mountain, Dieng, and Argopuro Mountain areas which have a narrower range of fractionation magma resulting andesite basaltic and andesite in compositions. The volcanic rocks from Garut show tholeiitic affinity and calc-alkaline affinity. The geothermal potential of Java is assumed to be related to the magma fractionation level. Geothermal potential of West Java (Garut) is higher than that of Central Java (Slamet Mountain, Dieng) and East Java (Argopuro Mountain).

Users' Satisfaction with Library Services: A Case Study of Delta State University Library

ERIC Educational Resources Information Center

Ikolo, Violet E.

2015-01-01

The study focused on users' satisfaction with library services at the Delta State University main Library, Abraka, Delta State. The objective was to find out if users are satisfied with the services, facilities, the library environment, information sources and staff of the library. Using the descriptive survey design, the population for the study…

LIBRARY-DEPENDENT MICROBIAL SOURCE TRACKING OF ENTEROCOCCUS SP. USING AFLP AND BOX-PCR

EPA Science Inventory

Library-dependent microbial source tracking (LD MST) methods are one of the approaches used to identify nonpoint sources of fecal contamination in support of total maximum daily load implementation. However, LD MST methods have been questioned due to the high temporal and spatial...

Information Source Characteristics and Environmental Scanning by Academic Library Managers

ERIC Educational Resources Information Center

Babalhavaeji, Fahimeh; Farhadpoor, Mohammad Reza

2013-01-01

Purpose: This article examines characteristics of the external environment of library and information centres of Islamic Azad University in Iran, focusing on perceived environmental uncertainty and perceived source accessibility and quality, and their impacts on the amount of scanning and the frequency of information source use. Methods: This…

Unviersity of Rhode Island Library Reference Sources in Gerontology.

ERIC Educational Resources Information Center

Morrison, Catherine E.

Thirty-two sources in gerontology, located at the University of Rhode Island Library, are listed in this annotated bibliography as well as some interdisciplinary sources. This bibliography contains material published as recently as 1996 and includes annotations of an "Older Americans Almanac," bibliographies, a biographical dictionary,…

Jewish Studies: A Guide to Reference Sources.

ERIC Educational Resources Information Center

McGill Univ., Montreal (Quebec). McLennan Library.

An annotated bibliography to the reference sources for Jewish Studies in the McLennan Library of McGill University (Canada) is presented. Any titles in Hebrew characters are listed by their transliterated equivalents. There is also a list of relevant Library of Congress Subject Headings. General reference sources listed are: encyclopedias,…

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…

Are We Alone in the Universe?

ERIC Educational Resources Information Center

Waring, Scott M.; Herlihy, Christine

2015-01-01

Primary sources, as defined by the Library of Congress, are the "raw materials of history--original documents and objects which were created at the time under study" (Library of Congress, 2014, p. 1). Primary sources differ from secondary sources, which interpret events without the benefit of firsthand experience. While often employed in…

Federal Legislative Policy of the American Library Association.

ERIC Educational Resources Information Center

American Library Association, Chicago, IL. Legislation Committee.

The American Library Association's policy on federal legislation is based on its objectives of promoting and improving library service and librarianship. Representing those who use libraries as well as those who operate them, the Association is a source of information on libraries and information services for those concerned with formulating and…

Determining Indirect Cost Rates in Research Libraries. SPEC Kit 34.

ERIC Educational Resources Information Center

Association of Research Libraries, Washington, DC. Office of Management Studies.

This kit prepared by the Association of Research Libraries (ARL) contains 15 primary source documents on determining indirect cost rates in research libraries. The kit comprises: (1) six library cost studies and surveys, "Allocation of Library Expenditures to Research and Instruction" (University of Pennsylvania), "Sampling of Current Monograph…

A Virtual "Hello": A Web-Based Orientation to the Library.

ERIC Educational Resources Information Center

Borah, Eloisa Gomez

1997-01-01

Describes the development of Web-based library services and resources available at the Rosenfeld Library of the Anderson Graduate School of Management at University of California at Los Angeles. Highlights include library orientation sessions; virtual tours of the library; a database of basic business sources; and research strategies, including…

The Difficult Patron in the Academic Library: Problem Issues or Problem Patrons?

ERIC Educational Resources Information Center

Simmonds Patience L.; Ingold, Jane L.

2002-01-01

Identifies difficult patron issues in academic libraries from the librarians' perspectives and offers solutions to try and prevent them from becoming problems. Topics include labeling academic library users; eliminating sources of conflict between faculty and library staff; and conflicts between students and library staff. (Author/LRW)

Finding Information on the State Virtual Libraries

ERIC Educational Resources Information Center

Pappas, Marjorie L.

2004-01-01

The number of state virtual libraries is rapidly expanding. These virtual libraries might include collections of subscription databases; state weblinks and resources; digital collections of primary source documents; and a state union catalog or links to school, public, and academic library catalogs. Most of these virtual libraries include an…

Library Standards: Evidence of Library Effectiveness and Accreditation.

ERIC Educational Resources Information Center

Ebbinghouse, Carol

1999-01-01

Discusses accreditation standards for libraries based on experiences in an academic law library. Highlights include the accreditation process; the impact of distance education and remote technologies on accreditation; and a list of Internet sources of standards and information. (LRW)

Building Interactive Simulations in Web Pages without Programming.

PubMed

Mailen Kootsey, J; McAuley, Grant; Bernal, Julie

2005-01-01

A software system is described for building interactive simulations and other numerical calculations in Web pages. The system is based on a new Java-based software architecture named NumberLinX (NLX) that isolates each function required to build the simulation so that a library of reusable objects could be assembled. The NLX objects are integrated into a commercial Web design program for coding-free page construction. The model description is entered through a wizard-like utility program that also functions as a model editor. The complete system permits very rapid construction of interactive simulations without coding. A wide range of applications are possible with the system beyond interactive calculations, including remote data collection and processing and collaboration over a network.

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

PubMed

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

Learning Extended Finite State Machines

NASA Technical Reports Server (NTRS)

Cassel, Sofia; Howar, Falk; Jonsson, Bengt; Steffen, Bernhard

2014-01-01

We present an active learning algorithm for inferring extended finite state machines (EFSM)s, combining data flow and control behavior. Key to our learning technique is a novel learning model based on so-called tree queries. The learning algorithm uses the tree queries to infer symbolic data constraints on parameters, e.g., sequence numbers, time stamps, identifiers, or even simple arithmetic. We describe sufficient conditions for the properties that the symbolic constraints provided by a tree query in general must have to be usable in our learning model. We have evaluated our algorithm in a black-box scenario, where tree queries are realized through (black-box) testing. Our case studies include connection establishment in TCP and a priority queue from the Java Class Library.

A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC.

PubMed

Song, Qingfeng; Chen, Dairui; Long, Stephen P; Zhu, Xin-Guang

2017-01-01

Windows Intuitive Model of Vegetation response to Atmosphere and Climate Change (WIMOVAC) has been used widely as a generic modular mechanistically rich model of plant production. It can predict the responses of leaf and canopy carbon balance, as well as production in different environmental conditions, in particular those relevant to global change. Here, we introduce an open source Java user-friendly version of WIMOVAC. This software is platform independent and can be easily downloaded to a laptop and used without any prior programming skills. In this article, we describe the structure, equations and user guide and illustrate some potential applications of WIMOVAC. © 2016 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

Multi-source water pollution in the Upper Citarum watershed, Indonesia, with special reference to its spatiotemporal variation.

PubMed

Parikesit; Salim, H; Triharyanto, E; Gunawan, B; Sunardi; Abdoellah, O S; Ohtsuka, R

2005-01-01

The Citarum River in West Java is the largest water supplier to the Saguling Dam, which plays a major role in electric power generation for the entire Java Island and is used for the aquaculture of marketed fish. To elucidate the extent of degradation in water quality and its causes in the Upper Citarum watershed, physical, chemical and biological parameters for water samples collected from various sites were analyzed. The results demonstrate large site-to-site variations in water qualities and pollutant loads derived from various human activities such as agriculture, cattle raising and the textile industry. To halt worsening conditions of the Citarum watershed, integrated mitigation efforts should be made, taking biophysical pollution mechanisms and local socioeconomic conditions into account.

ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

PubMed

Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

2016-01-01

To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

Integrating an Educational Game in Moodle LMS

ERIC Educational Resources Information Center

Minovic, Miroslav; Milovanovic, Milos; Minovic, Jelena; Starcevic, Dusan

2012-01-01

The authors present a learning platform based on a computer game. Learning games combine two industries: education and entertainment, which is often called "Edutainment." The game is realized as a strategic game (similar to Risk[TM]), implemented as a module for Moodle CMS, utilizing Java Applet technology. Moodle is an open-source course…

Biomolecules in the Computer: Jmol to the Rescue

ERIC Educational Resources Information Center

Herraez, Angel

2006-01-01

Jmol is free, open source software for interactive molecular visualization. Since it is written in the Java[TM] programming language, it is compatible with all major operating systems and, in the applet form, with most modern web browsers. This article summarizes Jmol development and features that make it a valid and promising replacement for…

LBNL Neutrino Astrophysics

Science.gov Websites

The KATRIN experiment The KATRIN experiment is designed to make a direct measurement of the mass experiment, scaled up by an order of magnitude in size, precision and tritium source intensity from previous experiments. Visit the experiment home page for more information. Gallery SimpleViewer requires JavaScript and

Vegetation Structure of Ebony Leaf Monkey (Trachypithecus auratus) Habitat in Kecubung Ulolanang Nature Preservation Central Java-Indonesia

NASA Astrophysics Data System (ADS)

Ervina, Rahmawati; Wasiq, Hidayat Jafron

2018-02-01

Kecubung Ulolanang Nature Preservation is ebony leaf monkey's habitats in Central Java Indonesia. Continuously degradation of their population is caused by illegal hunting and habitat degradation that made this species being vulnerable. Habitat conservation is one of important aspects to prevent them from extinction. The purpose of this research was to analyze the vegetation's structure and composition, which was potentially, becomes habitat and food source for the monkeys. Data collected using purposive sampling with line transect method of four different level of vegetation. Data analysis used Important Value Index and Diversity Index. There were 43 species of vegetation at seedling stage, 18 species at sapling stage, 8 species at poles stage and 27 species at trees stage. Species that had the highest important value index at seedling was Stenochlaena palustri , at the sapling was Gnetum gnemon, at pole was Swietenia mahagoni and at tree was Tectona grandis . Species of trees those were potentially to become habitat (food source) for ebony leaf monkey were T. grandis, Dipterocarpus gracilis, Quercus sundaica and Ficus superba. The highest diversity index was at seedling gwoth stage.

Application of a Java-based, univel geometry, neutral particle Monte Carlo code to the searchlight problem

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

Charles A. Wemple; Joshua J. Cogliati

2005-04-01

A univel geometry, neutral particle Monte Carlo transport code, written entirely in the Java programming language, is under development for medical radiotherapy applications. The code uses ENDF-VI based continuous energy cross section data in a flexible XML format. Full neutron-photon coupling, including detailed photon production and photonuclear reactions, is included. Charged particle equilibrium is assumed within the patient model so that detailed transport of electrons produced by photon interactions may be neglected. External beam and internal distributed source descriptions for mixed neutron-photon sources are allowed. Flux and dose tallies are performed on a univel basis. A four-tap, shift-register-sequence random numbermore » generator is used. Initial verification and validation testing of the basic neutron transport routines is underway. The searchlight problem was chosen as a suitable first application because of the simplicity of the physical model. Results show excellent agreement with analytic solutions. Computation times for similar numbers of histories are comparable to other neutron MC codes written in C and FORTRAN.« less

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/.

Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models.

PubMed

Jardine, Bartholomew; Raymond, Gary M; Bassingthwaighte, James B

2015-01-01

The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) ( http://www.physiome.org/jsim/) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle in writing complex models for physiological processes is the large amount of time it takes to model the myriad processes taking place simultaneously in cells, tissues, and organs. MPC replaces this task with code-generating algorithms that take model code from several different existing models and produce model code for a new JSim model. This is particularly useful during multi-scale model development where many variants are to be configured and tested against data. MPC encodes and preserves information about how a model is built from its simpler model modules, allowing the researcher to quickly substitute or update modules for hypothesis testing. MPC is implemented in Java and requires JSim to use its output. MPC source code and documentation are available at http://www.physiome.org/software/MPC/.

Passive acoustic source localization using sources of opportunity.

PubMed

Verlinden, Christopher M A; Sarkar, J; Hodgkiss, W S; Kuperman, W A; Sabra, K G

2015-07-01

The feasibility of using data derived replicas from ships of opportunity for implementing matched field processing is demonstrated. The Automatic Identification System (AIS) is used to provide the library coordinates for the replica library and a correlation based processing procedure is used to overcome the impediment that the replica library is constructed from sources with different spectra and will further be used to locate another source with its own unique spectral structure. The method is illustrated with simulation and then verified using acoustic data from a 2009 experiment for which AIS information was retrieved from the United States Coast Guard Navigation Center Nationwide AIS database.

Development of a Web-Based Distributed Interactive Simulation (DIS) Environment Using JavaScript

DTIC Science & Technology

2014-09-01

scripting that let users change or interact with web content depending on user input, which is in contrast with server-side scripts such as PHP, Java and...transfer, DIS usually broadcasts or multicasts its PDUs based on UDP socket. 3. JavaScript JavaScript is the scripting language of the web, and all...IDE) for developing desktop, mobile and web applications with JAVA , C++, HTML5, JavaScript and more. b. Framework The DIS implementation of

Direct comparison of linear and macrocyclic compound libraries as a source of protein ligands.

PubMed

Gao, Yu; Kodadek, Thomas

2015-03-09

There has been much discussion of the potential desirability of macrocyclic molecules for the development of tool compounds and drug leads. But there is little experimental data comparing otherwise equivalent macrocyclic and linear compound libraries as a source of protein ligands. In this Letter, we probe this point in the context of peptoid libraries. Bead-displayed libraries of macrocyclic and linear peptoids containing four variable positions and 0-2 fixed residues, to vary the ring size, were screened against streptavidin and the affinity of every hit for the target was measured. The data show that macrocyclization is advantageous, but only when the ring contains 17 atoms, not 20 or 23 atoms. This technology will be useful for conducting direct comparisons between many different types of chemical libraries to determine their relative utility as a source of protein ligands.

Chronology of KSC and KSC Related Events for 2000

NASA Technical Reports Server (NTRS)

Liston, Elaine E.; Atkins, Donna A.; Guelzow, Deborah A.

2001-01-01

This document is intended to serve as a record of Kennedy Space Center (KSC) events and is a reference source for historians and other researchers. Arrangement is by day and month and individual articles are attributed to published sources. Materials were researched and described by the KSC Library Archivist with assistance from KSC Library Librarians for KSC Library Services Contractor InDyne, Inc.