Sample records for java source code

  1. Java Source Code Analysis for API Migration to Embedded Systems

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

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

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

  2. MzJava: An open source library for mass spectrometry data processing.

    PubMed

    Horlacher, Oliver; Nikitin, Frederic; Alocci, Davide; Mariethoz, Julien; Müller, Markus; Lisacek, Frederique

    2015-11-03

    Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library's API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. 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.

  4. The r-Java 2.0 code: nuclear physics

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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++.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. Jannovar: a java library for exome annotation.

    PubMed

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

    2014-05-01

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

  18. SPV: a JavaScript Signaling Pathway Visualizer.

    PubMed

    Calderone, Alberto; Cesareni, Gianni

    2018-03-24

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

  19. 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.

  20. New Web Server - the Java Version of Tempest - Produced

    NASA Technical Reports Server (NTRS)

    York, David W.; Ponyik, Joseph G.

    2000-01-01

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

  1. 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

  2. Conversion of the agent-oriented domain-specific language ALAS into JavaScript

    NASA Astrophysics Data System (ADS)

    Sredojević, Dejan; Vidaković, Milan; Okanović, Dušan; Mitrović, Dejan; Ivanović, Mirjana

    2016-06-01

    This paper shows generation of JavaScript code from code written in agent-oriented domain-specific language ALAS. ALAS is an agent-oriented domain-specific language for writing software agents that are executed within XJAF middleware. Since the agents can be executed on various platforms, they must be converted into a language of the target platform. We also try to utilize existing tools and technologies to make the whole conversion process as simple as possible, as well as faster and more efficient. We use the Xtext framework that is compatible with Java to implement ALAS infrastructure - editor and code generator. Since Xtext supports Java, generation of Java code from ALAS code is straightforward. To generate a JavaScript code that will be executed within the target JavaScript XJAF implementation, Google Web Toolkit (GWT) is used.

  3. 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.

  4. 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.

  5. Java PathFinder: A Translator From Java to Promela

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus

    1999-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Marchetti, Luca; Manca, Vincenzo

    2015-04-15

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

  9. Monitoring Java Programs with Java PathExplorer

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  10. Practices in Code Discoverability: Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, A.; Teuben, P.; Nemiroff, R. J.; Shamir, L.

    2012-09-01

    Here we describe the Astrophysics Source Code Library (ASCL), which takes an active approach to sharing astrophysics source code. ASCL's editor seeks out both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and adds entries for the found codes to the library. This approach ensures that source codes are added without requiring authors to actively submit them, resulting in a comprehensive listing that covers a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL now has over 340 codes in it and continues to grow. In 2011, the ASCL has on average added 19 codes per month. An advisory committee has been established to provide input and guide the development and expansion of the new site, and a marketing plan has been developed and is being executed. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are freely available either via a download site or from an identified source. This paper provides the history and description of the ASCL. It lists the requirements for including codes, examines the advantages of the ASCL, and outlines some of its future plans.

  11. 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/

  12. TrackEtching - A Java based code for etched track profile calculations in SSNTDs

    NASA Astrophysics Data System (ADS)

    Muraleedhara Varier, K.; Sankar, V.; Gangadathan, M. P.

    2017-09-01

    A java code incorporating a user friendly GUI has been developed to calculate the parameters of chemically etched track profiles of ion-irradiated solid state nuclear track detectors. Huygen's construction of wavefronts based on secondary wavelets has been used to numerically calculate the etched track profile as a function of the etching time. Provision for normal incidence and oblique incidence on the detector surface has been incorporated. Results in typical cases are presented and compared with experimental data. Different expressions for the variation of track etch rate as a function of the ion energy have been utilized. The best set of values of the parameters in the expressions can be obtained by comparing with available experimental data. Critical angle for track development can also be calculated using the present code.

  13. 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

  14. Scientific Programming Using Java: A Remote Sensing Example

    NASA Technical Reports Server (NTRS)

    Prados, Don; Mohamed, Mohamed A.; Johnson, Michael; Cao, Changyong; Gasser, Jerry

    1999-01-01

    This paper presents results of a project to port remote sensing code from the C programming language to Java. The advantages and disadvantages of using Java versus C as a scientific programming language in remote sensing applications are discussed. Remote sensing applications deal with voluminous data that require effective memory management, such as buffering operations, when processed. Some of these applications also implement complex computational algorithms, such as Fast Fourier Transformation analysis, that are very performance intensive. Factors considered include performance, precision, complexity, rapidity of development, ease of code reuse, ease of maintenance, memory management, and platform independence. Performance of radiometric calibration code written in Java for the graphical user interface and of using C for the domain model are also presented.

  15. 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.

  16. 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.

  17. 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/.

  18. Version 4.0 of code Java for 3D simulation of the CCA model

    NASA Astrophysics Data System (ADS)

    Fan, Linyu; Liao, Jianwei; Zuo, Junsen; Zhang, Kebo; Li, Chao; Xiong, Hailing

    2018-07-01

    This paper presents a new version Java code for the three-dimensional simulation of Cluster-Cluster Aggregation (CCA) model to replace the previous version. Many redundant traverses of clusters-list in the program were totally avoided, so that the consumed simulation time is significantly reduced. In order to show the aggregation process in a more intuitive way, we have labeled different clusters with varied colors. Besides, a new function is added for outputting the particle's coordinates of aggregates in file to benefit coupling our model with other models.

  19. 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.

  20. Adaptive distributed source coding.

    PubMed

    Varodayan, David; Lin, Yao-Chung; Girod, Bernd

    2012-05-01

    We consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive the Slepian-Wolf bound and devise coding algorithms for a block-candidate model of this problem. The encoder sends, in addition to syndrome bits, a portion of the source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source symbols and the hidden statistical dependence variables. We also develop novel techniques based on density evolution (DE) to analyze the coding algorithms. We experimentally confirm that our DE analysis closely approximates practical performance. This result allows us to efficiently optimize parameters of the algorithms. In particular, we show that the system performs close to the Slepian-Wolf bound when an appropriate doping rate is selected. We then apply our coding and analysis techniques to a reduced-reference video quality monitoring system and show a bit rate saving of about 75% compared with fixed-length coding.

  1. Java Application Shell: A Framework for Piecing Together Java Applications

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  2. Authorship Attribution of Source Code

    ERIC Educational Resources Information Center

    Tennyson, Matthew F.

    2013-01-01

    Authorship attribution of source code is the task of deciding who wrote a program, given its source code. Applications include software forensics, plagiarism detection, and determining software ownership. A number of methods for the authorship attribution of source code have been presented in the past. A review of those existing methods is…

  3. Infrastructure for Rapid Development of Java GUI Programs

    NASA Technical Reports Server (NTRS)

    Jones, Jeremy; Hostetter, Carl F.; Wheeler, Philip

    2006-01-01

    The Java Application Shell (JAS) is a software framework that accelerates the development of Java graphical-user-interface (GUI) application programs by enabling the reuse of common, proven GUI elements, as distinguished from writing custom code for GUI elements. JAS is a software infrastructure upon which Java interactive application programs and graphical user interfaces (GUIs) for those programs can be built as sets of plug-ins. JAS provides an application- programming interface that is extensible by application-specific plugins that describe and encapsulate both specifications of a GUI and application-specific functionality tied to the specified GUI elements. The desired GUI elements are specified in Extensible Markup Language (XML) descriptions instead of in compiled code. JAS reads and interprets these descriptions, then creates and configures a corresponding GUI from a standard set of generic, reusable GUI elements. These elements are then attached (again, according to the XML descriptions) to application-specific compiled code and scripts. An application program constructed by use of JAS as its core can be extended by writing new plug-ins and replacing existing plug-ins. Thus, JAS solves many problems that Java programmers generally solve anew for each project, thereby reducing development and testing time.

  4. The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

    PubMed

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

    2015-09-01

    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/. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  6. Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, A.; DuPrie, K.; Berriman, B.; Hanisch, R. J.; Mink, J.; Teuben, P. J.

    2013-10-01

    The Astrophysics Source Code Library (ASCL), founded in 1999, is a free on-line registry for source codes of interest to astronomers and astrophysicists. The library is housed on the discussion forum for Astronomy Picture of the Day (APOD) and can be accessed at http://ascl.net. The ASCL has a comprehensive listing that covers a significant number of the astrophysics source codes used to generate results published in or submitted to refereed journals and continues to grow. The ASCL currently has entries for over 500 codes; its records are citable and are indexed by ADS. The editors of the ASCL and members of its Advisory Committee were on hand at a demonstration table in the ADASS poster room to present the ASCL, accept code submissions, show how the ASCL is starting to be used by the astrophysics community, and take questions on and suggestions for improving the resource.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  8. 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.

  9. Schroedinger’s code: Source code availability and transparency in astrophysics

    NASA Astrophysics Data System (ADS)

    Ryan, PW; Allen, Alice; Teuben, Peter

    2018-01-01

    Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.

  10. Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

    NASA Technical Reports Server (NTRS)

    Ancheta, T. C., Jr.

    1976-01-01

    A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

  11. Syndrome source coding and its universal generalization

    NASA Technical Reports Server (NTRS)

    Ancheta, T. C., Jr.

    1975-01-01

    A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A universal generalization of syndrome-source-coding is formulated which provides robustly-effective, distortionless, coding of source ensembles.

  12. 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…

  13. 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

  14. 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.

  15. Scientific Programming Using Java and C: A Remote Sensing Example

    NASA Technical Reports Server (NTRS)

    Prados, Donald; Johnson, Michael; Mohamed, Mohamed A.; Cao, Chang-Yong; Gasser, Jerry; Powell, Don; McGregor, Lloyd

    1999-01-01

    This paper presents results of a project to port code for processing remotely sensed data from the UNIX environment to Windows. Factors considered during this process include time schedule, cost, resource availability, reuse of existing code, rapid interface development, ease of integration, and platform independence. The approach selected for this project used both Java and C. By using Java for the graphical user interface and C for the domain model, the strengths of both languages were utilized and the resulting code can easily be ported to other platforms. The advantages of this approach are discussed in this paper.

  16. Supporting the Cybercrime Investigation Process: Effective Discrimination of Source Code Authors Based on Byte-Level Information

    NASA Astrophysics Data System (ADS)

    Frantzeskou, Georgia; Stamatatos, Efstathios; Gritzalis, Stefanos

    Source code authorship analysis is the particular field that attempts to identify the author of a computer program by treating each program as a linguistically analyzable entity. This is usually based on other undisputed program samples from the same author. There are several cases where the application of such a method could be of a major benefit, such as tracing the source of code left in the system after a cyber attack, authorship disputes, proof of authorship in court, etc. In this paper, we present our approach which is based on byte-level n-gram profiles and is an extension of a method that has been successfully applied to natural language text authorship attribution. We propose a simplified profile and a new similarity measure which is less complicated than the algorithm followed in text authorship attribution and it seems more suitable for source code identification since is better able to deal with very small training sets. Experiments were performed on two different data sets, one with programs written in C++ and the second with programs written in Java. Unlike the traditional language-dependent metrics used by previous studies, our approach can be applied to any programming language with no additional cost. The presented accuracy rates are much better than the best reported results for the same data sets.

  17. 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

  18. 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/.

  19. The Astrophysics Source Code Library: An Update

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Nemiroff, R. J.; Shamir, L.; Teuben, P. J.

    2012-01-01

    The Astrophysics Source Code Library (ASCL), founded in 1999, takes an active approach to sharing astrophysical source code. ASCL's editor seeks out both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and adds entries for the found codes to the library. This approach ensures that source codes are added without requiring authors to actively submit them, resulting in a comprehensive listing that covers a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL moved to a new location in 2010, and has over 300 codes in it and continues to grow. In 2011, the ASCL (http://asterisk.apod.com/viewforum.php?f=35) has on average added 19 new codes per month; we encourage scientists to submit their codes for inclusion. An advisory committee has been established to provide input and guide the development and expansion of its new site, and a marketing plan has been developed and is being executed. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are freely available either via a download site or from an identified source. This presentation covers the history of the ASCL and examines the current state and benefits of the ASCL, the means of and requirements for including codes, and outlines its future plans.

  20. 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.

  1. Model Checker for Java Programs

    NASA Technical Reports Server (NTRS)

    Visser, Willem

    2007-01-01

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

  2. 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

  3. 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.

  4. 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 .

  5. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  6. JIP: Java image processing on the Internet

    NASA Astrophysics Data System (ADS)

    Wang, Dongyan; Lin, Bo; Zhang, Jun

    1998-12-01

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

  7. 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

  8. Java simulations of embedded control systems.

    PubMed

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

    2010-01-01

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

  9. Java Simulations of Embedded Control Systems

    PubMed Central

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

    2010-01-01

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

  10. Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

    NASA Astrophysics Data System (ADS)

    Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

    2018-01-01

    The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

  11. 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.

  12. Multidimensional incremental parsing for universal source coding.

    PubMed

    Bae, Soo Hyun; Juang, Biing-Hwang

    2008-10-01

    A multidimensional incremental parsing algorithm (MDIP) for multidimensional discrete sources, as a generalization of the Lempel-Ziv coding algorithm, is investigated. It consists of three essential component schemes, maximum decimation matching, hierarchical structure of multidimensional source coding, and dictionary augmentation. As a counterpart of the longest match search in the Lempel-Ziv algorithm, two classes of maximum decimation matching are studied. Also, an underlying behavior of the dictionary augmentation scheme for estimating the source statistics is examined. For an m-dimensional source, m augmentative patches are appended into the dictionary at each coding epoch, thus requiring the transmission of a substantial amount of information to the decoder. The property of the hierarchical structure of the source coding algorithm resolves this issue by successively incorporating lower dimensional coding procedures in the scheme. In regard to universal lossy source coders, we propose two distortion functions, the local average distortion and the local minimax distortion with a set of threshold levels for each source symbol. For performance evaluation, we implemented three image compression algorithms based upon the MDIP; one is lossless and the others are lossy. The lossless image compression algorithm does not perform better than the Lempel-Ziv-Welch coding, but experimentally shows efficiency in capturing the source structure. The two lossy image compression algorithms are implemented using the two distortion functions, respectively. The algorithm based on the local average distortion is efficient at minimizing the signal distortion, but the images by the one with the local minimax distortion have a good perceptual fidelity among other compression algorithms. Our insights inspire future research on feature extraction of multidimensional discrete sources.

  13. Source Code Plagiarism--A Student Perspective

    ERIC Educational Resources Information Center

    Joy, M.; Cosma, G.; Yau, J. Y.-K.; Sinclair, J.

    2011-01-01

    This paper considers the problem of source code plagiarism by students within the computing disciplines and reports the results of a survey of students in Computing departments in 18 institutions in the U.K. This survey was designed to investigate how well students understand the concept of source code plagiarism and to discover what, if any,…

  14. Making your code citable with the Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, Alice; DuPrie, Kimberly; Schmidt, Judy; Berriman, G. Bruce; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

    2016-01-01

    The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. It also provides a method to quantify the impact of source codes in a fashion similar to the science metrics of journal articles. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL's mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don't formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.

  15. Using the Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Teuben, P. J.; Berriman, G. B.; DuPrie, K.; Hanisch, R. J.; Mink, J. D.; Nemiroff, R. J.; Shamir, L.; Wallin, J. F.

    2013-01-01

    The Astrophysics Source Code Library (ASCL) is a free on-line registry of source codes that are of interest to astrophysicists; with over 500 codes, it is the largest collection of scientist-written astrophysics programs in existence. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are available either via a download site or from an identified source. An advisory committee formed in 2011 provides input and guides the development and expansion of the ASCL, and since January 2012, all accepted ASCL entries are indexed by ADS. Though software is increasingly important for the advancement of science in astrophysics, these methods are still often hidden from view or difficult to find. The ASCL (ascl.net/) seeks to improve the transparency and reproducibility of research by making these vital methods discoverable, and to provide recognition and incentive to those who write and release programs useful for astrophysics research. This poster provides a description of the ASCL, an update on recent additions, and the changes in the astrophysics community we are starting to see because of the ASCL.

  16. A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

    NASA Technical Reports Server (NTRS)

    Reed, John A.; Afjeh, Abdollah A.

    1997-01-01

    This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

  17. 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.

  18. 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.

  19. Astrophysics Source Code Library: Incite to Cite!

    NASA Astrophysics Data System (ADS)

    DuPrie, K.; Allen, A.; Berriman, B.; Hanisch, R. J.; Mink, J.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P.; Wallen, J. F.

    2014-05-01

    The Astrophysics Source Code Library (ASCl,http://ascl.net/) is an on-line registry of over 700 source codes that are of interest to astrophysicists, with more being added regularly. The ASCL actively seeks out codes as well as accepting submissions from the code authors, and all entries are citable and indexed by ADS. All codes have been used to generate results published in or submitted to a refereed journal and are available either via a download site or from an identified source. In addition to being the largest directory of scientist-written astrophysics programs available, the ASCL is also an active participant in the reproducible research movement with presentations at various conferences, numerous blog posts and a journal article. This poster provides a description of the ASCL and the changes that we are starting to see in the astrophysics community as a result of the work we are doing.

  20. Java, Indonesia

    NASA Image and Video Library

    1996-01-20

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

  1. Practices in source code sharing in astrophysics

    NASA Astrophysics Data System (ADS)

    Shamir, Lior; Wallin, John F.; Allen, Alice; Berriman, Bruce; Teuben, Peter; Nemiroff, Robert J.; Mink, Jessica; Hanisch, Robert J.; DuPrie, Kimberly

    2013-02-01

    While software and algorithms have become increasingly important in astronomy, the majority of authors who publish computational astronomy research do not share the source code they develop, making it difficult to replicate and reuse the work. In this paper we discuss the importance of sharing scientific source code with the entire astrophysics community, and propose that journals require authors to make their code publicly available when a paper is published. That is, we suggest that a paper that involves a computer program not be accepted for publication unless the source code becomes publicly available. The adoption of such a policy by editors, editorial boards, and reviewers will improve the ability to replicate scientific results, and will also make computational astronomy methods more available to other researchers who wish to apply them to their data.

  2. 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.

  3. Astrophysics Source Code Library Enhancements

    NASA Astrophysics Data System (ADS)

    Hanisch, R. J.; Allen, A.; Berriman, G. B.; DuPrie, K.; Mink, J.; Nemiroff, R. J.; Schmidt, J.; Shamir, L.; Shortridge, K.; Taylor, M.; Teuben, P. J.; Wallin, J.

    2015-09-01

    The Astrophysics Source Code Library (ASCL)1 is a free online registry of codes used in astronomy research; it currently contains over 900 codes and is indexed by ADS. The ASCL has recently moved a new infrastructure into production. The new site provides a true database for the code entries and integrates the WordPress news and information pages and the discussion forum into one site. Previous capabilities are retained and permalinks to ascl.net continue to work. This improvement offers more functionality and flexibility than the previous site, is easier to maintain, and offers new possibilities for collaboration. This paper covers these recent changes to the ASCL.

  4. Using Java for distributed computing in the Gaia satellite data processing

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  5. Astronomy education and the Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Nemiroff, Robert J.

    2016-01-01

    The Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one's own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others' codes.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. Image authentication using distributed source coding.

    PubMed

    Lin, Yao-Chung; Varodayan, David; Girod, Bernd

    2012-01-01

    We present a novel approach using distributed source coding for image authentication. The key idea is to provide a Slepian-Wolf encoded quantized image projection as authentication data. This version can be correctly decoded with the help of an authentic image as side information. Distributed source coding provides the desired robustness against legitimate variations while detecting illegitimate modification. The decoder incorporating expectation maximization algorithms can authenticate images which have undergone contrast, brightness, and affine warping adjustments. Our authentication system also offers tampering localization by using the sum-product algorithm.

  11. Enhancing Web applications in radiology with Java: estimating MR imaging relaxation times.

    PubMed

    Dagher, A P; Fitzpatrick, M; Flanders, A E; Eng, J

    1998-01-01

    Java is a relatively new programming language that has been used to develop a World Wide Web-based tool for estimating magnetic resonance (MR) imaging relaxation times, thereby demonstrating how Java may be used for Web-based radiology applications beyond improving the user interface of teaching files. A standard processing algorithm coded with Java is downloaded along with the hypertext markup language (HTML) document. The user (client) selects the desired pulse sequence and inputs data obtained from a region of interest on the MR images. The algorithm is used to modify selected MR imaging parameters in an equation that models the phenomenon being evaluated. MR imaging relaxation times are estimated, and confidence intervals and a P value expressing the accuracy of the final results are calculated. Design features such as simplicity, object-oriented programming, and security restrictions allow Java to expand the capabilities of HTML by offering a more versatile user interface that includes dynamic annotations and graphics. Java also allows the client to perform more sophisticated information processing and computation than is usually associated with Web applications. Java is likely to become a standard programming option, and the development of stand-alone Java applications may become more common as Java is integrated into future versions of computer operating systems.

  12. 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.

  13. The Astrophysics Source Code Library by the numbers

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Teuben, Peter; Berriman, G. Bruce; DuPrie, Kimberly; Mink, Jessica; Nemiroff, Robert; Ryan, PW; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Wallin, John; Warmels, Rein

    2018-01-01

    The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear. It also discusses what changes have been made to the ASCL recently, and what its plans are for the future.

  14. Data processing with microcode designed with source coding

    DOEpatents

    McCoy, James A; Morrison, Steven E

    2013-05-07

    Programming for a data processor to execute a data processing application is provided using microcode source code. The microcode source code is assembled to produce microcode that includes digital microcode instructions with which to signal the data processor to execute the data processing application.

  15. Context-sensitive trace inlining for Java.

    PubMed

    Häubl, Christian; Wimmer, Christian; Mössenböck, Hanspeter

    2013-12-01

    Method inlining is one of the most important optimizations in method-based just-in-time (JIT) compilers. It widens the compilation scope and therefore allows optimizing multiple methods as a whole, which increases the performance. However, if method inlining is used too frequently, the compilation time increases and too much machine code is generated. This has negative effects on the performance. Trace-based JIT compilers only compile frequently executed paths, so-called traces, instead of whole methods. This may result in faster compilation, less generated machine code, and better optimized machine code. In the previous work, we implemented a trace recording infrastructure and a trace-based compiler for [Formula: see text], by modifying the Java HotSpot VM. Based on this work, we evaluate the effect of trace inlining on the performance and the amount of generated machine code. Trace inlining has several major advantages when compared to method inlining. First, trace inlining is more selective than method inlining, because only frequently executed paths are inlined. Second, the recorded traces may capture information about virtual calls, which simplify inlining. A third advantage is that trace information is context sensitive so that different method parts can be inlined depending on the specific call site. These advantages allow more aggressive inlining while the amount of generated machine code is still reasonable. We evaluate several inlining heuristics on the benchmark suites DaCapo 9.12 Bach, SPECjbb2005, and SPECjvm2008 and show that our trace-based compiler achieves an up to 51% higher peak performance than the method-based Java HotSpot client compiler. Furthermore, we show that the large compilation scope of our trace-based compiler has a positive effect on other compiler optimizations such as constant folding or null check elimination.

  16. 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

  17. Implementing the Gaia Astrometric Global Iterative Solution (AGIS) in Java

    NASA Astrophysics Data System (ADS)

    O'Mullane, William; Lammers, Uwe; Lindegren, Lennart; Hernandez, Jose; Hobbs, David

    2011-10-01

    This paper provides a description of the Java software framework which has been constructed to run the Astrometric Global Iterative Solution for the Gaia mission. This is the mathematical framework to provide the rigid reference frame for Gaia observations from the Gaia data itself. This process makes Gaia a self calibrated, and input catalogue independent, mission. The framework is highly distributed typically running on a cluster of machines with a database back end. All code is written in the Java language. We describe the overall architecture and some of the details of the implementation.

  18. Schroedinger’s Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Teuben, Peter J.; Ryan, P. Wesley

    2018-05-01

    We examined software usage in a sample set of astrophysics research articles published in 2015 and searched for the source codes for the software mentioned in these research papers. We categorized the software to indicate whether the source code is available for download and whether there are restrictions to accessing it, and if the source code is not available, whether some other form of the software, such as a binary, is. We also extracted hyperlinks from one journal’s 2015 research articles, as links in articles can serve as an acknowledgment of software use and lead to the data used in the research, and tested them to determine which of these URLs are still accessible. For our sample of 715 software instances in the 166 articles we examined, we were able to categorize 418 records as according to whether source code was available and found that 285 unique codes were used, 58% of which offered the source code for download. Of the 2558 hyperlinks extracted from 1669 research articles, at best, 90% of them were available over our testing period.

  19. Ptolemy Coding Style

    DTIC Science & Technology

    2014-09-05

    shell script that checks Java code and prints out an alphabetical list of unrec- ognized spellings. It properly handles namesWithEmbeddedCapitalization...local/bin/ispell. To run this script, type $PTII/util/testsuite/ptspell *.java • testsuite/chkjava is a shell script for checking various other...best if the svn:native property is set. Below is how to check the values for a file named README.txt: bash-3.2$ svn proplist README.txt Properties on

  20. 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…

  1. 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.

  2. 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.

  3. Streamlined Genome Sequence Compression using Distributed Source Coding

    PubMed Central

    Wang, Shuang; Jiang, Xiaoqian; Chen, Feng; Cui, Lijuan; Cheng, Samuel

    2014-01-01

    We aim at developing a streamlined genome sequence compression algorithm to support alternative miniaturized sequencing devices, which have limited communication, storage, and computation power. Existing techniques that require heavy client (encoder side) cannot be applied. To tackle this challenge, we carefully examined distributed source coding theory and developed a customized reference-based genome compression protocol to meet the low-complexity need at the client side. Based on the variation between source and reference, our protocol will pick adaptively either syndrome coding or hash coding to compress subsequences of changing code length. Our experimental results showed promising performance of the proposed method when compared with the state-of-the-art algorithm (GRS). PMID:25520552

  4. Estimation of toxicity using a Java based software tool

    EPA Science Inventory

    A software tool has been developed that will allow a user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be accessed using a web browser (or alternatively downloaded and ran as a stand alone applic...

  5. 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

  6. 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/

  7. 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.

  8. Distributed Joint Source-Channel Coding in Wireless Sensor Networks

    PubMed Central

    Zhu, Xuqi; Liu, Yu; Zhang, Lin

    2009-01-01

    Considering the fact that sensors are energy-limited and the wireless channel conditions in wireless sensor networks, there is an urgent need for a low-complexity coding method with high compression ratio and noise-resisted features. This paper reviews the progress made in distributed joint source-channel coding which can address this issue. The main existing deployments, from the theory to practice, of distributed joint source-channel coding over the independent channels, the multiple access channels and the broadcast channels are introduced, respectively. To this end, we also present a practical scheme for compressing multiple correlated sources over the independent channels. The simulation results demonstrate the desired efficiency. PMID:22408560

  9. 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

  10. Joint source-channel coding for motion-compensated DCT-based SNR scalable video.

    PubMed

    Kondi, Lisimachos P; Ishtiaq, Faisal; Katsaggelos, Aggelos K

    2002-01-01

    In this paper, we develop an approach toward joint source-channel coding for motion-compensated DCT-based scalable video coding and transmission. A framework for the optimal selection of the source and channel coding rates over all scalable layers is presented such that the overall distortion is minimized. The algorithm utilizes universal rate distortion characteristics which are obtained experimentally and show the sensitivity of the source encoder and decoder to channel errors. The proposed algorithm allocates the available bit rate between scalable layers and, within each layer, between source and channel coding. We present the results of this rate allocation algorithm for video transmission over a wireless channel using the H.263 Version 2 signal-to-noise ratio (SNR) scalable codec for source coding and rate-compatible punctured convolutional (RCPC) codes for channel coding. We discuss the performance of the algorithm with respect to the channel conditions, coding methodologies, layer rates, and number of layers.

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

    PubMed

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

    2010-04-01

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

  12. 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.

  13. Maximum aposteriori joint source/channel coding

    NASA Technical Reports Server (NTRS)

    Sayood, Khalid; Gibson, Jerry D.

    1991-01-01

    A maximum aposteriori probability (MAP) approach to joint source/channel coder design is presented in this paper. This method attempts to explore a technique for designing joint source/channel codes, rather than ways of distributing bits between source coders and channel coders. For a nonideal source coder, MAP arguments are used to design a decoder which takes advantage of redundancy in the source coder output to perform error correction. Once the decoder is obtained, it is analyzed with the purpose of obtaining 'desirable properties' of the channel input sequence for improving overall system performance. Finally, an encoder design which incorporates these properties is proposed.

  14. Model Checking Real Time Java Using Java PathFinder

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  15. Astrophysics Source Code Library -- Now even better!

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Schmidt, Judy; Berriman, Bruce; DuPrie, Kimberly; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

    2015-01-01

    The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. Indexed by ADS, it now contains nearly 1,000 codes and with recent major changes, is better than ever! The resource has a new infrastructure that offers greater flexibility and functionality for users, including an easier submission process, better browsing, one-click author search, and an RSS feeder for news. The new database structure is easier to maintain and offers new possibilities for collaboration. Come see what we've done!

  16. Operational rate-distortion performance for joint source and channel coding of images.

    PubMed

    Ruf, M J; Modestino, J W

    1999-01-01

    This paper describes a methodology for evaluating the operational rate-distortion behavior of combined source and channel coding schemes with particular application to images. In particular, we demonstrate use of the operational rate-distortion function to obtain the optimum tradeoff between source coding accuracy and channel error protection under the constraint of a fixed transmission bandwidth for the investigated transmission schemes. Furthermore, we develop information-theoretic bounds on performance for specific source and channel coding systems and demonstrate that our combined source-channel coding methodology applied to different schemes results in operational rate-distortion performance which closely approach these theoretical limits. We concentrate specifically on a wavelet-based subband source coding scheme and the use of binary rate-compatible punctured convolutional (RCPC) codes for transmission over the additive white Gaussian noise (AWGN) channel. Explicit results for real-world images demonstrate the efficacy of this approach.

  17. Towards Holography via Quantum Source-Channel Codes.

    PubMed

    Pastawski, Fernando; Eisert, Jens; Wilming, Henrik

    2017-07-14

    While originally motivated by quantum computation, quantum error correction (QEC) is currently providing valuable insights into many-body quantum physics, such as topological phases of matter. Furthermore, mounting evidence originating from holography research (AdS/CFT) indicates that QEC should also be pertinent for conformal field theories. With this motivation in mind, we introduce quantum source-channel codes, which combine features of lossy compression and approximate quantum error correction, both of which are predicted in holography. Through a recent construction for approximate recovery maps, we derive guarantees on its erasure decoding performance from calculations of an entropic quantity called conditional mutual information. As an example, we consider Gibbs states of the transverse field Ising model at criticality and provide evidence that they exhibit nontrivial protection from local erasure. This gives rise to the first concrete interpretation of a bona fide conformal field theory as a quantum error correcting code. We argue that quantum source-channel codes are of independent interest beyond holography.

  18. Towards Holography via Quantum Source-Channel Codes

    NASA Astrophysics Data System (ADS)

    Pastawski, Fernando; Eisert, Jens; Wilming, Henrik

    2017-07-01

    While originally motivated by quantum computation, quantum error correction (QEC) is currently providing valuable insights into many-body quantum physics, such as topological phases of matter. Furthermore, mounting evidence originating from holography research (AdS/CFT) indicates that QEC should also be pertinent for conformal field theories. With this motivation in mind, we introduce quantum source-channel codes, which combine features of lossy compression and approximate quantum error correction, both of which are predicted in holography. Through a recent construction for approximate recovery maps, we derive guarantees on its erasure decoding performance from calculations of an entropic quantity called conditional mutual information. As an example, we consider Gibbs states of the transverse field Ising model at criticality and provide evidence that they exhibit nontrivial protection from local erasure. This gives rise to the first concrete interpretation of a bona fide conformal field theory as a quantum error correcting code. We argue that quantum source-channel codes are of independent interest beyond holography.

  19. 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.

  20. JSXGraph--Dynamic Mathematics with JavaScript

    ERIC Educational Resources Information Center

    Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

    2010-01-01

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

  1. Distributed single source coding with side information

    NASA Astrophysics Data System (ADS)

    Vila-Forcen, Jose E.; Koval, Oleksiy; Voloshynovskiy, Sviatoslav V.

    2004-01-01

    In the paper we advocate image compression technique in the scope of distributed source coding framework. The novelty of the proposed approach is twofold: classical image compression is considered from the positions of source coding with side information and, contrarily to the existing scenarios, where side information is given explicitly, side information is created based on deterministic approximation of local image features. We consider an image in the transform domain as a realization of a source with a bounded codebook of symbols where each symbol represents a particular edge shape. The codebook is image independent and plays the role of auxiliary source. Due to the partial availability of side information at both encoder and decoder we treat our problem as a modification of Berger-Flynn-Gray problem and investigate a possible gain over the solutions when side information is either unavailable or available only at decoder. Finally, we present a practical compression algorithm for passport photo images based on our concept that demonstrates the superior performance in very low bit rate regime.

  2. 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.

  3. Model Checking JAVA Programs Using Java Pathfinder

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Pressburger, Thomas

    2000-01-01

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

  4. 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.

  5. 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).

  6. 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.

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  9. 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.

  10. Distributed Coding of Compressively Sensed Sources

    NASA Astrophysics Data System (ADS)

    Goukhshtein, Maxim

    In this work we propose a new method for compressing multiple correlated sources with a very low-complexity encoder in the presence of side information. Our approach uses ideas from compressed sensing and distributed source coding. At the encoder, syndromes of the quantized compressively sensed sources are generated and transmitted. The decoder uses side information to predict the compressed sources. The predictions are then used to recover the quantized measurements via a two-stage decoding process consisting of bitplane prediction and syndrome decoding. Finally, guided by the structure of the sources and the side information, the sources are reconstructed from the recovered measurements. As a motivating example, we consider the compression of multispectral images acquired on board satellites, where resources, such as computational power and memory, are scarce. Our experimental results exhibit a significant improvement in the rate-distortion trade-off when compared against approaches with similar encoder complexity.

  11. Java Programming Language

    NASA Technical Reports Server (NTRS)

    Shaykhian, Gholam Ali

    2007-01-01

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

  12. An Efficient Variable Length Coding Scheme for an IID Source

    NASA Technical Reports Server (NTRS)

    Cheung, K. -M.

    1995-01-01

    A scheme is examined for using two alternating Huffman codes to encode a discrete independent and identically distributed source with a dominant symbol. This combined strategy, or alternating runlength Huffman (ARH) coding, was found to be more efficient than ordinary coding in certain circumstances.

  13. Top ten reasons to register your code with the Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, Alice; DuPrie, Kimberly; Berriman, G. Bruce; Mink, Jessica D.; Nemiroff, Robert J.; Robitaille, Thomas; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Teuben, Peter J.; Wallin, John F.; Warmels, Rein

    2017-01-01

    With 1,400 codes, the Astrophysics Source Code Library (ASCL, ascl.net) is the largest indexed resource for codes used in astronomy research in existence. This free online registry was established in 1999, is indexed by Web of Science and ADS, and is citable, with citations to its entries tracked by ADS. Registering your code with the ASCL is easy with our online submissions system. Making your software available for examination shows confidence in your research and makes your research more transparent, reproducible, and falsifiable. ASCL registration allows your software to be cited on its own merits and provides a citation that is trackable and accepted by all astronomy journals and journals such as Science and Nature. Registration also allows others to find your code more easily. This presentation covers the benefits of registering astronomy research software with the ASCL.

  14. Joint inversion of active and passive seismic data in Central Java

    NASA Astrophysics Data System (ADS)

    Wagner, Diana; Koulakov, I.; Rabbel, W.; Luehr, B.-G.; Wittwer, A.; Kopp, H.; Bohm, M.; Asch, G.

    2007-08-01

    Seismic and volcanic activities in Central Java, Indonesia, the area of interest of this study, are directly or indirectly related to the subduction of the Indo-Australian plate. In the framework of the MERapi AMphibious EXperiments (MERAMEX), a network consisting of about 130 seismographic stations was installed onshore and offshore in Central Java and operated for more than 150 days. In addition, 3-D active seismic experiments were carried out offshore. In this paper, we present the results of processing combined active and passive seismic data, which contain traveltimes from 292 local earthquakes and additional airgun shots along three offshore profiles. The inversion was performed using the updated LOTOS-06 code that allows processing for active and passive source data. The joint inversion of the active and passive data set considerably improves the resolution of the upper crust, especially in the offshore area in comparison to only passive data. The inversion results are verified using a series of synthetic tests. The resulting images show an exceptionally strong low-velocity anomaly (-30 per cent) in the backarc crust northward of the active volcanoes. In the upper mantle beneath the volcanoes, we observe a low-velocity anomaly inclined towards the slab, which probably reflects the paths of fluids and partially melted materials in the mantle wedge. The crust in the forearc appears to be strongly heterogeneous. The onshore part consists of two high-velocity blocks separated by a narrow low-velocity anomaly, which can be interpreted as a weakened contact zone between two rigid crustal bodies. The recent Java Mw = 6.3 earthquake (2006/05/26-UTC) occurred at the lower edge of this zone. Its focal strike slip mechanism is consistent with the orientation of this contact.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  16. 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.

  17. Using National Drug Codes and drug knowledge bases to organize prescription records from multiple sources.

    PubMed

    Simonaitis, Linas; McDonald, Clement J

    2009-10-01

    The utility of National Drug Codes (NDCs) and drug knowledge bases (DKBs) in the organization of prescription records from multiple sources was studied. The master files of most pharmacy systems include NDCs and local codes to identify the products they dispense. We obtained a large sample of prescription records from seven different sources. These records carried a national product code or a local code that could be translated into a national product code via their formulary master. We obtained mapping tables from five DKBs. We measured the degree to which the DKB mapping tables covered the national product codes carried in or associated with the sample of prescription records. Considering the total prescription volume, DKBs covered 93.0-99.8% of the product codes from three outpatient sources and 77.4-97.0% of the product codes from four inpatient sources. Among the in-patient sources, invented codes explained 36-94% of the noncoverage. Outpatient pharmacy sources rarely invented codes, which comprised only 0.11-0.21% of their total prescription volume, compared with inpatient pharmacy sources for which invented codes comprised 1.7-7.4% of their prescription volume. The distribution of prescribed products was highly skewed, with 1.4-4.4% of codes accounting for 50% of the message volume and 10.7-34.5% accounting for 90% of the message volume. DKBs cover the product codes used by outpatient sources sufficiently well to permit automatic mapping. Changes in policies and standards could increase coverage of product codes used by inpatient sources.

  18. PDDL4J: a planning domain description library for java

    NASA Astrophysics Data System (ADS)

    Pellier, D.; Fiorino, H.

    2018-01-01

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

  19. An interactive HTML ocean nowcast GUI based on Perl and JavaScript

    NASA Astrophysics Data System (ADS)

    Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

    1999-02-01

    We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

  20. Continuation of research into language concepts for the mission support environment: Source code

    NASA Technical Reports Server (NTRS)

    Barton, Timothy J.; Ratner, Jeremiah M.

    1991-01-01

    Research into language concepts for the Mission Control Center is presented. A computer code for source codes is presented. The file contains the routines which allow source code files to be created and compiled. The build process assumes that all elements and the COMP exist in the current directory. The build process places as much code generation as possible on the preprocessor as possible. A summary is given of the source files as used and/or manipulated by the build routine.

  1. The FORTRAN static source code analyzer program (SAP) system description

    NASA Technical Reports Server (NTRS)

    Decker, W.; Taylor, W.; Merwarth, P.; Oneill, M.; Goorevich, C.; Waligora, S.

    1982-01-01

    A source code analyzer program (SAP) designed to assist personnel in conducting studies of FORTRAN programs is described. The SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. The processing performed by SAP and of the routines, COMMON blocks, and files used by SAP are described. The system generation procedure for SAP is also presented.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  4. The random energy model in a magnetic field and joint source channel coding

    NASA Astrophysics Data System (ADS)

    Merhav, Neri

    2008-09-01

    We demonstrate that there is an intimate relationship between the magnetic properties of Derrida’s random energy model (REM) of spin glasses and the problem of joint source-channel coding in Information Theory. In particular, typical patterns of erroneously decoded messages in the coding problem have “magnetization” properties that are analogous to those of the REM in certain phases, where the non-uniformity of the distribution of the source in the coding problem plays the role of an external magnetic field applied to the REM. We also relate the ensemble performance (random coding exponents) of joint source-channel codes to the free energy of the REM in its different phases.

  5. A Telemetry Browser Built with Java Components

    NASA Astrophysics Data System (ADS)

    Poupart, E.

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

  6. 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.

  7. FOUNTAIN: A JAVA open-source package to assist large sequencing projects

    PubMed Central

    Buerstedde, Jean-Marie; Prill, Florian

    2001-01-01

    Background Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences. Results We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented. Conclusions A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort. PMID:11591214

  8. 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.

  9. Volcanoes, Central Java, Indonesia

    NASA Technical Reports Server (NTRS)

    1992-01-01

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

  10. Volcanoes, Central Java, Indonesia

    NASA Image and Video Library

    1992-08-08

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

  11. Software Model Checking Without Source Code

    NASA Technical Reports Server (NTRS)

    Chaki, Sagar; Ivers, James

    2009-01-01

    We present a framework, called AIR, for verifying safety properties of assembly language programs via software model checking. AIR extends the applicability of predicate abstraction and counterexample guided abstraction refinement to the automated verification of low-level software. By working at the assembly level, AIR allows verification of programs for which source code is unavailable-such as legacy and COTS software-and programs that use features-such as pointers, structures, and object-orientation-that are problematic for source-level software verification tools. In addition, AIR makes no assumptions about the underlying compiler technology. We have implemented a prototype of AIR and present encouraging results on several non-trivial examples.

  12. Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey

    NASA Astrophysics Data System (ADS)

    Guillemot, Christine; Siohan, Pierre

    2005-12-01

    Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS) provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD) strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM) capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC) and variable-length source codes (VLC) widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2018-05-01

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

  15. Joint Source-Channel Coding by Means of an Oversampled Filter Bank Code

    NASA Astrophysics Data System (ADS)

    Marinkovic, Slavica; Guillemot, Christine

    2006-12-01

    Quantized frame expansions based on block transforms and oversampled filter banks (OFBs) have been considered recently as joint source-channel codes (JSCCs) for erasure and error-resilient signal transmission over noisy channels. In this paper, we consider a coding chain involving an OFB-based signal decomposition followed by scalar quantization and a variable-length code (VLC) or a fixed-length code (FLC). This paper first examines the problem of channel error localization and correction in quantized OFB signal expansions. The error localization problem is treated as an[InlineEquation not available: see fulltext.]-ary hypothesis testing problem. The likelihood values are derived from the joint pdf of the syndrome vectors under various hypotheses of impulse noise positions, and in a number of consecutive windows of the received samples. The error amplitudes are then estimated by solving the syndrome equations in the least-square sense. The message signal is reconstructed from the corrected received signal by a pseudoinverse receiver. We then improve the error localization procedure by introducing a per-symbol reliability information in the hypothesis testing procedure of the OFB syndrome decoder. The per-symbol reliability information is produced by the soft-input soft-output (SISO) VLC/FLC decoders. This leads to the design of an iterative algorithm for joint decoding of an FLC and an OFB code. The performance of the algorithms developed is evaluated in a wavelet-based image coding system.

  16. 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.

  17. Solving Semantic Searches for Source Code

    DTIC Science & Technology

    2012-11-01

    but of input and expected output pairs. In this domain, those inputs take the form of strings and outputs could be one of sev- eral datatypes ...for some relaxation of CPi that yields C ′ Pi . Encoding weakening is performed by systematically making the constraints on a particular datatype ...the datatypes that can hold concrete or symbolic values: integers, characters, booleans, and strings. The Java implementation uses all the data types

  18. Process Model Improvement for Source Code Plagiarism Detection in Student Programming Assignments

    ERIC Educational Resources Information Center

    Kermek, Dragutin; Novak, Matija

    2016-01-01

    In programming courses there are various ways in which students attempt to cheat. The most commonly used method is copying source code from other students and making minimal changes in it, like renaming variable names. Several tools like Sherlock, JPlag and Moss have been devised to detect source code plagiarism. However, for larger student…

  19. JaSTA-2: Second version of the Java Superposition T-matrix Application

    NASA Astrophysics Data System (ADS)

    Halder, Prithish; Das, Himadri Sekhar

    2017-12-01

    In this article, we announce the development of a new version of the Java Superposition T-matrix App (JaSTA-2), to study the light scattering properties of porous aggregate particles. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precision superposition T-matrix codes for multi-sphere clusters in random orientation, developed by Mackowski and Mischenko (1996). The new version consists of two options as part of the input parameters: (i) single wavelength and (ii) multiple wavelengths. The first option (which retains the applicability of older version of JaSTA) calculates the light scattering properties of aggregates of spheres for a single wavelength at a given instant of time whereas the second option can execute the code for a multiple numbers of wavelengths in a single run. JaSTA-2 provides convenient and quicker data analysis which can be used in diverse fields like Planetary Science, Atmospheric Physics, Nanoscience, etc. This version of the software is developed for Linux platform only, and it can be operated over all the cores of a processor using the multi-threading option.

  20. 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

  1. Java: An Explosion on the Internet.

    ERIC Educational Resources Information Center

    Read, Tim; Hall, Hazel

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

  2. 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

  3. Model-Based Least Squares Reconstruction of Coded Source Neutron Radiographs: Integrating the ORNL HFIR CG1D Source Model

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

    Santos-Villalobos, Hector J; Gregor, Jens; Bingham, Philip R

    2014-01-01

    At the present, neutron sources cannot be fabricated small and powerful enough in order to achieve high resolution radiography while maintaining an adequate flux. One solution is to employ computational imaging techniques such as a Magnified Coded Source Imaging (CSI) system. A coded-mask is placed between the neutron source and the object. The system resolution is increased by reducing the size of the mask holes and the flux is increased by increasing the size of the coded-mask and/or the number of holes. One limitation of such system is that the resolution of current state-of-the-art scintillator-based detectors caps around 50um. Tomore » overcome this challenge, the coded-mask and object are magnified by making the distance from the coded-mask to the object much smaller than the distance from object to detector. In previous work, we have shown via synthetic experiments that our least squares method outperforms other methods in image quality and reconstruction precision because of the modeling of the CSI system components. However, the validation experiments were limited to simplistic neutron sources. In this work, we aim to model the flux distribution of a real neutron source and incorporate such a model in our least squares computational system. We provide a full description of the methodology used to characterize the neutron source and validate the method with synthetic experiments.« less

  4. Java PathFinder User Guide

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus

    1999-01-01

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

  5. A distributed computing system for magnetic resonance imaging: Java-based processing and binding of XML.

    PubMed

    de Beer, R; Graveron-Demilly, D; Nastase, S; van Ormondt, D

    2004-03-01

    Recently we have developed a Java-based heterogeneous distributed computing system for the field of magnetic resonance imaging (MRI). It is a software system for embedding the various image reconstruction algorithms that we have created for handling MRI data sets with sparse sampling distributions. Since these data sets may result from multi-dimensional MRI measurements our system has to control the storage and manipulation of large amounts of data. In this paper we describe how we have employed the extensible markup language (XML) to realize this data handling in a highly structured way. To that end we have used Java packages, recently released by Sun Microsystems, to process XML documents and to compile pieces of XML code into Java classes. We have effectuated a flexible storage and manipulation approach for all kinds of data within the MRI system, such as data describing and containing multi-dimensional MRI measurements, data configuring image reconstruction methods and data representing and visualizing the various services of the system. We have found that the object-oriented approach, possible with the Java programming environment, combined with the XML technology is a convenient way of describing and handling various data streams in heterogeneous distributed computing systems.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  7. The Astrophysics Source Code Library: Supporting software publication and citation

    NASA Astrophysics Data System (ADS)

    Allen, Alice; Teuben, Peter

    2018-01-01

    The Astrophysics Source Code Library (ASCL, ascl.net), established in 1999, is a free online registry for source codes used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using the unique ascl ID assigned to each code. In addition to registering codes, the ASCL can house archive files for download and assign them DOIs. The ASCL advocations for software citation on par with article citation, participates in multidiscipinary events such as Force11, OpenCon, and the annual Workshop on Sustainable Software for Science, works with journal publishers, and organizes Special Sessions and Birds of a Feather meetings at national and international conferences such as Astronomical Data Analysis Software and Systems (ADASS), European Week of Astronomy and Space Science, and AAS meetings. In this presentation, I will discuss some of the challenges of gathering credit for publishing software and ideas and efforts from other disciplines that may be useful to astronomy.

  8. jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

    PubMed

    Helsens, Kenny; Brusniak, Mi-Youn; Deutsch, Eric; Moritz, Robert L; Martens, Lennart

    2011-11-04

    We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com . TraML files can also be converted online at http://iomics.ugent.be/jtraml .

  9. The Need for Vendor Source Code at NAS. Revised

    NASA Technical Reports Server (NTRS)

    Carter, Russell; Acheson, Steve; Blaylock, Bruce; Brock, David; Cardo, Nick; Ciotti, Bob; Poston, Alan; Wong, Parkson; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    The Numerical Aerodynamic Simulation (NAS) Facility has a long standing practice of maintaining buildable source code for installed hardware. There are two reasons for this: NAS's designated pathfinding role, and the need to maintain a smoothly running operational capacity given the widely diversified nature of the vendor installations. NAS has a need to maintain support capabilities when vendors are not able; diagnose and remedy hardware or software problems where applicable; and to support ongoing system software development activities whether or not the relevant vendors feel support is justified. This note provides an informal history of these activities at NAS, and brings together the general principles that drive the requirement that systems integrated into the NAS environment run binaries built from source code, onsite.

  10. 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/.

  11. HALO--a Java framework for precise transcript half-life determination.

    PubMed

    Friedel, Caroline C; Kaufmann, Stefanie; Dölken, Lars; Zimmer, Ralf

    2010-05-01

    Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives. Such transcript half-lives provide important insights into the regulation of biological processes and the relative contributions of RNA decay and de novo transcription to differential gene expression. In this article, we present HALO (Half-life Organizer), the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription or decay determined with microarrays or RNA-seq. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command-line tools and a well-documented Java application programming interface (API). Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the provided user interfaces as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines. Source code, executables and documentation are available at http://www.bio.ifi.lmu.de/software/halo.

  12. Towards a Certified Lightweight Array Bound Checker for Java Bytecode

    NASA Technical Reports Server (NTRS)

    Pichardie, David

    2009-01-01

    Dynamic array bound checks are crucial elements for the security of a Java Virtual Machines. These dynamic checks are however expensive and several static analysis techniques have been proposed to eliminate explicit bounds checks. Such analyses require advanced numerical and symbolic manipulations that 1) penalize bytecode loading or dynamic compilation, 2) complexify the trusted computing base. Following the Foundational Proof Carrying Code methodology, our goal is to provide a lightweight bytecode verifier for eliminating array bound checks that is both efficient and trustable. In this work, we define a generic relational program analysis for an imperative, stackoriented byte code language with procedures, arrays and global variables and instantiate it with a relational abstract domain as polyhedra. The analysis has automatic inference of loop invariants and method pre-/post-conditions, and efficient checking of analysis results by a simple checker. Invariants, which can be large, can be specialized for proving a safety policy using an automatic pruning technique which reduces their size. The result of the analysis can be checked efficiently by annotating the program with parts of the invariant together with certificates of polyhedral inclusions. The resulting checker is sufficiently simple to be entirely certified within the Coq proof assistant for a simple fragment of the Java bytecode language. During the talk, we will also report on our ongoing effort to scale this approach for the full sequential JVM.

  13. Source Authentication for Code Dissemination Supporting Dynamic Packet Size in Wireless Sensor Networks.

    PubMed

    Kim, Daehee; Kim, Dongwan; An, Sunshin

    2016-07-09

    Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption.

  14. SAP- FORTRAN STATIC SOURCE CODE ANALYZER PROGRAM (IBM VERSION)

    NASA Technical Reports Server (NTRS)

    Manteufel, R.

    1994-01-01

    The FORTRAN Static Source Code Analyzer program, SAP, was developed to automatically gather statistics on the occurrences of statements and structures within a FORTRAN program and to provide for the reporting of those statistics. Provisions have been made for weighting each statistic and to provide an overall figure of complexity. Statistics, as well as figures of complexity, are gathered on a module by module basis. Overall summed statistics are also accumulated for the complete input source file. SAP accepts as input syntactically correct FORTRAN source code written in the FORTRAN 77 standard language. In addition, code written using features in the following languages is also accepted: VAX-11 FORTRAN, IBM S/360 FORTRAN IV Level H Extended; and Structured FORTRAN. The SAP program utilizes two external files in its analysis procedure. A keyword file allows flexibility in classifying statements and in marking a statement as either executable or non-executable. A statistical weight file allows the user to assign weights to all output statistics, thus allowing the user flexibility in defining the figure of complexity. The SAP program is written in FORTRAN IV for batch execution and has been implemented on a DEC VAX series computer under VMS and on an IBM 370 series computer under MVS. The SAP program was developed in 1978 and last updated in 1985.

  15. 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.

  16. 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.

  17. SOURCELESS STARTUP. A MACHINE CODE FOR COMPUTING LOW-SOURCE REACTOR STARTUPS

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

    MacMillan, D.B.

    1960-06-01

    >A revision to the sourceless start-up code is presented. The code solves a system of differential equations encountered in computing the probability distribution of activity at an observed power level during reactor start-up from a very low source level. (J.R.D.)

  18. Automating RPM Creation from a Source Code Repository

    DTIC Science & Technology

    2012-02-01

    apps/usr --with- libpq=/apps/ postgres make rm -rf $RPM_BUILD_ROOT umask 0077 mkdir -p $RPM_BUILD_ROOT/usr/local/bin mkdir -p $RPM_BUILD_ROOT...from a source code repository. %pre %prep %setup %build ./autogen.sh ; ./configure --with-db=/apps/db --with-libpq=/apps/ postgres make

  19. The Astrophysics Source Code Library: Where Do We Go from Here?

    NASA Astrophysics Data System (ADS)

    Allen, A.; Berriman, B.; DuPrie, K.; Hanisch, R. J.; Mink, J.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P.; Wallen, J.

    2014-05-01

    The Astrophysics Source Code Library1, started in 1999, has in the past three years grown from a repository for 40 codes to a registry of over 700 codes that are now indexed by ADS. What comes next? We examine the future of the , the challenges facing it, the rationale behind its practices, and the need to balance what we might do with what we have the resources to accomplish.

  20. 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.

  1. CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

    PubMed Central

    Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H.; Lau, Ching C.; Behl, Sanjiv; Man, Tsz-Kwong

    2007-01-01

    With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License. PMID:19936083

  2. CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

    PubMed

    Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

    2007-10-06

    With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  3. 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.

  4. Design of batch audio/video conversion platform based on JavaEE

    NASA Astrophysics Data System (ADS)

    Cui, Yansong; Jiang, Lianpin

    2018-03-01

    With the rapid development of digital publishing industry, the direction of audio / video publishing shows the diversity of coding standards for audio and video files, massive data and other significant features. Faced with massive and diverse data, how to quickly and efficiently convert to a unified code format has brought great difficulties to the digital publishing organization. In view of this demand and present situation in this paper, basing on the development architecture of Sptring+SpringMVC+Mybatis, and combined with the open source FFMPEG format conversion tool, a distributed online audio and video format conversion platform with a B/S structure is proposed. Based on the Java language, the key technologies and strategies designed in the design of platform architecture are analyzed emphatically in this paper, designing and developing a efficient audio and video format conversion system, which is composed of “Front display system”, "core scheduling server " and " conversion server ". The test results show that, compared with the ordinary audio and video conversion scheme, the use of batch audio and video format conversion platform can effectively improve the conversion efficiency of audio and video files, and reduce the complexity of the work. Practice has proved that the key technology discussed in this paper can be applied in the field of large batch file processing, and has certain practical application value.

  5. Machine learning techniques to predict sensitive patterns to fault attack in the Java Card application

    NASA Astrophysics Data System (ADS)

    Chahrazed, Yahiaoui; Jean-Louis, Lanet; Mohamed, Mezghiche; Karim, Tamine

    2018-01-01

    Fault attack represents one of the serious threats against Java Card security. It consists of physical perturbation of chip components to introduce faults in the code execution. A fault may be induced using a laser beam to impact opcodes and operands of instructions. This could lead to a mutation of the application code in such a way that it becomes hostile. Any successful attack may reveal a secret information stored in the card or grant an undesired authorisation. We propose a methodology to recognise, during the development step, the sensitive patterns to the fault attack in the Java Card applications. It is based on the concepts from text categorisation and machine learning. In fact, in this method, we represented the patterns using opcodes n-grams as features, and we evaluated different machine learning classifiers. The results show that the classifiers performed poorly when classifying dangerous sensitive patterns, due to the imbalance of our data-set. The number of dangerous sensitive patterns is much lower than the number of not dangerous patterns. We used resampling techniques to balance the class distribution in our data-set. The experimental results indicated that the resampling techniques improved the accuracy of the classifiers. In addition, our proposed method reduces the execution time of sensitive patterns classification in comparison to the SmartCM tool. This tool is used in our study to evaluate the effect of faults on Java Card applications.

  6. Bringing Interactivity to the Web: The JAVA Solution.

    ERIC Educational Resources Information Center

    Knee, Richard H.; Cafolla, Ralph

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

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

    PubMed

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

    2014-06-14

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

  8. Data integration of structured and unstructured sources for assigning clinical codes to patient stays

    PubMed Central

    Luyckx, Kim; Luyten, Léon; Daelemans, Walter; Van den Bulcke, Tim

    2016-01-01

    Objective Enormous amounts of healthcare data are becoming increasingly accessible through the large-scale adoption of electronic health records. In this work, structured and unstructured (textual) data are combined to assign clinical diagnostic and procedural codes (specifically ICD-9-CM) to patient stays. We investigate whether integrating these heterogeneous data types improves prediction strength compared to using the data types in isolation. Methods Two separate data integration approaches were evaluated. Early data integration combines features of several sources within a single model, and late data integration learns a separate model per data source and combines these predictions with a meta-learner. This is evaluated on data sources and clinical codes from a broad set of medical specialties. Results When compared with the best individual prediction source, late data integration leads to improvements in predictive power (eg, overall F-measure increased from 30.6% to 38.3% for International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnostic codes), while early data integration is less consistent. The predictive strength strongly differs between medical specialties, both for ICD-9-CM diagnostic and procedural codes. Discussion Structured data provides complementary information to unstructured data (and vice versa) for predicting ICD-9-CM codes. This can be captured most effectively by the proposed late data integration approach. Conclusions We demonstrated that models using multiple electronic health record data sources systematically outperform models using data sources in isolation in the task of predicting ICD-9-CM codes over a broad range of medical specialties. PMID:26316458

  9. AN OPEN-SOURCE NEUTRINO RADIATION HYDRODYNAMICS CODE FOR CORE-COLLAPSE SUPERNOVAE

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

    O’Connor, Evan, E-mail: evanoconnor@ncsu.edu; CITA, Canadian Institute for Theoretical Astrophysics, Toronto, M5S 3H8

    2015-08-15

    We present an open-source update to the spherically symmetric, general-relativistic hydrodynamics, core-collapse supernova (CCSN) code GR1D. The source code is available at http://www.GR1Dcode.org. We extend its capabilities to include a general-relativistic treatment of neutrino transport based on the moment formalisms of Shibata et al. and Cardall et al. We pay special attention to implementing and testing numerical methods and approximations that lessen the computational demand of the transport scheme by removing the need to invert large matrices. This is especially important for the implementation and development of moment-like transport methods in two and three dimensions. A critical component of neutrinomore » transport calculations is the neutrino–matter interaction coefficients that describe the production, absorption, scattering, and annihilation of neutrinos. In this article we also describe our open-source neutrino interaction library NuLib (available at http://www.nulib.org). We believe that an open-source approach to describing these interactions is one of the major steps needed to progress toward robust models of CCSNe and robust predictions of the neutrino signal. We show, via comparisons to full Boltzmann neutrino-transport simulations of CCSNe, that our neutrino transport code performs remarkably well. Furthermore, we show that the methods and approximations we employ to increase efficiency do not decrease the fidelity of our results. We also test the ability of our general-relativistic transport code to model failed CCSNe by evolving a 40-solar-mass progenitor to the onset of collapse to a black hole.« less

  10. Source Authentication for Code Dissemination Supporting Dynamic Packet Size in Wireless Sensor Networks †

    PubMed Central

    Kim, Daehee; Kim, Dongwan; An, Sunshin

    2016-01-01

    Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption. PMID:27409616

  11. 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.

  12. Optimal power allocation and joint source-channel coding for wireless DS-CDMA visual sensor networks

    NASA Astrophysics Data System (ADS)

    Pandremmenou, Katerina; Kondi, Lisimachos P.; Parsopoulos, Konstantinos E.

    2011-01-01

    In this paper, we propose a scheme for the optimal allocation of power, source coding rate, and channel coding rate for each of the nodes of a wireless Direct Sequence Code Division Multiple Access (DS-CDMA) visual sensor network. The optimization is quality-driven, i.e. the received quality of the video that is transmitted by the nodes is optimized. The scheme takes into account the fact that the sensor nodes may be imaging scenes with varying levels of motion. Nodes that image low-motion scenes will require a lower source coding rate, so they will be able to allocate a greater portion of the total available bit rate to channel coding. Stronger channel coding will mean that such nodes will be able to transmit at lower power. This will both increase battery life and reduce interference to other nodes. Two optimization criteria are considered. One that minimizes the average video distortion of the nodes and one that minimizes the maximum distortion among the nodes. The transmission powers are allowed to take continuous values, whereas the source and channel coding rates can assume only discrete values. Thus, the resulting optimization problem lies in the field of mixed-integer optimization tasks and is solved using Particle Swarm Optimization. Our experimental results show the importance of considering the characteristics of the video sequences when determining the transmission power, source coding rate and channel coding rate for the nodes of the visual sensor network.

  13. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

    PubMed

    Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

    2012-03-01

    We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. JAVA PathFinder

    NASA Technical Reports Server (NTRS)

    Mehhtz, Peter

    2005-01-01

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

  15. 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.

  16. SAP- FORTRAN STATIC SOURCE CODE ANALYZER PROGRAM (DEC VAX VERSION)

    NASA Technical Reports Server (NTRS)

    Merwarth, P. D.

    1994-01-01

    The FORTRAN Static Source Code Analyzer program, SAP, was developed to automatically gather statistics on the occurrences of statements and structures within a FORTRAN program and to provide for the reporting of those statistics. Provisions have been made for weighting each statistic and to provide an overall figure of complexity. Statistics, as well as figures of complexity, are gathered on a module by module basis. Overall summed statistics are also accumulated for the complete input source file. SAP accepts as input syntactically correct FORTRAN source code written in the FORTRAN 77 standard language. In addition, code written using features in the following languages is also accepted: VAX-11 FORTRAN, IBM S/360 FORTRAN IV Level H Extended; and Structured FORTRAN. The SAP program utilizes two external files in its analysis procedure. A keyword file allows flexibility in classifying statements and in marking a statement as either executable or non-executable. A statistical weight file allows the user to assign weights to all output statistics, thus allowing the user flexibility in defining the figure of complexity. The SAP program is written in FORTRAN IV for batch execution and has been implemented on a DEC VAX series computer under VMS and on an IBM 370 series computer under MVS. The SAP program was developed in 1978 and last updated in 1985.

  17. Supporting Source Code Comprehension during Software Evolution and Maintenance

    ERIC Educational Resources Information Center

    Alhindawi, Nouh

    2013-01-01

    This dissertation addresses the problems of program comprehension to support the evolution of large-scale software systems. The research concerns how software engineers locate features and concepts along with categorizing changes within very large bodies of source code along with their versioned histories. More specifically, advanced Information…

  18. East Java Maritime Connectivity and Its Regional Development Support

    NASA Astrophysics Data System (ADS)

    Purboyo, H.; Ibad, M. Z.

    2017-07-01

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

  19. 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.

  20. Robust video transmission with distributed source coded auxiliary channel.

    PubMed

    Wang, Jiajun; Majumdar, Abhik; Ramchandran, Kannan

    2009-12-01

    We propose a novel solution to the problem of robust, low-latency video transmission over lossy channels. Predictive video codecs, such as MPEG and H.26x, are very susceptible to prediction mismatch between encoder and decoder or "drift" when there are packet losses. These mismatches lead to a significant degradation in the decoded quality. To address this problem, we propose an auxiliary codec system that sends additional information alongside an MPEG or H.26x compressed video stream to correct for errors in decoded frames and mitigate drift. The proposed system is based on the principles of distributed source coding and uses the (possibly erroneous) MPEG/H.26x decoder reconstruction as side information at the auxiliary decoder. The distributed source coding framework depends upon knowing the statistical dependency (or correlation) between the source and the side information. We propose a recursive algorithm to analytically track the correlation between the original source frame and the erroneous MPEG/H.26x decoded frame. Finally, we propose a rate-distortion optimization scheme to allocate the rate used by the auxiliary encoder among the encoding blocks within a video frame. We implement the proposed system and present extensive simulation results that demonstrate significant gains in performance both visually and objectively (on the order of 2 dB in PSNR over forward error correction based solutions and 1.5 dB in PSNR over intrarefresh based solutions for typical scenarios) under tight latency constraints.

  1. 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.

  2. A Java Applet for Illustrating Internet Error Control

    ERIC Educational Resources Information Center

    Holliday, Mark A.

    2004-01-01

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

  3. User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)

    DTIC Science & Technology

    2014-06-01

    User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) by James P. Larentzos...Laboratory Aberdeen Proving Ground, MD 21005-5069 ARL-SR-290 June 2014 User Manual and Source Code for a LAMMPS Implementation of Constant...3. DATES COVERED (From - To) September 2013–February 2014 4. TITLE AND SUBTITLE User Manual and Source Code for a LAMMPS Implementation of

  4. 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

  5. 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.

  6. A source-channel coding approach to digital image protection and self-recovery.

    PubMed

    Sarreshtedari, Saeed; Akhaee, Mohammad Ali

    2015-07-01

    Watermarking algorithms have been widely applied to the field of image forensics recently. One of these very forensic applications is the protection of images against tampering. For this purpose, we need to design a watermarking algorithm fulfilling two purposes in case of image tampering: 1) detecting the tampered area of the received image and 2) recovering the lost information in the tampered zones. State-of-the-art techniques accomplish these tasks using watermarks consisting of check bits and reference bits. Check bits are used for tampering detection, whereas reference bits carry information about the whole image. The problem of recovering the lost reference bits still stands. This paper is aimed at showing that having the tampering location known, image tampering can be modeled and dealt with as an erasure error. Therefore, an appropriate design of channel code can protect the reference bits against tampering. In the present proposed method, the total watermark bit-budget is dedicated to three groups: 1) source encoder output bits; 2) channel code parity bits; and 3) check bits. In watermark embedding phase, the original image is source coded and the output bit stream is protected using appropriate channel encoder. For image recovery, erasure locations detected by check bits help channel erasure decoder to retrieve the original source encoded image. Experimental results show that our proposed scheme significantly outperforms recent techniques in terms of image quality for both watermarked and recovered image. The watermarked image quality gain is achieved through spending less bit-budget on watermark, while image recovery quality is considerably improved as a consequence of consistent performance of designed source and channel codes.

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

    PubMed

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

    2018-05-21

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

  8. Implementation issues in source coding

    NASA Technical Reports Server (NTRS)

    Sayood, Khalid; Chen, Yun-Chung; Hadenfeldt, A. C.

    1989-01-01

    An edge preserving image coding scheme which can be operated in both a lossy and a lossless manner was developed. The technique is an extension of the lossless encoding algorithm developed for the Mars observer spectral data. It can also be viewed as a modification of the DPCM algorithm. A packet video simulator was also developed from an existing modified packet network simulator. The coding scheme for this system is a modification of the mixture block coding (MBC) scheme described in the last report. Coding algorithms for packet video were also investigated.

  9. 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.

  10. HELIOS-R: An Ultrafast, Open-Source Retrieval Code For Exoplanetary Atmosphere Characterization

    NASA Astrophysics Data System (ADS)

    LAVIE, Baptiste

    2015-12-01

    Atmospheric retrieval is a growing, new approach in the theory of exoplanet atmosphere characterization. Unlike self-consistent modeling it allows us to fully explore the parameter space, as well as the degeneracies between the parameters using a Bayesian framework. We present HELIOS-R, a very fast retrieving code written in Python and optimized for GPU computation. Once it is ready, HELIOS-R will be the first open-source atmospheric retrieval code accessible to the exoplanet community. As the new generation of direct imaging instruments (SPHERE, GPI) have started to gather data, the first version of HELIOS-R focuses on emission spectra. We use a 1D two-stream forward model for computing fluxes and couple it to an analytical temperature-pressure profile that is constructed to be in radiative equilibrium. We use our ultra-fast opacity calculator HELIOS-K (also open-source) to compute the opacities of CO2, H2O, CO and CH4 from the HITEMP database. We test both opacity sampling (which is typically used by other workers) and the method of k-distributions. Using this setup, we compute a grid of synthetic spectra and temperature-pressure profiles, which is then explored using a nested sampling algorithm. By focusing on model selection (Occam’s razor) through the explicit computation of the Bayesian evidence, nested sampling allows us to deal with current sparse data as well as upcoming high-resolution observations. Once the best model is selected, HELIOS-R provides posterior distributions of the parameters. As a test for our code we studied HR8799 system and compared our results with the previous analysis of Lee, Heng & Irwin (2013), which used the proprietary NEMESIS retrieval code. HELIOS-R and HELIOS-K are part of the set of open-source community codes we named the Exoclimes Simulation Platform (www.exoclime.org).

  11. A plug-in to Eclipse for VHDL source codes: functionalities

    NASA Astrophysics Data System (ADS)

    Niton, B.; Poźniak, K. T.; Romaniuk, R. S.

    The paper presents an original application, written by authors, which supports writing and edition of source codes in VHDL language. It is a step towards fully automatic, augmented code writing for photonic and electronic systems, also systems based on FPGA and/or DSP processors. An implementation is described, based on VEditor. VEditor is a free license program. Thus, the work presented in this paper supplements and extends this free license. The introduction characterizes shortly available tools on the market which serve for aiding the design processes of electronic systems in VHDL. Particular attention was put on plug-ins to the Eclipse environment and Emacs program. There are presented detailed properties of the written plug-in such as: programming extension conception, and the results of the activities of formatter, re-factorizer, code hider, and other new additions to the VEditor program.

  12. Utilities for master source code distribution: MAX and Friends

    NASA Technical Reports Server (NTRS)

    Felippa, Carlos A.

    1988-01-01

    MAX is a program for the manipulation of FORTRAN master source code (MSC). This is a technique by which one maintains one and only one master copy of a FORTRAN program under a program developing system, which for MAX is assumed to be VAX/VMS. The master copy is not intended to be directly compiled. Instead it must be pre-processed by MAX to produce compilable instances. These instances may correspond to different code versions (for example, double precision versus single precision), different machines (for example, IBM, CDC, Cray) or different operating systems (i.e., VAX/VMS versus VAX/UNIX). The advantage os using a master source is more pronounced in complex application programs that are developed and maintained over many years and are to be transported and executed on several computer environments. The version lag problem that plagues many such programs is avoided by this approach. MAX is complemented by several auxiliary programs that perform nonessential functions. The ensemble is collectively known as MAX and Friends. All of these programs, including MAX, are executed as foreign VAX/VMS commands and can easily be hidden in customized VMS command procedures.

  13. The FORTRAN static source code analyzer program (SAP) user's guide, revision 1

    NASA Technical Reports Server (NTRS)

    Decker, W.; Taylor, W.; Eslinger, S.

    1982-01-01

    The FORTRAN Static Source Code Analyzer Program (SAP) User's Guide (Revision 1) is presented. SAP is a software tool designed to assist Software Engineering Laboratory (SEL) personnel in conducting studies of FORTRAN programs. SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. This document is a revision of the previous SAP user's guide, Computer Sciences Corporation document CSC/TM-78/6045. SAP Revision 1 is the result of program modifications to provide several new reports, additional complexity analysis, and recognition of all statements described in the FORTRAN 77 standard. This document provides instructions for operating SAP and contains information useful in interpreting SAP output.

  14. Development of Educational Support System for Learning Image Processing Enabling Client-Side Programming Aided by Java Servlet Technology

    NASA Astrophysics Data System (ADS)

    Furukawa, Tatsuya; Aoki, Noriyuki; Ohchi, Masashi; Nakao, Masaki

    The image proccessing has become a useful and important technology in various reserch and development fields. According to such demands for engineering problems, we have designed and implemented the educational support system for that using a Java Applet technology. However in the conventional system, it required the tedious procedure for the end user to code his own programs. Therefore, in this study, we have improved the defect in the previous system by using a Java Servlet technology. The new system will make it possible for novice user to experience a practical digital image proccessing and an advanced programming with ease. We will describe the architecture of the proposed system function, that has been introduced to facilitate the client-side programming.

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

    NASA Astrophysics Data System (ADS)

    Fienen, M. N.; Lowry, C.

    2013-12-01

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

  16. Muria Volcano, Island of Java, Indonesia

    NASA Technical Reports Server (NTRS)

    1991-01-01

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

  17. Hybrid polylingual object model: an efficient and seamless integration of Java and native components on the Dalvik virtual machine.

    PubMed

    Huang, Yukun; Chen, Rong; Wei, Jingbo; Pei, Xilong; Cao, Jing; Prakash Jayaraman, Prem; Ranjan, Rajiv

    2014-01-01

    JNI in the Android platform is often observed with low efficiency and high coding complexity. Although many researchers have investigated the JNI mechanism, few of them solve the efficiency and the complexity problems of JNI in the Android platform simultaneously. In this paper, a hybrid polylingual object (HPO) model is proposed to allow a CAR object being accessed as a Java object and as vice in the Dalvik virtual machine. It is an acceptable substitute for JNI to reuse the CAR-compliant components in Android applications in a seamless and efficient way. The metadata injection mechanism is designed to support the automatic mapping and reflection between CAR objects and Java objects. A prototype virtual machine, called HPO-Dalvik, is implemented by extending the Dalvik virtual machine to support the HPO model. Lifespan management, garbage collection, and data type transformation of HPO objects are also handled in the HPO-Dalvik virtual machine automatically. The experimental result shows that the HPO model outweighs the standard JNI in lower overhead on native side, better executing performance with no JNI bridging code being demanded.

  18. 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.

  19. 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

  20. Generating code adapted for interlinking legacy scalar code and extended vector code

    DOEpatents

    Gschwind, Michael K

    2013-06-04

    Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

  1. Plagiarism Detection Algorithm for Source Code in Computer Science Education

    ERIC Educational Resources Information Center

    Liu, Xin; Xu, Chan; Ouyang, Boyu

    2015-01-01

    Nowadays, computer programming is getting more necessary in the course of program design in college education. However, the trick of plagiarizing plus a little modification exists among some students' home works. It's not easy for teachers to judge if there's plagiarizing in source code or not. Traditional detection algorithms cannot fit this…

  2. 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.

  3. Vernier caliper and micrometer computer models using Easy Java Simulation and its pedagogical design features—ideas for augmenting learning with real instruments

    NASA Astrophysics Data System (ADS)

    Wee, Loo Kang; Tiang Ning, Hwee

    2014-09-01

    This paper presents the customization of Easy Java Simulation models, used with actual laboratory instruments, to create active experiential learning for measurements. The laboratory instruments are the vernier caliper and the micrometer. Three computer model design ideas that complement real equipment are discussed. These ideas involve (1) a simple two-dimensional view for learning from pen and paper questions and the real world; (2) hints, answers, different scale options and the inclusion of zero error; (3) assessment for learning feedback. The initial positive feedback from Singaporean students and educators indicates that these tools could be successfully shared and implemented in learning communities. Educators are encouraged to change the source code for these computer models to suit their own purposes; they have creative commons attribution licenses for the benefit of all.

  4. Chromaticity calculations and code comparisons for x-ray lithography source XLS and SXLS rings

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

    Parsa, Z.

    1988-06-16

    This note presents the chromaticity calculations and code comparison results for the (x-ray lithography source) XLS (Chasman Green, XUV Cosy lattice) and (2 magnet 4T) SXLS lattices, with the standard beam optic codes, including programs SYNCH88.5, MAD6, PATRICIA88.4, PATPET88.2, DIMAD, BETA, and MARYLIE. This analysis is a part of our ongoing accelerator physics code studies. 4 figs., 10 tabs.

  5. 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.

  6. Java and its future in biomedical computing.

    PubMed Central

    Rodgers, R P

    1996-01-01

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

  7. Sources of financial pressure and up coding behavior in French public hospitals.

    PubMed

    Georgescu, Irène; Hartmann, Frank G H

    2013-05-01

    Drawing upon role theory and the literature concerning unintended consequences of financial pressure, this study investigates the effects of health care decision pressure from the hospital's administration and from the professional peer group on physician's inclination to engage in up coding. We explore two kinds of up coding, information-related and action-related, and develop hypothesis that connect these kinds of data manipulation to the sources of pressure via the intermediate effect of role conflict. Qualitative data from initial interviews with physicians and subsequent questionnaire evidence from 578 physicians in 14 French hospitals suggest that the source of pressure is a relevant predictor of physicians' inclination to engage in data-manipulation. We further find that this effect is partly explained by the extent to which these pressures create role conflict. Given the concern about up coding in treatment-based reimbursement systems worldwide, our analysis adds to understanding how the design of the hospital's management control system may enhance this undesired type of behavior. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  8. D-DSC: Decoding Delay-based Distributed Source Coding for Internet of Sensing Things

    PubMed Central

    Akan, Ozgur B.

    2018-01-01

    Spatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (IoST). PMID:29538405

  9. D-DSC: Decoding Delay-based Distributed Source Coding for Internet of Sensing Things.

    PubMed

    Aktas, Metin; Kuscu, Murat; Dinc, Ergin; Akan, Ozgur B

    2018-01-01

    Spatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (IoST).

  10. Hybrid PolyLingual Object Model: An Efficient and Seamless Integration of Java and Native Components on the Dalvik Virtual Machine

    PubMed Central

    Huang, Yukun; Chen, Rong; Wei, Jingbo; Pei, Xilong; Cao, Jing; Prakash Jayaraman, Prem; Ranjan, Rajiv

    2014-01-01

    JNI in the Android platform is often observed with low efficiency and high coding complexity. Although many researchers have investigated the JNI mechanism, few of them solve the efficiency and the complexity problems of JNI in the Android platform simultaneously. In this paper, a hybrid polylingual object (HPO) model is proposed to allow a CAR object being accessed as a Java object and as vice in the Dalvik virtual machine. It is an acceptable substitute for JNI to reuse the CAR-compliant components in Android applications in a seamless and efficient way. The metadata injection mechanism is designed to support the automatic mapping and reflection between CAR objects and Java objects. A prototype virtual machine, called HPO-Dalvik, is implemented by extending the Dalvik virtual machine to support the HPO model. Lifespan management, garbage collection, and data type transformation of HPO objects are also handled in the HPO-Dalvik virtual machine automatically. The experimental result shows that the HPO model outweighs the standard JNI in lower overhead on native side, better executing performance with no JNI bridging code being demanded. PMID:25110745

  11. Distributed nuclear medicine applications using World Wide Web and Java technology.

    PubMed

    Knoll, P; Höll, K; Mirzaei, S; Koriska, K; Köhn, H

    2000-01-01

    At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT).

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

    NASA Astrophysics Data System (ADS)

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

    2005-10-01

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

  13. Comparison of TG-43 dosimetric parameters of brachytherapy sources obtained by three different versions of MCNP codes.

    PubMed

    Zaker, Neda; Zehtabian, Mehdi; Sina, Sedigheh; Koontz, Craig; Meigooni, Ali S

    2016-03-08

    Monte Carlo simulations are widely used for calculation of the dosimetric parameters of brachytherapy sources. MCNP4C2, MCNP5, MCNPX, EGS4, EGSnrc, PTRAN, and GEANT4 are among the most commonly used codes in this field. Each of these codes utilizes a cross-sectional library for the purpose of simulating different elements and materials with complex chemical compositions. The accuracies of the final outcomes of these simulations are very sensitive to the accuracies of the cross-sectional libraries. Several investigators have shown that inaccuracies of some of the cross section files have led to errors in 125I and 103Pd parameters. The purpose of this study is to compare the dosimetric parameters of sample brachytherapy sources, calculated with three different versions of the MCNP code - MCNP4C, MCNP5, and MCNPX. In these simulations for each source type, the source and phantom geometries, as well as the number of the photons, were kept identical, thus eliminating the possible uncertainties. The results of these investigations indicate that for low-energy sources such as 125I and 103Pd there are discrepancies in gL(r) values. Discrepancies up to 21.7% and 28% are observed between MCNP4C and other codes at a distance of 6 cm for 103Pd and 10 cm for 125I from the source, respectively. However, for higher energy sources, the discrepancies in gL(r) values are less than 1.1% for 192Ir and less than 1.2% for 137Cs between the three codes.

  14. JPARSS: A Java Parallel Network Package for Grid Computing

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

    Chen, Jie; Akers, Walter; Chen, Ying

    2002-03-01

    The emergence of high speed wide area networks makes grid computinga reality. However grid applications that need reliable data transfer still have difficulties to achieve optimal TCP performance due to network tuning of TCP window size to improve bandwidth and to reduce latency on a high speed wide area network. This paper presents a Java package called JPARSS (Java Parallel Secure Stream (Socket)) that divides data into partitions that are sent over several parallel Java streams simultaneously and allows Java or Web applications to achieve optimal TCP performance in a grid environment without the necessity of tuning TCP window size.more » This package enables single sign-on, certificate delegation and secure or plain-text data transfer using several security components based on X.509 certificate and SSL. Several experiments will be presented to show that using Java parallelstreams is more effective than tuning TCP window size. In addition a simple architecture using Web services« less

  15. Safe, Multiphase Bounds Check Elimination in Java

    DTIC Science & Technology

    2010-01-28

    production of mobile code from source code, JIT compilation in the virtual ma- chine, and application code execution. The code producer uses...invariants, and inequality constraint analysis) to identify and prove redundancy of bounds checks. During class-loading and JIT compilation, the virtual...unoptimized code if the speculated invariants do not hold. The combined effect of the multiple phases is to shift the effort as- sociated with bounds

  16. Instrumentation of Java Bytecode for Runtime Analysis

    NASA Technical Reports Server (NTRS)

    Goldberg, Allen; Haveland, Klaus

    2003-01-01

    This paper describes JSpy, a system for high-level instrumentation of Java bytecode and its use with JPaX, OUT system for runtime analysis of Java programs. JPaX monitors the execution of temporal logic formulas and performs predicative analysis of deadlocks and data races. JSpy s input is an instrumentation specification, which consists of a collection of rules, where a rule is a predicate/action pair The predicate is a conjunction of syntactic constraints on a Java statement, and the action is a description of logging information to be inserted in the bytecode corresponding to the statement. JSpy is built using JTrek an instrumentation package at a lower level of abstraction.

  17. 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).

  18. 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.

  19. Hybrid digital-analog coding with bandwidth expansion for correlated Gaussian sources under Rayleigh fading

    NASA Astrophysics Data System (ADS)

    Yahampath, Pradeepa

    2017-12-01

    Consider communicating a correlated Gaussian source over a Rayleigh fading channel with no knowledge of the channel signal-to-noise ratio (CSNR) at the transmitter. In this case, a digital system cannot be optimal for a range of CSNRs. Analog transmission however is optimal at all CSNRs, if the source and channel are memoryless and bandwidth matched. This paper presents new hybrid digital-analog (HDA) systems for sources with memory and channels with bandwidth expansion, which outperform both digital-only and analog-only systems over a wide range of CSNRs. The digital part is either a predictive quantizer or a transform code, used to achieve a coding gain. Analog part uses linear encoding to transmit the quantization error which improves the performance under CSNR variations. The hybrid encoder is optimized to achieve the minimum AMMSE (average minimum mean square error) over the CSNR distribution. To this end, analytical expressions are derived for the AMMSE of asymptotically optimal systems. It is shown that the outage CSNR of the channel code and the analog-digital power allocation must be jointly optimized to achieve the minimum AMMSE. In the case of HDA predictive quantization, a simple algorithm is presented to solve the optimization problem. Experimental results are presented for both Gauss-Markov sources and speech signals.

  20. 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.

  1. 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.

  2. Real-time Java for flight applications: an update

    NASA Technical Reports Server (NTRS)

    Dvorak, D.

    2003-01-01

    The RTSJ is a specification for supporting real-time execution in the Java programming language. The specification has been shaped by several guiding principles, particularly: predictable execution as the first priority in all tradeoffs, no syntactic extensions to Java, and backward compatibility.

  3. Comparison of TG‐43 dosimetric parameters of brachytherapy sources obtained by three different versions of MCNP codes

    PubMed Central

    Zaker, Neda; Sina, Sedigheh; Koontz, Craig; Meigooni1, Ali S.

    2016-01-01

    Monte Carlo simulations are widely used for calculation of the dosimetric parameters of brachytherapy sources. MCNP4C2, MCNP5, MCNPX, EGS4, EGSnrc, PTRAN, and GEANT4 are among the most commonly used codes in this field. Each of these codes utilizes a cross‐sectional library for the purpose of simulating different elements and materials with complex chemical compositions. The accuracies of the final outcomes of these simulations are very sensitive to the accuracies of the cross‐sectional libraries. Several investigators have shown that inaccuracies of some of the cross section files have led to errors in  125I and  103Pd parameters. The purpose of this study is to compare the dosimetric parameters of sample brachytherapy sources, calculated with three different versions of the MCNP code — MCNP4C, MCNP5, and MCNPX. In these simulations for each source type, the source and phantom geometries, as well as the number of the photons, were kept identical, thus eliminating the possible uncertainties. The results of these investigations indicate that for low‐energy sources such as  125I and  103Pd there are discrepancies in gL(r) values. Discrepancies up to 21.7% and 28% are observed between MCNP4C and other codes at a distance of 6 cm for  103Pd and 10 cm for  125I from the source, respectively. However, for higher energy sources, the discrepancies in gL(r) values are less than 1.1% for  192Ir and less than 1.2% for  137Cs between the three codes. PACS number(s): 87.56.bg PMID:27074460

  4. Phase 1 Validation Testing and Simulation for the WEC-Sim Open Source Code

    NASA Astrophysics Data System (ADS)

    Ruehl, K.; Michelen, C.; Gunawan, B.; Bosma, B.; Simmons, A.; Lomonaco, P.

    2015-12-01

    WEC-Sim is an open source code to model wave energy converters performance in operational waves, developed by Sandia and NREL and funded by the US DOE. The code is a time-domain modeling tool developed in MATLAB/SIMULINK using the multibody dynamics solver SimMechanics, and solves the WEC's governing equations of motion using the Cummins time-domain impulse response formulation in 6 degrees of freedom. The WEC-Sim code has undergone verification through code-to-code comparisons; however validation of the code has been limited to publicly available experimental data sets. While these data sets provide preliminary code validation, the experimental tests were not explicitly designed for code validation, and as a result are limited in their ability to validate the full functionality of the WEC-Sim code. Therefore, dedicated physical model tests for WEC-Sim validation have been performed. This presentation provides an overview of the WEC-Sim validation experimental wave tank tests performed at the Oregon State University's Directional Wave Basin at Hinsdale Wave Research Laboratory. Phase 1 of experimental testing was focused on device characterization and completed in Fall 2015. Phase 2 is focused on WEC performance and scheduled for Winter 2015/2016. These experimental tests were designed explicitly to validate the performance of WEC-Sim code, and its new feature additions. Upon completion, the WEC-Sim validation data set will be made publicly available to the wave energy community. For the physical model test, a controllable model of a floating wave energy converter has been designed and constructed. The instrumentation includes state-of-the-art devices to measure pressure fields, motions in 6 DOF, multi-axial load cells, torque transducers, position transducers, and encoders. The model also incorporates a fully programmable Power-Take-Off system which can be used to generate or absorb wave energy. Numerical simulations of the experiments using WEC-Sim will be

  5. 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.

  6. An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.

    PubMed

    Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R; Ellis, Heidi Jc; Hinman, M Lee; Vyas, Jay; Gryk, Michael R

    2012-01-01

    Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org).

  7. Unitals and ovals of symmetric block designs in LDPC and space-time coding

    NASA Astrophysics Data System (ADS)

    Andriamanalimanana, Bruno R.

    2004-08-01

    An approach to the design of LDPC (low density parity check) error-correction and space-time modulation codes involves starting with known mathematical and combinatorial structures, and deriving code properties from structure properties. This paper reports on an investigation of unital and oval configurations within generic symmetric combinatorial designs, not just classical projective planes, as the underlying structure for classes of space-time LDPC outer codes. Of particular interest are the encoding and iterative (sum-product) decoding gains that these codes may provide. Various small-length cases have been numerically implemented in Java and Matlab for a number of channel models.

  8. Prototyping Faithful Execution in a Java virtual machine.

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

    Tarman, Thomas David; Campbell, Philip LaRoche; Pierson, Lyndon George

    2003-09-01

    This report presents the implementation of a stateless scheme for Faithful Execution, the design for which is presented in a companion report, ''Principles of Faithful Execution in the Implementation of Trusted Objects'' (SAND 2003-2328). We added a simple cryptographic capability to an already simplified class loader and its associated Java Virtual Machine (JVM) to provide a byte-level implementation of Faithful Execution. The extended class loader and JVM we refer to collectively as the Sandia Faithfully Executing Java architecture (or JavaFE for short). This prototype is intended to enable exploration of more sophisticated techniques which we intend to implement in hardware.

  9. Creating Web-Based Scientific Applications Using Java Servlets

    NASA Technical Reports Server (NTRS)

    Palmer, Grant; Arnold, James O. (Technical Monitor)

    2001-01-01

    There are many advantages to developing web-based scientific applications. Any number of people can access the application concurrently. The application can be accessed from a remote location. The application becomes essentially platform-independent because it can be run from any machine that has internet access and can run a web browser. Maintenance and upgrades to the application are simplified since only one copy of the application exists in a centralized location. This paper details the creation of web-based applications using Java servlets. Java is a powerful, versatile programming language that is well suited to developing web-based programs. A Java servlet provides the interface between the central server and the remote client machines. The servlet accepts input data from the client, runs the application on the server, and sends the output back to the client machine. The type of servlet that supports the HTTP protocol will be discussed in depth. Among the topics the paper will discuss are how to write an http servlet, how the servlet can run applications written in Java and other languages, and how to set up a Java web server. The entire process will be demonstrated by building a web-based application to compute stagnation point heat transfer.

  10. Particle-in-cell code library for numerical simulation of the ECR source plasma

    NASA Astrophysics Data System (ADS)

    Shirkov, G.; Alexandrov, V.; Preisendorf, V.; Shevtsov, V.; Filippov, A.; Komissarov, R.; Mironov, V.; Shirkova, E.; Strekalovsky, O.; Tokareva, N.; Tuzikov, A.; Vatulin, V.; Vasina, E.; Fomin, V.; Anisimov, A.; Veselov, R.; Golubev, A.; Grushin, S.; Povyshev, V.; Sadovoi, A.; Donskoi, E.; Nakagawa, T.; Yano, Y.

    2003-05-01

    The project ;Numerical simulation and optimization of ion accumulation and production in multicharged ion sources; is funded by the International Science and Technology Center (ISTC). A summary of recent project development and the first version of a computer code library for simulation of electron-cyclotron resonance (ECR) source plasmas based on the particle-in-cell method are presented.

  11. Carbon source-dependent expansion of the genetic code in bacteria

    PubMed Central

    Prat, Laure; Heinemann, Ilka U.; Aerni, Hans R.; Rinehart, Jesse; O’Donoghue, Patrick; Söll, Dieter

    2012-01-01

    Despite the fact that the genetic code is known to vary between organisms in rare cases, it is believed that in the lifetime of a single cell the code is stable. We found Acetohalobium arabaticum cells grown on pyruvate genetically encode 20 amino acids, but in the presence of trimethylamine (TMA), A. arabaticum dynamically expands its genetic code to 21 amino acids including pyrrolysine (Pyl). A. arabaticum is the only known organism that modulates the size of its genetic code in response to its environment and energy source. The gene cassette pylTSBCD, required to biosynthesize and genetically encode UAG codons as Pyl, is present in the genomes of 24 anaerobic archaea and bacteria. Unlike archaeal Pyl-decoding organisms that constitutively encode Pyl, we observed that A. arabaticum controls Pyl encoding by down-regulating transcription of the entire Pyl operon under growth conditions lacking TMA, to the point where no detectable Pyl-tRNAPyl is made in vivo. Pyl-decoding archaea adapted to an expanded genetic code by minimizing TAG codon frequency to typically ∼5% of ORFs, whereas Pyl-decoding bacteria (∼20% of ORFs contain in-frame TAGs) regulate Pyl-tRNAPyl formation and translation of UAG by transcriptional deactivation of genes in the Pyl operon. We further demonstrate that Pyl encoding occurs in a bacterium that naturally encodes the Pyl operon, and identified Pyl residues by mass spectrometry in A. arabaticum proteins including two methylamine methyltransferases. PMID:23185002

  12. HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

    ERIC Educational Resources Information Center

    Machovec, George S., Ed.

    1995-01-01

    Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

  13. An Adaptive Source-Channel Coding with Feedback for Progressive Transmission of Medical Images

    PubMed Central

    Lo, Jen-Lung; Sanei, Saeid; Nazarpour, Kianoush

    2009-01-01

    A novel adaptive source-channel coding with feedback for progressive transmission of medical images is proposed here. In the source coding part, the transmission starts from the region of interest (RoI). The parity length in the channel code varies with respect to both the proximity of the image subblock to the RoI and the channel noise, which is iteratively estimated in the receiver. The overall transmitted data can be controlled by the user (clinician). In the case of medical data transmission, it is vital to keep the distortion level under control as in most of the cases certain clinically important regions have to be transmitted without any visible error. The proposed system significantly reduces the transmission time and error. Moreover, the system is very user friendly since the selection of the RoI, its size, overall code rate, and a number of test features such as noise level can be set by the users in both ends. A MATLAB-based TCP/IP connection has been established to demonstrate the proposed interactive and adaptive progressive transmission system. The proposed system is simulated for both binary symmetric channel (BSC) and Rayleigh channel. The experimental results verify the effectiveness of the design. PMID:19190770

  14. Evaluation of Diagnostic Codes in Morbidity and Mortality Data Sources for Heat-Related Illness Surveillance

    PubMed Central

    Watkins, Sharon

    2017-01-01

    Objectives: The primary objective of this study was to identify patients with heat-related illness (HRI) using codes for heat-related injury diagnosis and external cause of injury in 3 administrative data sets: emergency department (ED) visit records, hospital discharge records, and death certificates. Methods: We obtained data on ED visits, hospitalizations, and deaths for Florida residents for May 1 through October 31, 2005-2012. To identify patients with HRI, we used codes from the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) to search data on ED visits and hospitalizations and codes from the International Classification of Diseases, Tenth Revision (ICD-10) to search data on deaths. We stratified the results by data source and whether the HRI was work related. Results: We identified 23 981 ED visits, 4816 hospitalizations, and 140 deaths in patients with non–work-related HRI and 2979 ED visits, 415 hospitalizations, and 23 deaths in patients with work-related HRI. The most common diagnosis codes among patients were for severe HRI (heat exhaustion or heatstroke). The proportion of patients with a severe HRI diagnosis increased with data source severity. If ICD-9-CM code E900.1 and ICD-10 code W92 (excessive heat of man-made origin) were used as exclusion criteria for HRI, 5.0% of patients with non–work-related deaths, 3.0% of patients with work-related ED visits, and 1.7% of patients with work-related hospitalizations would have been removed. Conclusions: Using multiple data sources and all diagnosis fields may improve the sensitivity of HRI surveillance. Future studies should evaluate the impact of converting ICD-9-CM to ICD-10-CM codes on HRI surveillance of ED visits and hospitalizations. PMID:28379784

  15. Neutrons Flux Distributions of the Pu-Be Source and its Simulation by the MCNP-4B Code

    NASA Astrophysics Data System (ADS)

    Faghihi, F.; Mehdizadeh, S.; Hadad, K.

    Neutron Fluence rate of a low intense Pu-Be source is measured by Neutron Activation Analysis (NAA) of 197Au foils. Also, the neutron fluence rate distribution versus energy is calculated using the MCNP-4B code based on ENDF/B-V library. Theoretical simulation as well as our experimental performance are a new experience for Iranians to make reliability with the code for further researches. In our theoretical investigation, an isotropic Pu-Be source with cylindrical volume distribution is simulated and relative neutron fluence rate versus energy is calculated using MCNP-4B code. Variation of the fast and also thermal neutrons fluence rate, which are measured by NAA method and MCNP code, are compared.

  16. Benchmarking Defmod, an open source FEM code for modeling episodic fault rupture

    NASA Astrophysics Data System (ADS)

    Meng, Chunfang

    2017-03-01

    We present Defmod, an open source (linear) finite element code that enables us to efficiently model the crustal deformation due to (quasi-)static and dynamic loadings, poroelastic flow, viscoelastic flow and frictional fault slip. Ali (2015) provides the original code introducing an implicit solver for (quasi-)static problem, and an explicit solver for dynamic problem. The fault constraint is implemented via Lagrange Multiplier. Meng (2015) combines these two solvers into a hybrid solver that uses failure criteria and friction laws to adaptively switch between the (quasi-)static state and dynamic state. The code is capable of modeling episodic fault rupture driven by quasi-static loadings, e.g. due to reservoir fluid withdraw or injection. Here, we focus on benchmarking the Defmod results against some establish results.

  17. MODTOHAFSD — A GUI based JAVA code for gravity analysis of strike limited sedimentary basins by means of growing bodies with exponential density contrast-depth variation: A space domain approach

    NASA Astrophysics Data System (ADS)

    Chakravarthi, V.; Sastry, S. Rajeswara; Ramamma, B.

    2013-07-01

    Based on the principles of modeling and inversion, two interpretation methods are developed in the space domain along with a GUI based JAVA code, MODTOHAFSD, to analyze the gravity anomalies of strike limited sedimentary basins using a prescribed exponential density contrast-depth function. A stack of vertical prisms all having equal widths, but each one possesses its own limited strike length and thickness, describes the structure of a sedimentary basin above the basement complex. The thicknesses of prisms represent the depths to the basement and are the unknown parameters to be estimated from the observed gravity anomalies. Forward modeling is realized in the space domain using a combination of analytical and numerical approaches. The algorithm estimates the initial depths of a sedimentary basin and improves them, iteratively, based on the differences between the observed and modeled gravity anomalies within the specified convergence criteria. The present code, works on Model-View-Controller (MVC) pattern, reads the Bouguer gravity anomalies, constructs/modifies regional gravity background in an interactive approach, estimates residual gravity anomalies and performs automatic modeling or inversion based on user specification for basement topography. Besides generating output in both ASCII and graphical forms, the code displays (i) the changes in the depth structure, (ii) nature of fit between the observed and modeled gravity anomalies, (iii) changes in misfit, and (iv) variation of density contrast with iteration in animated forms. The code is used to analyze both synthetic and real field gravity anomalies. The proposed technique yielded information that is consistent with the assumed parameters in case of synthetic structure and with available drilling depths in case of field example. The advantage of the code is that it can be used to analyze the gravity anomalies of sedimentary basins even when the profile along which the interpretation is intended fails to

  18. Interactive Analysis of General Beam Configurations using Finite Element Methods and JavaScript

    NASA Astrophysics Data System (ADS)

    Hernandez, Christopher

    Advancements in computer technology have contributed to the widespread practice of modelling and solving engineering problems through the use of specialized software. The wide use of engineering software comes with the disadvantage to the user of costs from the required purchase of software licenses. The creation of accurate, trusted, and freely available applications capable of conducting meaningful analysis of engineering problems is a way to mitigate to the costs associated with every-day engineering computations. Writing applications in the JavaScript programming language allows the applications to run within any computer browser, without the need to install specialized software, since all internet browsers are equipped with virtual machines (VM) that allow the browsers to execute JavaScript code. The objective of this work is the development of an application that performs the analysis of a completely general beam through use of the finite element method. The app is written in JavaScript and embedded in a web page so it can be downloaded and executed by a user with an internet connection. This application allows the user to analyze any uniform or non-uniform beam, with any combination of applied forces, moments, distributed loads, and boundary conditions. Outputs for this application include lists the beam deformations and slopes, as well as lateral and slope deformation graphs, bending stress distributions, and shear and a moment diagrams. To validate the methodology of the GBeam finite element app, its results are verified using the results from obtained from two other established finite element solvers for fifteen separate test cases.

  19. Tactical Applications (TACAPPS) JavaScript Framework Investigation

    DTIC Science & Technology

    2017-02-01

    frameworks explored were Angular JavaScript (AngularJS), jQuery UI, Meteor, Ember, React JavaScript (ReactJS) and Web Components. The team evaluated the...10 Issues and Risks 11 Web Components 11 Benefits 13 Issues and Risks 13 Conclusions 14 Bibliography 15 Distribution List 19...3 Basic Flux flow 10 4 Shadow DOM tree hierarchy 12 5 Web Components browser support 13 UNCLASSIFIED Approved for

  20. 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).

  1. Almost stochastic dominance for poverty level in Central Java Province

    NASA Astrophysics Data System (ADS)

    Slamet, Isnandar; Agus Wibowo, Aryanto; Roswitha, Mania

    2017-12-01

    The criteria for the domination of the distribution function has been used in the investment issues, momentum, agricultural production, and so on. One criteria of domination is stochastic dominance (SD). When this criteria is applied to the dominating area that has smaller value than the dominated area, then almost stochastic dominance (ASD) can be used. It this research, we apply the ASD criteria on data of expenditure per capita based on districts/cities in Central Java. Furthermore, we determine which year the expenditure per capita in the period 2009-2013 is the most dominating to know the level of poverty in Central Java. From the discussion, it can be concluded that the expenditure per capita in Central Java in 2013 dominates expenditure per capita in Central Java in 2009-2012. In other words, the level of poverty in Central Java in 2013 is lower than in 2009-2012.

  2. 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.

  3. Java for flight software

    NASA Technical Reports Server (NTRS)

    Benowitz, E. G.; Niessner, A. F.

    2003-01-01

    We have successfully demonstrated a portion of the spacecraft attitude control and fault protection, running on a standard Java platform, and are currently in the process of taking advantage of the features provided by the RTSJ.

  4. 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.

  5. 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.

  6. RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

    NASA Astrophysics Data System (ADS)

    Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

    RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

  7. 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

  8. 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

  9. 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).

  10. Dynamic Learning Objects to Teach Java Programming Language

    ERIC Educational Resources Information Center

    Narasimhamurthy, Uma; Al Shawkani, Khuloud

    2010-01-01

    This article describes a model for teaching Java Programming Language through Dynamic Learning Objects. The design of the learning objects was based on effective learning design principles to help students learn the complex topic of Java Programming. Visualization was also used to facilitate the learning of the concepts. (Contains 1 figure and 2…

  11. LinguisticBelief: a java application for linguistic evaluation using belief, fuzzy sets, and approximate reasoning.

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

    Darby, John L.

    LinguisticBelief is a Java computer code that evaluates combinations of linguistic variables using an approximate reasoning rule base. Each variable is comprised of fuzzy sets, and a rule base describes the reasoning on combinations of variables fuzzy sets. Uncertainty is considered and propagated through the rule base using the belief/plausibility measure. The mathematics of fuzzy sets, approximate reasoning, and belief/ plausibility are complex. Without an automated tool, this complexity precludes their application to all but the simplest of problems. LinguisticBelief automates the use of these techniques, allowing complex problems to be evaluated easily. LinguisticBelief can be used free of chargemore » on any Windows XP machine. This report documents the use and structure of the LinguisticBelief code, and the deployment package for installation client machines.« less

  12. Java: A New Brew for Educators, Administrators and Students.

    ERIC Educational Resources Information Center

    Gordon, Barbara

    1996-01-01

    Java is an object-oriented programming language developed by Sun Microsystems; its benefits include platform independence, security, and interactivity. Within the college community, Java is being used in programming courses, collaborative technology research projects, computer graphics instruction, and distance education. (AEF)

  13. FastScript3D - A Companion to Java 3D

    NASA Technical Reports Server (NTRS)

    Koenig, Patti

    2005-01-01

    FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

  14. 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.

  15. Image2000: A Free, Innovative, Java Based Imaging Package

    NASA Technical Reports Server (NTRS)

    Pell, Nicholas; Wheeler, Phil; Cornwell, Carl; Matusow, David; Obenschain, Arthur F. (Technical Monitor)

    2001-01-01

    The National Aeronautics and Space Administration (NASA) Goddard Space Flight Center's (GSFC) Scientific and Educational Endeavors (SEE) and the Center for Image Processing in Education (CIPE) use satellite image processing as part of their science lessons developed for students and educators. The image processing products that they use, as part of these lessons, no longer fulfill the needs of SEE and CIPE because these products are either dependent on a particular computing platform, hard to customize and extend, or do not have enough functionality. SEE and CIPE began looking for what they considered the "perfect" image processing tool that was platform independent, rich in functionality and could easily be extended and customized for their purposes. At the request of SEE, NASA's GSFC, code 588 the Advanced Architectures and Automation Branch developed a powerful new Java based image processing endeavors.

  16. Study of an External Neutron Source for an Accelerator-Driven System using the PHITS Code

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

    Sugawara, Takanori; Iwasaki, Tomohiko; Chiba, Takashi

    A code system for the Accelerator Driven System (ADS) has been under development for analyzing dynamic behaviors of a subcritical core coupled with an accelerator. This code system named DSE (Dynamics calculation code system for a Subcritical system with an External neutron source) consists of an accelerator part and a reactor part. The accelerator part employs a database, which is calculated by using PHITS, for investigating the effect related to the accelerator such as the changes of beam energy, beam diameter, void generation, and target level. This analysis method using the database may introduce some errors into dynamics calculations sincemore » the neutron source data derived from the database has some errors in fitting or interpolating procedures. In this study, the effects of various events are investigated to confirm that the method based on the database is appropriate.« less

  17. 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

  18. Fan Noise Prediction System Development: Source/Radiation Field Coupling and Workstation Conversion for the Acoustic Radiation Code

    NASA Technical Reports Server (NTRS)

    Meyer, H. D.

    1993-01-01

    The Acoustic Radiation Code (ARC) is a finite element program used on the IBM mainframe to predict far-field acoustic radiation from a turbofan engine inlet. In this report, requirements for developers of internal aerodynamic codes regarding use of their program output an input for the ARC are discussed. More specifically, the particular input needed from the Bolt, Beranek and Newman/Pratt and Whitney (turbofan source noise generation) Code (BBN/PWC) is described. In a separate analysis, a method of coupling the source and radiation models, that recognizes waves crossing the interface in both directions, has been derived. A preliminary version of the coupled code has been developed and used for initial evaluation of coupling issues. Results thus far have shown that reflection from the inlet is sufficient to indicate that full coupling of the source and radiation fields is needed for accurate noise predictions ' Also, for this contract, the ARC has been modified for use on the Sun and Silicon Graphics Iris UNIX workstations. Changes and additions involved in this effort are described in an appendix.

  19. Java for flight software

    NASA Technical Reports Server (NTRS)

    Benowitz, E.; Niessner, A.

    2003-01-01

    This work involves developing representative mission-critical spacecraft software using the Real-Time Specification for Java (RTSJ). This work currently leverages actual flight software used in the design of actual flight software in the NASA's Deep Space 1 (DSI), which flew in 1998.

  20. The concept of geothermal exploration in west Java based on geophysical data

    NASA Astrophysics Data System (ADS)

    Gaffar, Eddy Z.

    2018-02-01

    Indonesia has the largest geothermal prospects in the world and most of them are concentrated in Java and Sumatera. The ones on Sumatra island are generally controlled by Sumatra Fault, either the main fault or the second and the third order fault. Geothermal in Java is still influenced by the subduction of oceanic plates from the south of Java island that forms the southern mountains extending from West Java to East Java. From a geophysical point of view, there is still no clue or concept that accelerates the process of geothermal exploration. The concept is that geothermal is located around the volcano (referred to the volcano as a host) and around the fault (fault as a host). There is another method from remote sensing analysis that often shows circular feature. In a study conducted by LIPI, we proposed a new concept for geothermal exploration which is from gravity analysis using Bouguer anomaly data from Java Island, which also show circular feature. The feature is supposed to be an "ancient crater" or a hidden caldera. Therefore, with this hypothesis, LIPI Geophysics team will try to prove whether this symptom can help accelerate the process of geothermal exploration on the island of West Java. Geophysical methods might simplify the exploration of geothermal prospect in West Java. Around the small circular feature, there are some large geothermal prospect areas such as Guntur, Kamojang, Drajat, Papandayan, Karaha Bodas, Patuha. The concept proposed by our team will try be applied to explore geothermal in Java Island for future work.

  1. 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

  2. Experience in the application of Java Technologies in telemedicine

    PubMed Central

    Fedyukin, IV; Reviakin, YG; Orlov, OI; Doarn, CR; Harnett, BM; Merrell, RC

    2002-01-01

    Java language has been demonstrated to be an effective tool in supporting medical image viewing in Russia. This evaluation was completed by obtaining a maximum of 20 images, depending on the client's computer workstation from one patient using a commercially available computer tomography (CT) scanner. The images were compared against standard CT images that were viewed at the site of capture. There was no appreciable difference. The client side is a lightweight component that provides an intuitive interface for end users. Each image is loaded in its own thread and the user can begin work after the first image has been loaded. This feature is especially useful on slow connection speed, 9.6 Kbps for example. The server side, which is implemented by the Java Servlet Engine works more effective than common gateway interface (CGI) programs do. Advantages of the Java Technology place this program on the next level of application development. This paper presents a unique application of Java in telemedicine. PMID:12459045

  3. Experience in the application of Java Technologies in telemedicine.

    PubMed

    Fedyukin, IV; Reviakin, YG; Orlov, OI; Doarn, CR; Harnett, BM; Merrell, RC

    2002-09-17

    Java language has been demonstrated to be an effective tool in supporting medical image viewing in Russia. This evaluation was completed by obtaining a maximum of 20 images, depending on the client's computer workstation from one patient using a commercially available computer tomography (CT) scanner. The images were compared against standard CT images that were viewed at the site of capture. There was no appreciable difference. The client side is a lightweight component that provides an intuitive interface for end users. Each image is loaded in its own thread and the user can begin work after the first image has been loaded. This feature is especially useful on slow connection speed, 9.6 Kbps for example. The server side, which is implemented by the Java Servlet Engine works more effective than common gateway interface (CGI) programs do. Advantages of the Java Technology place this program on the next level of application development. This paper presents a unique application of Java in telemedicine.

  4. 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

  5. Pre-coding method and apparatus for multiple source or time-shifted single source data and corresponding inverse post-decoding method and apparatus

    NASA Technical Reports Server (NTRS)

    Yeh, Pen-Shu (Inventor)

    1997-01-01

    A pre-coding method and device for improving data compression performance by removing correlation between a first original data set and a second original data set, each having M members, respectively. The pre-coding method produces a compression-efficiency-enhancing double-difference data set. The method and device produce a double-difference data set, i.e., an adjacent-delta calculation performed on a cross-delta data set or a cross-delta calculation performed on two adjacent-delta data sets, from either one of (1) two adjacent spectral bands coming from two discrete sources, respectively, or (2) two time-shifted data sets coming from a single source. The resulting double-difference data set is then coded using either a distortionless data encoding scheme (entropy encoding) or a lossy data compression scheme. Also, a post-decoding method and device for recovering a second original data set having been represented by such a double-difference data set.

  6. Pre-coding method and apparatus for multiple source or time-shifted single source data and corresponding inverse post-decoding method and apparatus

    NASA Technical Reports Server (NTRS)

    Yeh, Pen-Shu (Inventor)

    1998-01-01

    A pre-coding method and device for improving data compression performance by removing correlation between a first original data set and a second original data set, each having M members, respectively. The pre-coding method produces a compression-efficiency-enhancing double-difference data set. The method and device produce a double-difference data set, i.e., an adjacent-delta calculation performed on a cross-delta data set or a cross-delta calculation performed on two adjacent-delta data sets, from either one of (1) two adjacent spectral bands coming from two discrete sources, respectively, or (2) two time-shifted data sets coming from a single source. The resulting double-difference data set is then coded using either a distortionless data encoding scheme (entropy encoding) or a lossy data compression scheme. Also, a post-decoding method and device for recovering a second original data set having been represented by such a double-difference data set.

  7. 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.

  8. Sequence alignment visualization in HTML5 without Java.

    PubMed

    Gille, Christoph; Birgit, Weyand; Gille, Andreas

    2014-01-01

    Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary. Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons. Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software. Under GPL at: http://www.bioinformatics.org/strap/toHTML/.

  9. An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities

    PubMed Central

    Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R.; Ellis, Heidi JC; Hinman, M. Lee; Vyas, Jay; Gryk, Michael R.

    2012-01-01

    Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org). PMID:25328913

  10. 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.

  11. 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

  12. First geodetic measurement of convergence across the Java Trench

    NASA Technical Reports Server (NTRS)

    Tregoning, P.; Brunner, F. K.; Bock, Y.; Puntodewo, S. S. O.; Mccraffrey, R.; Genrich, J. F.; Calais, E.; Rais, J.; Subarya, C.

    1994-01-01

    Convergence across the Java Trench has been estimated for the first time, from annual Global Positioning System (GPS) measurements commencing in 1989. The directions of motion of Christmas and Cocos Island are within 1 deg of that predicted by the No-Net Rotation (NNR) NUVEL-1 plate motion model for the Australian plate although their rates are 25% and 37% less than predcited, respectively. The motion of West Java differs significantly from the NNR NUVEL-1 prediction for the Eurasian plate with a 1 deg difference in direction and a 40% increase in rate. We infer that either West Java moves with a distinct Southeast Asian plate or this region experiences plate margin deformation. The convergence of Christmas Island with respect to West Java is 67 +/- mm/yr in a direction N11 deg E +/- 4 deg which is orthogonal to the trench. The magnitude of convergence agrees well with rescaled NUVEL-1 relative plate model which predicts a value of 71 mm/yr between Australia and Eurasia. The direction of motion matches the direction inferred from earthquake slip vectors at the trench but may be more northerly than the N20 deg E +/- 3 deg predicted by NUVEL-1. On June 2, 1994, almost a year after the last GPS survey, an M(sub W) = 7.5 earthquake with slip vector direction N5 deg occurred south of central Java.

  13. Facilitating Internet-Scale Code Retrieval

    ERIC Educational Resources Information Center

    Bajracharya, Sushil Krishna

    2010-01-01

    Internet-Scale code retrieval deals with the representation, storage, and access of relevant source code from a large amount of source code available on the Internet. Internet-Scale code retrieval systems support common emerging practices among software developers related to finding and reusing source code. In this dissertation we focus on some…

  14. Urbanization in Central Java and Yogyakarta.

    PubMed

    Soehartadji

    1980-06-01

    The author examines urbanization in the provinces of Central Java and Yogyakarta, Indonesia. Changes in the number and definition of rural and urban areas and in the proportion of the population living in these areas between 1930 and 1971 are analyzed. Causes of urbanization are then discussed, with attention to income levels, push and pull factors, and trade and communication. The study reveals that the rate of urbanization is comparatively low because economic conditions in the cities and towns of Central Java and Yogyakarta are less favorable than in the urban areas of other provinces, with the result that migrants tend to choose destinations in these other provinces.

  15. Developmental Process Model for the Java Intelligent Tutoring System

    ERIC Educational Resources Information Center

    Sykes, Edward

    2007-01-01

    The Java Intelligent Tutoring System (JITS) was designed and developed to support the growing trend of Java programming around the world. JITS is an advanced web-based personalized tutoring system that is unique in several ways. Most programming Intelligent Tutoring Systems require the teacher to author problems with corresponding solutions. JITS,…

  16. Java-based remote viewing and processing of nuclear medicine images: toward "the imaging department without walls".

    PubMed

    Slomka, P J; Elliott, E; Driedger, A A

    2000-01-01

    In nuclear medicine practice, images often need to be reviewed and reports prepared from locations outside the department, usually in the form of hard copy. Although hard-copy images are simple and portable, they do not offer electronic data search and image manipulation capabilities. On the other hand, picture archiving and communication systems or dedicated workstations cannot be easily deployed at numerous locations. To solve this problem, we propose a Java-based remote viewing station (JaRViS) for the reading and reporting of nuclear medicine images using Internet browser technology. JaRViS interfaces to the clinical patient database of a nuclear medicine workstation. All JaRViS software resides on a nuclear medicine department server. The contents of the clinical database can be searched by a browser interface after providing a password. Compressed images with the Java applet and color lookup tables are downloaded on the client side. This paradigm does not require nuclear medicine software to reside on remote computers, which simplifies support and deployment of such a system. To enable versatile reporting of the images, color tables and thresholds can be interactively manipulated and images can be displayed in a variety of layouts. Image filtering, frame grouping (adding frames), and movie display are available. Tomographic mode displays are supported, including gated SPECT. The time to display 14 lung perfusion images in 128 x 128 matrix together with the Java applet and color lookup tables over a V.90 modem is <1 min. SPECT and PET slice reorientation is interactive (<1 s). JaRViS could run on a Windows 95/98/NT or a Macintosh platform with Netscape Communicator or Microsoft Intemet Explorer. The performance of Java code for bilinear interpolation, cine display, and filtering approaches that of a standard imaging workstation. It is feasible to set up a remote nuclear medicine viewing station using Java and an Internet or intranet browser. Images can be made

  17. JavaScript: Convenient Interactivity for the Class Web Page.

    ERIC Educational Resources Information Center

    Gray, Patricia

    This paper shows how JavaScript can be used within HTML pages to add interactive review sessions and quizzes incorporating graphics and sound files. JavaScript has the advantage of providing basic interactive functions without the use of separate software applications and players. Because it can be part of a standard HTML page, it is…

  18. Database Entity Persistence with Hibernate for the Network Connectivity Analysis Model

    DTIC Science & Technology

    2014-04-01

    time savings in the Java coding development process. Appendices A and B describe address setup procedures for installing the MySQL database...development environment is required: • The open source MySQL Database Management System (DBMS) from Oracle, which is a Java Database Connectivity (JDBC...compliant DBMS • MySQL JDBC Driver library that comes as a plug-in with the Netbeans distribution • The latest Java Development Kit with the latest

  19. Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project.

    PubMed

    Limou, Sophie; Taverner, Andrew M; Winkler, Cheryl A

    2016-07-15

    The 1000 Genomes (1KG) Project provides a near-comprehensive resource on human genetic variation in worldwide reference populations. 1KG variants can be accessed through a browser and through the raw and annotated data that are regularly released on an ftp server. We developed Ferret, a user-friendly Java tool, to easily extract genetic variation information from these large and complex data files. From a locus, gene(s) or SNP(s) of interest, Ferret retrieves genotype data for 1KG SNPs and indels, and computes allelic frequencies for 1KG populations and optionally, for the Exome Sequencing Project populations. By converting the 1KG data into files that can be imported into popular pre-existing tools (e.g. PLINK and HaploView), Ferret offers a straightforward way, even for non-bioinformatics specialists, to manipulate, explore and merge 1KG data with the user's dataset, as well as visualize linkage disequilibrium pattern, infer haplotypes and design tagSNPs. Ferret tool and source code are publicly available at http://limousophie35.github.io/Ferret/ ferret@nih.gov Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

  20. The 17 July 2006 Tsunami earthquake in West Java, Indonesia

    USGS Publications Warehouse

    Mori, J.; Mooney, W.D.; Afnimar,; Kurniawan, S.; Anaya, A.I.; Widiyantoro, S.

    2007-01-01

    A tsunami earthquake (Mw = 7.7) occurred south of Java on 17 July 2006. The event produced relatively low levels of high-frequency radiation, and local felt reports indicated only weak shaking in Java. There was no ground motion damage from the earthquake, but there was extensive damage and loss of life from the tsunami along 250 km of the southern coasts of West Java and Central Java. An inspection of the area a few days after the earthquake showed extensive damage to wooden and unreinforced masonry buildings that were located within several hundred meters of the coast. Since there was no tsunami warning system in place, efforts to escape the large waves depended on how people reacted to the earthquake shaking, which was only weakly felt in the coastal areas. This experience emphasizes the need for adequate tsunami warning systems for the Indian Ocean region.

  1. Experimental benchmark of the NINJA code for application to the Linac4 H- ion source plasma

    NASA Astrophysics Data System (ADS)

    Briefi, S.; Mattei, S.; Rauner, D.; Lettry, J.; Tran, M. Q.; Fantz, U.

    2017-10-01

    For a dedicated performance optimization of negative hydrogen ion sources applied at particle accelerators, a detailed assessment of the plasma processes is required. Due to the compact design of these sources, diagnostic access is typically limited to optical emission spectroscopy yielding only line-of-sight integrated results. In order to allow for a spatially resolved investigation, the electromagnetic particle-in-cell Monte Carlo collision code NINJA has been developed for the Linac4 ion source at CERN. This code considers the RF field generated by the ICP coil as well as the external static magnetic fields and calculates self-consistently the resulting discharge properties. NINJA is benchmarked at the diagnostically well accessible lab experiment CHARLIE (Concept studies for Helicon Assisted RF Low pressure Ion sourcEs) at varying RF power and gas pressure. A good general agreement is observed between experiment and simulation although the simulated electron density trends for varying pressure and power as well as the absolute electron temperature values deviate slightly from the measured ones. This can be explained by the assumption of strong inductive coupling in NINJA, whereas the CHARLIE discharges show the characteristics of loosely coupled plasmas. For the Linac4 plasma, this assumption is valid. Accordingly, both the absolute values of the accessible plasma parameters and their trends for varying RF power agree well in measurement and simulation. At varying RF power, the H- current extracted from the Linac4 source peaks at 40 kW. For volume operation, this is perfectly reflected by assessing the processes in front of the extraction aperture based on the simulation results where the highest H- density is obtained for the same power level. In surface operation, the production of negative hydrogen ions at the converter surface can only be considered by specialized beam formation codes, which require plasma parameters as input. It has been demonstrated that

  2. Auditory presentation and synchronization in Adobe Flash and HTML5/JavaScript Web experiments.

    PubMed

    Reimers, Stian; Stewart, Neil

    2016-09-01

    Substantial recent research has examined the accuracy of presentation durations and response time measurements for visually presented stimuli in Web-based experiments, with a general conclusion that accuracy is acceptable for most kinds of experiments. However, many areas of behavioral research use auditory stimuli instead of, or in addition to, visual stimuli. Much less is known about auditory accuracy using standard Web-based testing procedures. We used a millisecond-accurate Black Box Toolkit to measure the actual durations of auditory stimuli and the synchronization of auditory and visual presentation onsets. We examined the distribution of timings for 100 presentations of auditory and visual stimuli across two computers with difference specs, three commonly used browsers, and code written in either Adobe Flash or JavaScript. We also examined different coding options for attempting to synchronize the auditory and visual onsets. Overall, we found that auditory durations were very consistent, but that the lags between visual and auditory onsets varied substantially across browsers and computer systems.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  4. Code Sharing and Collaboration: Experiences from the Scientist's Expert Assistant Project and their Relevance to the Virtual Observatory

    NASA Technical Reports Server (NTRS)

    Jones, Jeremy; Grosvenor, Sandy; Wolf, Karl; Li, Connie; Koratkar, Anuradha; Powers, Edward I. (Technical Monitor)

    2001-01-01

    In the Virtual Observatory (VO), software tools will perform the functions that have traditionally been performed by physical observatories and their instruments. These tools will not be adjuncts to VO functionality but will make up the very core of the VO. Consequently, the tradition of observatory and system independent tools serving a small user base is not valid for the VO. For the VO to succeed, we must improve software collaboration and code sharing between projects and groups. A significant goal of the Scientist's Expert Assistant (SEA) project has been promoting effective collaboration and code sharing between groups. During the past three years, the SEA project has been developing prototypes for new observation planning software tools and strategies. Initially funded by the Next Generation Space Telescope, parts of the SEA code have since been adopted by the Space Telescope Science Institute. SEA has also supplied code for SOFIA, the SIRTF planning tools, and the JSky Open Source Java library. The potential benefits of sharing code are clear. The recipient gains functionality for considerably less cost. The provider gains additional developers working with their code. If enough users groups adopt a set of common code and tools, defacto standards can emerge (as demonstrated by the success of the FITS standard). Code sharing also raises a number of challenges related to the management of the code. In this talk, we will review our experiences with SEA - both successes and failures - and offer some lessons learned that may promote further successes in collaboration and re-use.

  5. Code Sharing and Collaboration: Experiences From the Scientist's Expert Assistant Project and Their Relevance to the Virtual Observatory

    NASA Technical Reports Server (NTRS)

    Korathkar, Anuradha; Grosvenor, Sandy; Jones, Jeremy; Li, Connie; Mackey, Jennifer; Neher, Ken; Obenschain, Arthur F. (Technical Monitor)

    2001-01-01

    In the Virtual Observatory (VO), software tools will perform the functions that have traditionally been performed by physical observatories and their instruments. These tools will not be adjuncts to VO functionality but will make up the very core of the VO. Consequently, the tradition of observatory and system independent tools serving a small user base is not valid for the VO. For the VO to succeed, we must improve software collaboration and code sharing between projects and groups. A significant goal of the Scientist's Expert Assistant (SEA) project has been promoting effective collaboration and code sharing among groups. During the past three years, the SEA project has been developing prototypes for new observation planning software tools and strategies. Initially funded by the Next Generation Space Telescope, parts of the SEA code have since been adopted by the Space Telescope Science Institute. SEA has also supplied code for the SIRTF (Space Infrared Telescope Facility) planning tools, and the JSky Open Source Java library. The potential benefits of sharing code are clear. The recipient gains functionality for considerably less cost. The provider gains additional developers working with their code. If enough users groups adopt a set of common code and tools, de facto standards can emerge (as demonstrated by the success of the FITS standard). Code sharing also raises a number of challenges related to the management of the code. In this talk, we will review our experiences with SEA--both successes and failures, and offer some lessons learned that might promote further successes in collaboration and re-use.

  6. A Comparison of Source Code Plagiarism Detection Engines

    NASA Astrophysics Data System (ADS)

    Lancaster, Thomas; Culwin, Fintan

    2004-06-01

    Automated techniques for finding plagiarism in student source code submissions have been in use for over 20 years and there are many available engines and services. This paper reviews the literature on the major modern detection engines, providing a comparison of them based upon the metrics and techniques they deploy. Generally the most common and effective techniques are seen to involve tokenising student submissions then searching pairs of submissions for long common substrings, an example of what is defined to be a paired structural metric. Computing academics are recommended to use one of the two Web-based detection engines, MOSS and JPlag. It is shown that whilst detection is well established there are still places where further research would be useful, particularly where visual support of the investigation process is possible.

  7. Measuring Diagnoses: ICD Code Accuracy

    PubMed Central

    O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

    2005-01-01

    Objective To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. Data Sources/Study Setting The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. Study Design/Methods We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Principle Findings Main error sources along the “patient trajectory” include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the “paper trail” include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. Conclusions By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways. PMID:16178999

  8. Paintbrush of Discovery: Using Java Applets to Enhance Mathematics Education

    ERIC Educational Resources Information Center

    Eason, Ray; Heath, Garrett

    2004-01-01

    This article addresses the enhancement of the learning environment by using Java applets in the mathematics classroom. Currently, the first year mathematics program at the United States Military Academy involves one semester of modeling with discrete dynamical systems (DDS). Several faculty members from the Academy have integrated Java applets…

  9. 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.

  10. OpenSWPC: an open-source integrated parallel simulation code for modeling seismic wave propagation in 3D heterogeneous viscoelastic media

    NASA Astrophysics Data System (ADS)

    Maeda, Takuto; Takemura, Shunsuke; Furumura, Takashi

    2017-07-01

    We have developed an open-source software package, Open-source Seismic Wave Propagation Code (OpenSWPC), for parallel numerical simulations of seismic wave propagation in 3D and 2D (P-SV and SH) viscoelastic media based on the finite difference method in local-to-regional scales. This code is equipped with a frequency-independent attenuation model based on the generalized Zener body and an efficient perfectly matched layer for absorbing boundary condition. A hybrid-style programming using OpenMP and the Message Passing Interface (MPI) is adopted for efficient parallel computation. OpenSWPC has wide applicability for seismological studies and great portability to allowing excellent performance from PC clusters to supercomputers. Without modifying the code, users can conduct seismic wave propagation simulations using their own velocity structure models and the necessary source representations by specifying them in an input parameter file. The code has various modes for different types of velocity structure model input and different source representations such as single force, moment tensor and plane-wave incidence, which can easily be selected via the input parameters. Widely used binary data formats, the Network Common Data Form (NetCDF) and the Seismic Analysis Code (SAC) are adopted for the input of the heterogeneous structure model and the outputs of the simulation results, so users can easily handle the input/output datasets. All codes are written in Fortran 2003 and are available with detailed documents in a public repository.[Figure not available: see fulltext.

  11. 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

  12. 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.

  13. A Java application for tissue section image analysis.

    PubMed

    Kamalov, R; Guillaud, M; Haskins, D; Harrison, A; Kemp, R; Chiu, D; Follen, M; MacAulay, C

    2005-02-01

    The medical industry has taken advantage of Java and Java technologies over the past few years, in large part due to the language's platform-independence and object-oriented structure. As such, Java provides powerful and effective tools for developing tissue section analysis software. The background and execution of this development are discussed in this publication. Object-oriented structure allows for the creation of "Slide", "Unit", and "Cell" objects to simulate the corresponding real-world objects. Different functions may then be created to perform various tasks on these objects, thus facilitating the development of the software package as a whole. At the current time, substantial parts of the initially planned functionality have been implemented. Getafics 1.0 is fully operational and currently supports a variety of research projects; however, there are certain features of the software that currently introduce unnecessary complexity and inefficiency. In the future, we hope to include features that obviate these problems.

  14. Sedimentary deposits study of the 2006 Java tsunami, in Pangandaran, West Java (preliminary result)

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

    Maemunah, Imun, E-mail: imun-m2001@yahoo.com; Institute Technology of Bandung; Suparka, Emmy, E-mail: emmy@gc.itb.ac.id

    The 2006 Java Earthquake (Mw 7.2) has generated a tsunami that reached Pangandaran coastal plain with 9.7 m above sea level height of wave. In 2014 we examined the tsunami deposit exposed in shallow trenches along a∼300 m at 5 transect from shoreline to inland on Karapyak and Madasari, Pangandaran. We documented stratigraphically and sedimentologically, the characteristics of Java Tsunami deposit on Karapyak and Madasari and compared both sediments. In local farmland a moderately-sorted, brown soil is buried by a poorly-sorted, grey, medium-grained sand-sheet. The tsunami deposit was distinguished from the underlying soil by a pronounced increase in grain size that becomesmore » finner upwards and landwards. Decreasing concentration of coarse size particles with distance toward inland are in agreement with grain size analysis. The thickest tsunami deposit is about 25 cm found at 84 m from shoreline in Madasari and about 15 cm found at 80 m from shoreline in Karapyak. The thickness of tsunami deposits in some transect become thinner landward but in some other transect lack a consistent suggested strongly affected by local topography. Tsunami deposits at Karapyak and Madasari show many similarities. Both deposits consist of coarse sand that sharply overlies a finer sandy soil. The presence mud drapes and other sedimentary structure like graded bedding, massive beds, mud clasts in many locations shows a dynamics process of tsunami waves. The imbrication coarse and shell fragments of the 2006 Java, tsunami deposits also provide information about the curent direction, allowing us to distinguish run up deposits from backwash deposits.« less

  15. Dynamic Detection of Malicious Code in COTS Software

    DTIC Science & Technology

    2000-04-01

    run the following documented hostile applets or ActiveX of these tools work only on mobile code (Java, ActiveX , controls: 16-11 Hostile Applets Tiny...Killer App Exploder Runner ActiveX Check Spy eSafe Protect Desktop 9/9 blocked NB B NB 13/17 blocked NB Surfinshield Online 9/9 blocked NB B B 13/17...Exploder is an ActiveX control top (@). that performs a clean shutdown of your computer. The interface is attractive, although rather complex, as McLain’s

  16. Measuring diagnoses: ICD code accuracy.

    PubMed

    O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

    2005-10-01

    To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Main error sources along the "patient trajectory" include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the "paper trail" include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways.

  17. Differences in the causes of death of HIV-positive patients in a cohort study by data sources and coding algorithms.

    PubMed

    Hernando, Victoria; Sobrino-Vegas, Paz; Burriel, M Carmen; Berenguer, Juan; Navarro, Gemma; Santos, Ignacio; Reparaz, Jesús; Martínez, M Angeles; Antela, Antonio; Gutiérrez, Félix; del Amo, Julia

    2012-09-10

    To compare causes of death (CoDs) from two independent sources: National Basic Death File (NBDF) and deaths reported to the Spanish HIV Research cohort [Cohort de adultos con infección por VIH de la Red de Investigación en SIDA CoRIS)] and compare the two coding algorithms: International Classification of Diseases, 10th revision (ICD-10) and revised version of Coding Causes of Death in HIV (revised CoDe). Between 2004 and 2008, CoDs were obtained from the cohort records (free text, multiple causes) and also from NBDF (ICD-10). CoDs from CoRIS were coded according to ICD-10 and revised CoDe by a panel. Deaths were compared by 13 disease groups: HIV/AIDS, liver diseases, malignancies, infections, cardiovascular, blood disorders, pulmonary, central nervous system, drug use, external, suicide, other causes and ill defined. There were 160 deaths. Concordance for the 13 groups was observed in 111 (69%) cases for the two sources and in 115 (72%) cases for the two coding algorithms. According to revised CoDe, the commonest CoDs were HIV/AIDS (53%), non-AIDS malignancies (11%) and liver related (9%), these percentages were similar, 57, 10 and 8%, respectively, for NBDF (coded as ICD-10). When using ICD-10 to code deaths in CoRIS, wherein HIV infection was known in everyone, the proportion of non-AIDS malignancies was 13%, liver-related accounted for 3%, while HIV/AIDS reached 70% due to liver-related, infections and ill-defined causes being coded as HIV/AIDS. There is substantial variation in CoDs in HIV-infected persons according to sources and algorithms. ICD-10 in patients known to be HIV-positive overestimates HIV/AIDS-related deaths at the expense of underestimating liver-related diseases, infections and ill defined causes. CoDe seems as the best option for cohort studies.

  18. 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.

  19. 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

  20. Absence of plague in certain mammals from Java and Kalimantan (Borneo).

    PubMed

    Van Peenen, P F; Joseph, S W; Cavanaugh, D C; Williams, J E; Luyster, L F; Saroso, J S

    1976-09-01

    Antibodies against plague were lacking in 237 wild mammal sera from Java and 103 from Kalimantan. Wild mammal spleens, 114 from Java and 18 from Kalimantan were negative for plague bacilli. A variety of mammalian species and areas was examined.

  1. 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

  2. Symbolic PathFinder: Symbolic Execution of Java Bytecode

    NASA Technical Reports Server (NTRS)

    Pasareanu, Corina S.; Rungta, Neha

    2010-01-01

    Symbolic Pathfinder (SPF) combines symbolic execution with model checking and constraint solving for automated test case generation and error detection in Java programs with unspecified inputs. In this tool, programs are executed on symbolic inputs representing multiple concrete inputs. Values of variables are represented as constraints generated from the analysis of Java bytecode. The constraints are solved using off-the shelf solvers to generate test inputs guaranteed to achieve complex coverage criteria. SPF has been used successfully at NASA, in academia, and in industry.

  3. 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.

  4. Modelling of cayenne production in Central Java using ARIMA-GARCH

    NASA Astrophysics Data System (ADS)

    Tarno; Sudarno; Ispriyanti, Dwi; Suparti

    2018-05-01

    Some regencies/cities in Central Java Province are known as producers of horticultural crops in Indonesia, for example, Brebes which is the largest area of shallot producer in Central Java, while the others, such as Cilacap and Wonosobo are the areas of cayenne commodities production. Currently, cayenne is a strategic commodity and it has broad impact to Indonesian economic development. Modelling the cayenne production is necessary to predict about the commodity to meet the need for society. The needs fulfillment of society will affect stability of the concerned commodity price. Based on the reality, the decreasing of cayenne production will cause the increasing of society’s basic needs price, and finally it will affect the inflation level at that area. This research focused on autoregressive integrated moving average (ARIMA) modelling by considering the effect of autoregressive conditional heteroscedasticity (ARCH) to study about cayenne production in Central Java. The result of empirical study of ARIMA-GARCH modelling for cayenne production in Central Java from January 2003 to November 2015 is ARIMA([1,3],0,0)-GARCH(1,0) as the best model.

  5. Implications of the Java language on computer-based patient records.

    PubMed

    Pollard, D; Kucharz, E; Hammond, W E

    1996-01-01

    The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

  6. Professional Practice and Innovation: Level of Agreement between Coding Sources of Percentage Total Body Surface Area Burnt (%TBSA).

    PubMed

    Watterson, Dina; Cleland, Heather; Picton, Natalie; Simpson, Pam M; Gabbe, Belinda J

    2011-03-01

    The percentage of total body surface area burnt (%TBSA) is a critical measure of burn injury severity and a key predictor of burn injury outcome. This study evaluated the level of agreement between four sources of %TBSA using 120 cases identified through the Victorian State Trauma Registry. Expert clinician, ICD-10-AM, Abbreviated Injury Scale, and burns registry coding were compared using measures of agreement. There was near-perfect agreement (weighted Kappa statistic 0.81-1) between all sources of data, suggesting that ICD-10-AM is a valid source of %TBSA and use of ICD-10-AM codes could reduce the resource used by trauma and burns registries capturing this information.

  7. Scalar collapse in AdS with an OpenCL open source code

    NASA Astrophysics Data System (ADS)

    Liebling, Steven L.; Khanna, Gaurav

    2017-10-01

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

  8. 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…

  9. 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

  10. Multimedia consultation session recording and playback using Java-based browser in global PACS

    NASA Astrophysics Data System (ADS)

    Martinez, Ralph; Shah, Pinkesh J.; Yu, Yuan-Pin

    1998-07-01

    The current version of the Global PACS software system uses a Java-based implementation of the Remote Consultation and Diagnosis (RCD) system. The Java RCD includes a multimedia consultation session between physicians that includes text, static image, image annotation, and audio data. The JAVA RCD allows 2-4 physicians to collaborate on a patient case. It allows physicians to join the session via WWW Java-enabled browsers or stand alone RCD application. The RCD system includes a distributed database archive system for archiving and retrieving patient and session data. The RCD system can be used for store and forward scenarios, case reviews, and interactive RCD multimedia sessions. The RCD system operates over the Internet, telephone lines, or in a private Intranet. A multimedia consultation session can be recorded, and then played back at a later time for review, comments, and education. A session can be played back using Java-enabled WWW browsers on any operating system platform. The JAVA RCD system shows that a case diagnosis can be captured digitally and played back with the original real-time temporal relationships between data streams. In this paper, we describe design and implementation of the RCD session playback.

  11. The state of the Java universe

    ScienceCinema

    Gosling, James

    2018-05-22

    Speaker Bio: James Gosling received a B.Sc. in computer science from the University of Calgary, Canada in 1977. He received a Ph.D. in computer science from Carnegie-Mellon University in 1983. The title of his thesis was The Algebraic Manipulation of Constraints. He has built satellite data acquisition systems, a multiprocessor version of UNIX®, several compilers, mail systems, and window managers. He has also built a WYSIWYG text editor, a constraint-based drawing editor, and a text editor called Emacs, for UNIX systems. At Sun his early activity was as lead engineer of the NeWS window system. He did the original design of the Java programming language and implemented its original compiler and virtual machine. He has recently been a contributor to the Real-Time Specification for Java.

  12. OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

    PubMed Central

    2011-01-01

    Background Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. Results OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. Conclusions OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. Availability http://www.ontocat.org PMID:21619703

  13. OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

    PubMed

    Adamusiak, Tomasz; Burdett, Tony; Kurbatova, Natalja; Joeri van der Velde, K; Abeygunawardena, Niran; Antonakaki, Despoina; Kapushesky, Misha; Parkinson, Helen; Swertz, Morris A

    2011-05-29

    Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. http://www.ontocat.org.

  14. Evaluation and utilization of beam simulation codes for the SNS ion source and low energy beam transport developmenta)

    NASA Astrophysics Data System (ADS)

    Han, B. X.; Welton, R. F.; Stockli, M. P.; Luciano, N. P.; Carmichael, J. R.

    2008-02-01

    Beam simulation codes PBGUNS, SIMION, and LORENTZ-3D were evaluated by modeling the well-diagnosed SNS base line ion source and low energy beam transport (LEBT) system. Then, an investigation was conducted using these codes to assist our ion source and LEBT development effort which is directed at meeting the SNS operational and also the power-upgrade project goals. A high-efficiency H- extraction system as well as magnetic and electrostatic LEBT configurations capable of transporting up to 100mA is studied using these simulation tools.

  15. Developing a java android application of KMV-Merton default rate model

    NASA Astrophysics Data System (ADS)

    Yusof, Norliza Muhamad; Anuar, Aini Hayati; Isa, Norsyaheeda Natasha; Zulkafli, Sharifah Nursyuhada Syed; Sapini, Muhamad Luqman

    2017-11-01

    This paper presents a developed java android application for KMV-Merton model in predicting the defaut rate of a firm. Predicting default rate is essential in the risk management area as default risk can be immediately transmitted from one entity to another entity. This is the reason default risk is known as a global risk. Although there are several efforts, instruments and methods used to manage the risk, it is said to be insufficient. To the best of our knowledge, there has been limited innovation in developing the default risk mathematical model into a mobile application. Therefore, through this study, default risk is predicted quantitatively using the KMV-Merton model. The KMV-Merton model has been integrated in the form of java program using the Android Studio Software. The developed java android application is tested by predicting the levels of default risk of the three different rated companies. It is found that the levels of default risk are equivalent to the ratings of the respective companies. This shows that the default rate predicted by the KMV-Merton model using the developed java android application can be a significant tool to the risk mangement field. The developed java android application grants users an alternative to predict level of default risk within less procedure.

  16. Development of a Long-Range Gliding Underwater Vehicle Utilizing Java Sun SPOT Technology

    DTIC Science & Technology

    2008-09-01

    release; distribution is unlimited DEVELOPMENT OF A LONG-RANGE GLIDING UNMANNED UNDERWATER VEHICLE UTILIZING JAVA SUN SPOT TECHNOLOGY by...TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE: Development of a Long-Range Gliding Underwater Vehicle Utilizing Java Sun SPOT...vehicle. Further work is needed to demonstrate the efficiency and effectiveness of this design. 15. NUMBER OF PAGES 117 14. SUBJECT TERMS Java

  17. Towards Crustal Structure of Java Island (Sunda Arc) from Ambient Seismic Noise Tomography

    NASA Astrophysics Data System (ADS)

    Widiyantoro, Sri; Zulhan, Zulfakriza; Martha, Agustya; Saygin, Erdinc; Cummins, Phil

    2015-04-01

    In our previous studies, P- and S-wave velocity structures beneath the Sunda Arc were successfully imaged using a global data set and a nested regional-global tomographic method was employed. To obtain more detailed P- and S-wave velocity structures beneath Java, in the central part of the Sunda Arc, we then used local data sets, i.e. newline from the MErapi AMphibious EXperiment (MERAMEX) and the Meteorological, Climatological and Geophysical Agency (MCGA), as well as employed a double-difference technique for tomographic imaging. The results of the imaging show e.g. that P- and S-wave velocities are significantly reduced in the uppermost mantle beneath central Java. In order to obtain detailed crustal structure information beneath Java, the Ambient Noise Tomography (ANT) method was used. The application of this method to the MERAMEX data has produced a good crustal model beneath central Java. We continue our experiment to image crustal structure of eastern Java. We have used seismic waveform data recorded by 22 MCGA stationary seismographic stations and 25 portable seismographs installed for 2 to 8 weeks. The data were processed to obtain waveforms of cross-correlated noise between pairs of seismographic stations. Our preliminary results presented here indicate that the Kendeng zone, an area of low gravity anomaly, is associated with a low velocity zone. On the other hand, the southern mountain range, which has a high gravity anomaly, is related to a high velocity anomaly (as shown by our tomographic images). In future work we will install more seismographic stations in eastern Java as well as in western Java to conduct ANT imaging for the whole of Java Island. The expected result combined with the mantle velocity models resulting from our body wave tomography will allow for accurate location of earthquake hypocenters and determination of regional tectonic structures. Both of these are valuable for understanding seismic hazard in Java, the most densely populated

  18. 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.

  19. JAVA CLASSES FOR NONPROCEDURAL VARIOGRAM MONITORING. JOURNAL OF COMPUTERS AND GEOSCIENCE

    EPA Science Inventory

    NRMRL-ADA-00229 Faulkner*, B.P. Java Classes for Nonprocedural Variogram Monitoring. Journal of Computers and Geosciences ( Elsevier Science, Ltd.) 28:387-397 (2002). EPA/600/J-02/235. A set of Java classes was written for variogram modeling to support research for US EPA's Reg...

  20. PrismTech Data Distribution Service Java API Evaluation

    NASA Technical Reports Server (NTRS)

    Riggs, Cortney

    2008-01-01

    My internship duties with Launch Control Systems required me to start performance testing of an Object Management Group's (OMG) Data Distribution Service (DDS) specification implementation by PrismTech Limited through the Java programming language application programming interface (API). DDS is a networking middleware for Real-Time Data Distribution. The performance testing involves latency, redundant publishers, extended duration, redundant failover, and read performance. Time constraints allowed only for a data throughput test. I have designed the testing applications to perform all performance tests when time is allowed. Performance evaluation data such as megabits per second and central processing unit (CPU) time consumption were not easily attainable through the Java programming language; they required new methods and classes created in the test applications. Evaluation of this product showed the rate that data can be sent across the network. Performance rates are better on Linux platforms than AIX and Sun platforms. Compared to previous C++ programming language API, the performance evaluation also shows the language differences for the implementation. The Java API of the DDS has a lower throughput performance than the C++ API.

  1. Java PathExplorer: A Runtime Verification Tool

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

    We describe recent work on designing an environment called Java PathExplorer for monitoring the execution of Java programs. This environment facilitates the testing of execution traces against high level specifications, including temporal logic formulae. In addition, it contains algorithms for detecting classical error patterns in concurrent programs, such as deadlocks and data races. An initial prototype of the tool has been applied to the executive module of the planetary Rover K9, developed at NASA Ames. In this paper we describe the background and motivation for the development of this tool, including comments on how it relates to formal methods tools as well as to traditional testing, and we then present the tool itself.

  2. 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.

  3. Review of subduction and its association with geothermal system in Sumatera-Java

    NASA Astrophysics Data System (ADS)

    Ladiba, A. F.; Putriyana, L.; Sibarani, B. br.; Soekarno, H.

    2017-12-01

    Java and Sumatera have the largest geothermal resources in Indonesia, in which mostly are spatially associated with volcanoes of subduction zones. However, those volcanoes are not distributed in a regular pattern due to the difference of subduction position. Subduction position in java is relatively more perpendicular to the trench than in Sumatera. In addition, Java has a concentration of large productive geothermal field with vapour dominated system in the western part of Java, which may be caused by the various subduction dip along the island. In order to understand the relationship between the subduction process and geothermal system in the subduction zone volcanoes, we examined several kinematic parameters of subduction that potentially relevant to the formation of geothermal system in overriding plate such as slab dip, subduction rate, and direction of subduction. Data and information regarding tectonic setting of Sumatera and Java and productive geothermal field in Sumatera and Java have been collected and evaluated. In conclusion, there are three condition that caused the geothermal fluid to be more likely being in vapour phase, which are: the subduction is in an orthogonal position, the slab dip is high, and rate of subduction is high. Although there are plenty researches of subduction zone volcanoes, only a few of them present information about its formation and implication to the geothermal system. The result of this study may be used as reference in exploration of geothermal field in mutual geologic environment.

  4. Using XML and Java for Astronomical Instrument Control

    NASA Astrophysics Data System (ADS)

    Koons, L.; Ames, T.; Evans, R.; Warsaw, C.; Sall, K.

    1999-12-01

    Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests. Instrument description is too tightly coupled with details of implementation. NASA/Goddard Space Flight Center and AppNet, Inc. are developing a very general and highly extensible framework that applies to virtually any kind of instrument that can be controlled by a computer (e.g., telescopes, microscopes and printers). A key aspect of the object-oriented architecture, implemented in Java, involves software that is driven by an instrument description. The Astronomical Instrument Markup Language (AIML) is a domain-specific implementation of the more generalized Instrument Markup Language (IML). The software architecture combines the platform-independent processing capabilities of Java with the vendor-independent data description syntax of Extensible Markup Language (XML), a human-readable and machine-understandable way to describe structured data. IML is used to describe command sets (including parameters, datatypes, and constraints) and their associated formats, telemetry, and communication mechanisms. The software uses this description to present graphical user interfaces to control and monitor the instrument. Recent efforts have extended to command procedures (scripting) and representation of data pipeline inputs, outputs, and connections. Near future efforts are likely to include an XML description of data visualizations, as well as the potential use of XSL (Extensible Stylesheet Language) to permit astronomers to customize the user interface on several levels: per user, instrument, subsystem, or observatory-wide. Our initial prototyping effort was targeted for HAWC (High-resolution Airborne Wideband Camera), a first-light instrument of SOFIA (the Stratospheric Observatory for Infrared Astronomy

  5. [Radiology information system using HTML, JavaScript, and Web server].

    PubMed

    Sone, M; Sasaki, M; Oikawa, H; Yoshioka, K; Ehara, S; Tamakawa, Y

    1997-12-01

    We have developed a radiology information system using intranet techniques, including hypertext markup language, JavaScript, and Web server. JavaScript made it possible to develop an easy-to-use application, as well as to reduce network traffic and load on the server. The system we have developed is inexpensive and flexible, and its development and maintenance are much easier than with the previous system.

  6. Study on Design and Implementation of JAVA Programming Procedural Assessment Standard

    ERIC Educational Resources Information Center

    Tingting, Xu; Hua, Ma; Xiujuan, Wang; Jing, Wang

    2015-01-01

    The traditional JAVA course examination is just a list of questions from which we cannot know students' skills of programming. According to the eight abilities in curriculum objectives, we designed an assessment standard of JAVA programming course that is based on employment orientation and apply it to practical teaching to check the teaching…

  7. 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

  8. Wedge geometry, frictional properties and interseismic coupling of the Java megathrust

    NASA Astrophysics Data System (ADS)

    Koulali, Achraf; McClusky, Simon; Cummins, Phil; Tregoning, Paul

    2018-06-01

    The mechanical interaction between rocks at fault zones is a key element for understanding how earthquakes nucleate and propagate. Therefore, estimating frictional properties along fault planes allows us to infer the degree of elastic strain accumulation throughout the seismic cycle. The Java subduction zone is an active plate boundary where high seismic activity has long been documented. However, very little is known about the seismogenic processes of the megathrust, especially its shallowest portion where onshore geodetic networks are insensitive to recover the pattern of elastic strain. Here, we use the geometry of the offshore accretionary prism to infer frictional properties along the Java subduction zone, using Coulomb critical taper theory. We show that large portions of the inner wedge in the eastern part of the Java subduction megathrust are in a critical state, where the wedge is on the verge of failure everywhere. We identify four clusters with an internal coefficient of friction μint of ∼ 0.8 and hydrostatic pore pressure within the wedge. The average effective coefficient of friction ranges between 0.3 and 0.4, reflecting a strong décollement. Our results also show that the aftershock sequence of the 1994 Mw 7.9 earthquake halted adjacent to a critical segment of the wedge, suggesting that critical taper wedge areas in the eastern Java subduction interface may behave as a permanent barrier to large earthquake rupture. In contrast, in western Java topographic slope and slab dip profiles suggest that the wedge is mechanically stable, i.e deformation is restricted to sliding along the décollement, and likely to coincide with a seismogenic portion of the megathrust. We discuss the seismic hazard implications and highlight the importance of considering the segmentation of the Java subduction zone when assessing the seismic hazard of this region.

  9. Collaborative Scheduling Using JMS in a Mixed Java and .NET Environment

    NASA Technical Reports Server (NTRS)

    Wang, Yeou-Fang; Wax, Allan; Lam, Ray; Baldwin, John; Borden, Chet

    2006-01-01

    A viewgraph presentation to demonstrate collaborative scheduling using Java Message Service (JMS) in a mixed Java and .Net environment is given. The topics include: 1) NASA Deep Space Network scheduling; 2) Collaborative scheduling concept; 3) Distributed computing environment; 4) Platform concerns in a distributed environment; 5) Messaging and data synchronization; and 6) The prototype.

  10. Optimal source coding, removable noise elimination, and natural coordinate system construction for general vector sources using replicator neural networks

    NASA Astrophysics Data System (ADS)

    Hecht-Nielsen, Robert

    1997-04-01

    A new universal one-chart smooth manifold model for vector information sources is introduced. Natural coordinates (a particular type of chart) for such data manifolds are then defined. Uniformly quantized natural coordinates form an optimal vector quantization code for a general vector source. Replicator neural networks (a specialized type of multilayer perceptron with three hidden layers) are the introduced. As properly configured examples of replicator networks approach minimum mean squared error (e.g., via training and architecture adjustment using randomly chosen vectors from the source), these networks automatically develop a mapping which, in the limit, produces natural coordinates for arbitrary source vectors. The new concept of removable noise (a noise model applicable to a wide variety of real-world noise processes) is then discussed. Replicator neural networks, when configured to approach minimum mean squared reconstruction error (e.g., via training and architecture adjustment on randomly chosen examples from a vector source, each with randomly chosen additive removable noise contamination), in the limit eliminate removable noise and produce natural coordinates for the data vector portions of the noise-corrupted source vectors. Consideration regarding selection of the dimension of a data manifold source model and the training/configuration of replicator neural networks are discussed.

  11. 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.

  12. The kinematics of crustal deformation in Java from GPS observations: Implications for fault slip partitioning

    NASA Astrophysics Data System (ADS)

    Koulali, A.; McClusky, S.; Susilo, S.; Leonard, Y.; Cummins, P.; Tregoning, P.; Meilano, I.; Efendi, J.; Wijanarto, A. B.

    2017-01-01

    Our understanding of seismic risk in Java has been focused primarily on the subduction zone, where the seismic records during the last century have shown the occurrence of a number of tsunami earthquakes. However, the potential of the existence of active crustal structures within the island of Java itself is less well known. Historical archives show the occurrence of several devastating earthquake ruptures north of the volcanic arc in west Java during the 18th and the 19th centuries, suggesting the existence of active faults that need to be identified in order to guide seismic hazard assessment. Here we use geodetic constraints from the Global Positioning System (GPS) to quantify the present day crustal deformation in Java. The GPS velocities reveal a homogeneous counterclockwise rotation of the Java Block independent of Sunda Block, consistent with a NE-SW convergence between the Australian Plate and southeast Asia. Continuous GPS observations show a time-dependent change in the linear rate of surface motion in west Java, which we interpret as an ongoing long-term post-seismic deformation following the 2006 Mw 7.7 Java earthquake. We use an elastic block model in combination with a viscoelastic model to correct for this post-seismic transient and derive the long-term inter-seismic velocity, which we interpret as a combination of tectonic block motions and crustal faults strain related deformation. There is a north-south gradient in the resulting velocity field with a decrease in the magnitude towards the North across the Kendeng Thrust in the east and the Baribis Thrust in the west. We suggest that the Baribis Thrust is active and accommodating a slow relative motion between Java and the Sunda Block at about 5 ± 0.2 mm /yr. We propose a kinematic model of convergence of the Australian Plate and the Sunda Block, involving a slip partitioning between the Java Trench and a left-lateral structure extending E-W along Java with most of the convergence being

  13. An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code, with Application to WASP-12b

    NASA Astrophysics Data System (ADS)

    Harrington, Joseph; Blecic, Jasmina; Cubillos, Patricio; Rojo, Patricio; Loredo, Thomas J.; Bowman, M. Oliver; Foster, Andrew S. D.; Stemm, Madison M.; Lust, Nate B.

    2015-01-01

    Atmospheric retrievals for solar-system planets typically fit, either with a minimizer or by eye, a synthetic spectrum to high-resolution (Δλ/λ ~ 1000-100,000) data with S/N > 100 per point. In contrast, exoplanet data often have S/N ~ 10 per point, and may have just a few points representing bandpasses larger than 1 um. To derive atmospheric constraints and robust parameter uncertainty estimates from such data requires a Bayesian approach. To date there are few investigators with the relevant codes, none of which are publicly available. We are therefore pleased to announce the open-source Bayesian Atmospheric Radiative Transfer (BART) code. BART uses a Bayesian phase-space explorer to drive a radiative-transfer model through the parameter phase space, producing the most robust estimates available for the thermal profile and chemical abundances in the atmosphere. We present an overview of the code and an initial application to Spitzer eclipse data for WASP-12b. We invite the community to use and improve BART via the open-source development site GitHub.com. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

  14. An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code, and Application to WASP-12b

    NASA Astrophysics Data System (ADS)

    Harrington, Joseph; Blecic, Jasmina; Cubillos, Patricio; Rojo, Patricio M.; Loredo, Thomas J.; Bowman, Matthew O.; Foster, Andrew S.; Stemm, Madison M.; Lust, Nate B.

    2014-11-01

    Atmospheric retrievals for solar-system planets typically fit, either with a minimizer or by eye, a synthetic spectrum to high-resolution (Δλ/λ ~ 1000-100,000) data with S/N > 100 per point. In contrast, exoplanet data often have S/N ~ 10 per point, and may have just a few points representing bandpasses larger than 1 um. To derive atmospheric constraints and robust parameter uncertainty estimates from such data requires a Bayesian approach. To date there are few investigators with the relevant codes, none of which are publicly available. We are therefore pleased to announce the open-source Bayesian Atmospheric Radiative Transfer (BART) code. BART uses a Bayesian phase-space explorer to drive a radiative-transfer model through the parameter phase space, producing the most robust estimates available for the thermal profile and chemical abundances in the atmosphere. We present an overview of the code and an initial application to Spitzer eclipse data for WASP-12b. We invite the community to use and improve BART via the open-source development site GitHub.com. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

  15. 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

  16. JAVA CLASSES FOR NONPROCEDURAL VARIOGRAM MONITORING

    EPA Science Inventory

    A set of Java classes was written for variogram modeling to support research for US EPA's Regional Vulnerability Assessment Program (ReVA). The modeling objectives of this research program are to use conceptual programming tools for numerical analysis for regional risk assessm...

  17. BioLayout(Java): versatile network visualisation of structural and functional relationships.

    PubMed

    Goldovsky, Leon; Cases, Ildefonso; Enright, Anton J; Ouzounis, Christos A

    2005-01-01

    Visualisation of biological networks is becoming a common task for the analysis of high-throughput data. These networks correspond to a wide variety of biological relationships, such as sequence similarity, metabolic pathways, gene regulatory cascades and protein interactions. We present a general approach for the representation and analysis of networks of variable type, size and complexity. The application is based on the original BioLayout program (C-language implementation of the Fruchterman-Rheingold layout algorithm), entirely re-written in Java to guarantee portability across platforms. BioLayout(Java) provides broader functionality, various analysis techniques, extensions for better visualisation and a new user interface. Examples of analysis of biological networks using BioLayout(Java) are presented.

  18. Cytoscape.js: a graph theory library for visualisation and analysis.

    PubMed

    Franz, Max; Lopes, Christian T; Huck, Gerardo; Dong, Yue; Sumer, Onur; Bader, Gary D

    2016-01-15

    Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. gary.bader@utoronto.ca. © The Author 2015. Published by Oxford University Press.

  19. Prevalence of antibodies to Japanese encephalitis virus among pigs in Bali and East Java, Indonesia, 2008.

    PubMed

    Yamanaka, Atsushi; Mulyatno, Kris Cahyo; Susilowati, Helen; Hendrianto, Eryk; Utsumi, Takako; Amin, Mochamad; Lusida, Maria Inge; Soegijanto, Soegeng; Konishi, Eiji

    2010-01-01

    Japanese encephalitis virus (JEV) is a fatal disease in Asia. Pigs are considered to be the effective amplifying host for JEV in the peridomestic environment. Bali Island and Java Island in Indonesia provide a model to assess the effect of pigs on JEV transmission, since the pig density is nearly 100-fold higher in Bali than Java, while the geographic and climatologic environments are equivalent in these areas. We surveyed antibodies to JEV among 123 pigs in Mengwi (Bali) and 96 pigs in Tulungagung (East Java) in 2008 by the hemagglutination-inhibition (HAI) test. Overall prevalences were 49% in Bali and 6% in Java, with a significant difference between them (P < 0.001). Monthly infection rates estimated from age-dependent antibody prevalences were 11% in Bali and 2% in Java. In addition, 2-mercaptoethanol-sensitive antibodies were found only from Bali samples. Further, the average HAI antibody titer obtained from positive samples was significantly higher in Bali (1:52) than Java (1:10; P < 0.001). These results indicated that JEV transmission in nature is more active in Bali than East Java.

  20. Using XML and Java for Astronomical Instrumentation Control

    NASA Technical Reports Server (NTRS)

    Ames, Troy; Koons, Lisa; Sall, Ken; Warsaw, Craig

    2000-01-01

    Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). ]ML is used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, and communication mechanisms. Although the current effort is targeted for the High-resolution Airborne Wideband Camera, a first-light instrument of the Stratospheric Observatory for Infrared Astronomy, the framework is designed to be generic and extensible so that it can be applied to any instrument.

  1. Tsunami Disaster Risk Assessment and Prevention in West Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Deng, H.; Harris, R. A.; Horns, D. M.; Yulianto, E.; Bunds, M. P.; Prasetyadi, C.; Emmett, C.; Hall, S.

    2016-12-01

    Java Island, Indonesia is the most populated area and one of the most tectonically active coastal nations on Earth. This island is the volcanic arc and accretionary wedge of the subduction zone of the Sunda and the Australia plate, where the Java Trench is located. However, the Java Trench hasn't had a mega or giant earthquake for at least 430 years according to historical records. Up to 30 m of slip may have accumulated on the subduction zone interface during this time, which is enough to produce a Mw 9.0 earthquake and large tsunami. One of the largest seismic gaps along the Sunda Arc is a 640 km section of the coast of west Java. The largest population center in this region is Pelabuhan Ratu, with is partially built on ridge and swale coastal plain topography. Candidate tsunami deposits were found in swales that may indicate inundation up to 1 km inland. Numerical modeling of various possible tsunami scenarios indicate that the configuration of the coastline may amplify a tsunami and cause high run-up in the most populated areas or the coast. Also, data from questionnaire surveys administered in Pelabuhan Ratu show a lack of awareness about how tsunamis threaten these communities and plans of action.

  2. Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

    NASA Astrophysics Data System (ADS)

    Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; Kalinkin, Alexander A.

    2017-02-01

    Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,'bottom-up' and 'top-down', are illustrated. Preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.

  3. Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

    DOE PAGES

    Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; ...

    2017-03-20

    Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, whichmore » is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,‘bottom-up’ and ‘top-down’, are illustrated. Here, preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.« less

  4. Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

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

    Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha

    Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, whichmore » is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,‘bottom-up’ and ‘top-down’, are illustrated. Here, preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.« less

  5. Two-terminal video coding.

    PubMed

    Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

    2009-03-01

    Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

  6. 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/.

  7. 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.

  8. 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

  9. Aeroacoustic Prediction Codes

    NASA Technical Reports Server (NTRS)

    Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

    2000-01-01

    This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor

  10. Developing Interactive Educational Engineering Software for the World Wide Web with Java.

    ERIC Educational Resources Information Center

    Reed, John A.; Afjeh, Abdollah A.

    1998-01-01

    Illustrates the design and implementation of a Java applet for use in educational propulsion engineering curricula. The Java Gas Turbine Simulator applet provides an interactive graphical environment which allows the rapid, efficient construction and analysis of arbitrary gas turbine systems. The simulator can be easily accessed from the World…

  11. Annual risks of tuberculous infection in East Nusa Tenggara and Central Java Provinces, Indonesia.

    PubMed

    Bachtiar, A; Miko, T Y; Machmud, R; Besral, B; Yudarini, P; Mehta, F; Chadha, V K; Basri, C; Loprang, F; Jitendra, R

    2009-01-01

    East Nusa Tenggara (NTT) and Central Java Provinces, Indonesia. To estimate the average annual risk of tuberculous infection (ARTI) among school children aged 6-9 years in each province. Children attending Classes 1-4 in 65 schools in NTT and 79 in Central Java, selected by two-stage sampling, were intradermally administered 2 tuberculin units of purified protein derivative RT23 with Tween 80 on the mid-volar aspect of the left forearm. The maximum transverse diameter of induration was measured 72 h later. The analysis was carried out among 5479 satisfactorily test-read children in NTT and 6943 in Central Java. One hundred and fifty-five new sputum smear-positive pulmonary tuberculosis (PTB) cases (78 in NTT and 77 in Central Java) were also tuberculin tested. Based on the frequency distribution of reaction sizes among the children and PTB cases, the prevalence of infection was estimated by the mirror-image method using the modes of tuberculous reactions at 15 and 17 mm. Using the 15 mm mode, ARTI was estimated at 1% in NTT and 0.9% in Central Java. Using the 17 mm mode, ARTI was estimated at 0.5% in NTT and 0.4% in Central Java. Transmission of tuberculous infection may be further reduced by intensification of tuberculosis control efforts.

  12. Java 3D Interactive Visualization for Astrophysics

    NASA Astrophysics Data System (ADS)

    Chae, K.; Edirisinghe, D.; Lingerfelt, E. J.; Guidry, M. W.

    2003-05-01

    We are developing a series of interactive 3D visualization tools that employ the Java 3D API. We have applied this approach initially to a simple 3-dimensional galaxy collision model (restricted 3-body approximation), with quite satisfactory results. Running either as an applet under Web browser control, or as a Java standalone application, this program permits real-time zooming, panning, and 3-dimensional rotation of the galaxy collision simulation under user mouse and keyboard control. We shall also discuss applications of this technology to 3-dimensional visualization for other problems of astrophysical interest such as neutron star mergers and the time evolution of element/energy production networks in X-ray bursts. *Managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.

  13. Characteristic and Behavior of Rainfall Induced Landslides in Java Island, Indonesia : an Overview

    NASA Astrophysics Data System (ADS)

    Christanto, N.; Hadmoko, D. S.; Westen, C. J.; Lavigne, F.; Sartohadi, J.; Setiawan, M. A.

    2009-04-01

    Landslides are important natural hazards occurring on mountainous area situated in the wet tropical climate like in Java, Indonesia. As a central of economic and government activity, Java become the most populated island in Indonesia and is increasing every year. This condition create population more vulnerable to hazard. Java is populated by 120 million inhabitants or equivalent with 60% of Indonesian population in only 6,9% of the total surface of Indonesia. Due to its geological setting, its topographical characteristics, and its climatic characteristics, Java is the most exposed regions to landslide hazard and closely related to several factors: (1) located on a subduction zone, 60% of Java is mountainous, with volcano-tectonic mountain chains and 36 active volcanoes out of the 129 in Indonesia, and these volcanic materials are intensively weathered (2) Java is under a humid tropical climate associated with heavy rainfall during the rainy season from October to April. On top of these "natural" conditions, the human activity is an additional factor of landslide occurrence, driven by a high demographic density The purpose of this paper was to collect and analyze spatial and temporal data concerning landslide hazard for the period 1981-2007 and to evaluate and analyze the characteristic and the behavior of landslide in Java. The results provides a new insight into our understanding of landslide hazard and characteristic in the humid tropics, and a basis for predicting future landslides and assessing related hazards at a regional scale. An overview of characteristic and behavior of landslides in Java is given. The result of this work would be valuable for decision makers and communities in the frame of future landslide risk reduction programs. Landslide inventory data was collected from internal database at the different institutions. The result is then georefenced. The temporal changes of landslide activities was done by examining the changes in number and

  14. 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

  15. Lisp as an Alternative to Java

    NASA Technical Reports Server (NTRS)

    Gat, E.

    2000-01-01

    In a recent study, Prechelt compared the relative performance of Java and C++ in terms of execution time and memory utilization. Unlike many benchmark studies, Prechelt compared mulitple implementations of the same task by multiple programmers in order to control for the effects of difference in programmer skill.

  16. Distributed Object Technology with CORBA and Java: Key Concepts and Implications.

    DTIC Science & Technology

    1997-06-01

    commercial use should be addressed to the SEI Licensing Agent. NO WARRANTY THIS CARNEGIE MELLON UNIVERSITY AND SOFTWARE ENGINEERING INSTITUTE MATERIAL...retrieval. This power is not derived from the language per se, but from the architecture-neutral approach used by Java. The Java Virtual Machine...pattern that is focused on performance considerations, the PCo archi- tecture also uses CORBA interface definition language (IDL) to model the

  17. Installation of the National Transport Code Collaboration Data Server at the ITPA International Multi-tokamak Confinement Profile Database

    NASA Astrophysics Data System (ADS)

    Roach, Colin; Carlsson, Johan; Cary, John R.; Alexander, David A.

    2002-11-01

    The National Transport Code Collaboration (NTCC) has developed an array of software, including a data client/server. The data server, which is written in C++, serves local data (in the ITER Profile Database format) as well as remote data (by accessing one or several MDS+ servers). The client, a web-invocable Java applet, provides a uniform, intuitive, user-friendly, graphical interface to the data server. The uniformity of the interface relieves the user from the trouble of mastering the differences between different data formats and lets him/her focus on the essentials: plotting and viewing the data. The user runs the client by visiting a web page using any Java capable Web browser. The client is automatically downloaded and run by the browser. A reference to the data server is then retrieved via the standard Web protocol (HTTP). The communication between the client and the server is then handled by the mature, industry-standard CORBA middleware. CORBA has bindings for all common languages and many high-quality implementations are available (both Open Source and commercial). The NTCC data server has been installed at the ITPA International Multi-tokamak Confinement Profile Database, which is hosted by the UKAEA at Culham Science Centre. The installation of the data server is protected by an Internet firewall. To make it accessible to clients outside the firewall some modifications of the server were required. The working version of the ITPA confinement profile database is not open to the public. Authentification of legitimate users is done utilizing built-in Java security features to demand a password to download the client. We present an overview of the NTCC data client/server and some details of how the CORBA firewall-traversal issues were resolved and how the user authentification is implemented.

  18. LENSED: a code for the forward reconstruction of lenses and sources from strong lensing observations

    NASA Astrophysics Data System (ADS)

    Tessore, Nicolas; Bellagamba, Fabio; Metcalf, R. Benton

    2016-12-01

    Robust modelling of strong lensing systems is fundamental to exploit the information they contain about the distribution of matter in galaxies and clusters. In this work, we present LENSED, a new code which performs forward parametric modelling of strong lenses. LENSED takes advantage of a massively parallel ray-tracing kernel to perform the necessary calculations on a modern graphics processing unit (GPU). This makes the precise rendering of the background lensed sources much faster, and allows the simultaneous optimization of tens of parameters for the selected model. With a single run, the code is able to obtain the full posterior probability distribution for the lens light, the mass distribution and the background source at the same time. LENSED is first tested on mock images which reproduce realistic space-based observations of lensing systems. In this way, we show that it is able to recover unbiased estimates of the lens parameters, even when the sources do not follow exactly the assumed model. Then, we apply it to a subsample of the Sloan Lens ACS Survey lenses, in order to demonstrate its use on real data. The results generally agree with the literature, and highlight the flexibility and robustness of the algorithm.

  19. Interface Generation and Compositional Verification in JavaPathfinder

    NASA Technical Reports Server (NTRS)

    Giannakopoulou, Dimitra; Pasareanu, Corina

    2009-01-01

    We present a novel algorithm for interface generation of software components. Given a component, our algorithm uses learning techniques to compute a permissive interface representing legal usage of the component. Unlike our previous work, this algorithm does not require knowledge about the component s environment. Furthermore, in contrast to other related approaches, our algorithm computes permissive interfaces even in the presence of non-determinism in the component. Our algorithm is implemented in the JavaPathfinder model checking framework for UML statechart components. We have also added support for automated assume-guarantee style compositional verification in JavaPathfinder, using component interfaces. We report on the application of the presented approach to the generation of interfaces for flight software components.

  20. Joint design of QC-LDPC codes for coded cooperation system with joint iterative decoding

    NASA Astrophysics Data System (ADS)

    Zhang, Shunwai; Yang, Fengfan; Tang, Lei; Ejaz, Saqib; Luo, Lin; Maharaj, B. T.

    2016-03-01

    In this paper, we investigate joint design of quasi-cyclic low-density-parity-check (QC-LDPC) codes for coded cooperation system with joint iterative decoding in the destination. First, QC-LDPC codes based on the base matrix and exponent matrix are introduced, and then we describe two types of girth-4 cycles in QC-LDPC codes employed by the source and relay. In the equivalent parity-check matrix corresponding to the jointly designed QC-LDPC codes employed by the source and relay, all girth-4 cycles including both type I and type II are cancelled. Theoretical analysis and numerical simulations show that the jointly designed QC-LDPC coded cooperation well combines cooperation gain and channel coding gain, and outperforms the coded non-cooperation under the same conditions. Furthermore, the bit error rate performance of the coded cooperation employing jointly designed QC-LDPC codes is better than those of random LDPC codes and separately designed QC-LDPC codes over AWGN channels.

  1. Server-Side JavaScript Debugging: Viewing the Contents of an Object

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

    Hampton, J.; Simons, R.

    1999-04-21

    JavaScript allows the definition and use of large, complex objects. Unlike some other object-oriented languages, it also allows run-time modifications not only of the values of object components, but also of the very structure of the object itself. This feature is powerful and sometimes very convenient, but it can be difficult to keep track of the object's structure and values throughout program execution. What's needed is a simple way to view the current state of an object at any point during execution. There is a debug function that is included in the Netscape server-side JavaScript environment. The function outputs themore » value(s) of the expression given as the argument to the function in the JavaScript Application Manager's debug window [SSJS].« less

  2. Surface wave tomography of the Ontong Java Plateau: Seismic probing of the largest igneous province

    NASA Astrophysics Data System (ADS)

    Richardson, William Philip

    1998-12-01

    Large igneous provinces (LIP), such as the gigantic Cretaceous oceanic plateaus, the Ontong-Java, the Manihiki and the Kerguelen, are part of a globally distributed diverse suite of massive crustal features considered to be episodic representations of mantle dynamics (Coffin and Eldholm, 1994). The Ontong Java Plateau in the central western Pacific is by far the largest (and presumably thickest) of these provinces and is believed to have been emplaced rapidly in the Aptian, ˜122 Ma (Tarduno et al., 1991). From 1994 to 1996 four PASSCAL broadband seismic stations were deployed in an array north of the OJP. Analysis was conducted on vertical component broadband seismograms from events recorded on the Micronesian Seismic Experiment array between January 1994 and March 1996. The purpose of this experiment is to investigate the crustal and upper mantle structure of the Ontong Java Plateau (OJP) employing surface wave tomographic methods. Using the partitioned waveform inversion method (Nolet, 1990) and earthquakes with published Centroid Moment Tensor (Dziewonski et al., 1981) solutions, we produce waveform fits from source-to-receiver paths that primarily sample the OJP. From these waveform fits, linearized constraints on shear velocity suggest: (1) a massively thickened crust over the center of the OJP-greater than 35km over central areas of the plateau while thinning off-center; (2) a pronounced low-velocity zone down to ˜300km depth-a robust result in agreement with recent geochemical predictions (Neal et al., 1997); (3) the probability of lateral heterogeneity across the OJP. Finally, by combining many single waveform inversions (van der Lee and Nolet, 1997b) a 3-D shear velocity model can be computed for the Ontong Java Plateau and the nearby Caroline Basin. New constraints on the crustal thickness (and hence the volume extruded) are presented, thereby adding to the understanding of the overall tectonic setting and possible emplacement mechanism of the structure.

  3. JVM: Java Visual Mapping tool for next generation sequencing read.

    PubMed

    Yang, Ye; Liu, Juan

    2015-01-01

    We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

  4. Imaging of upper crustal structure beneath East Java-Bali, Indonesia with ambient noise tomography

    NASA Astrophysics Data System (ADS)

    Martha, Agustya Adi; Cummins, Phil; Saygin, Erdinc; Sri Widiyantoro; Masturyono

    2017-12-01

    The complex geological structures in East Java and Bali provide important opportunities for natural resource exploitation, but also harbor perils associated with natural disasters. Such a condition makes the East Java region an important area for exploration of the subsurface seismic wave velocity structure, especially in its upper crust. We employed the ambient noise tomography method to image the upper crustal structure under this study area. We used seismic data recorded at 24 seismographs of BMKG spread over East Java and Bali. In addition, we installed 28 portable seismographs in East Java from April 2013 to January 2014 for 2-8 weeks, and we installed an additional 28 seismographs simultaneously throughout East Java from August 2015 to April 2016. We constructed inter-station Rayleigh wave Green's functions through cross-correlations of the vertical component of seismic noise recordings at 1500 pairs of stations. We used the Neighborhood Algorithm to construct depth profiles of shear wave velocity (Vs). The main result obtained from this study is the thickness of sediment cover. East Java's southern mountain zone is dominated by higher Vs, the Kendeng basin in the center is dominated by very low Vs, and the Rembang zone (to the North of Kendeng zone) is associated with medium Vs. The existence of structures with oil and gas potential in the Kendeng and Rembang zones can be identified by low Vs.

  5. Classification of java tea (Orthosiphon aristatus) quality using FTIR spectroscopy and chemometrics

    NASA Astrophysics Data System (ADS)

    Heryanto, R.; Pradono, D. I.; Marlina, E.; Darusman, L. K.

    2017-05-01

    Java tea (Orthosiphon aristatus) is a plant that widely used as a medicinal herb in Indonesia. Its quality is varying depends on various factors, such as cultivating area, climate and harvesting time. This study aimed to investigate the effectiveness of FTIR spectroscopy coupled with chemometrics for discriminating the quality of java tea from different cultivating area. FTIR spectra of ethanolic extracts were collected from five different regions of origin of java tea. Prior to chemometrics evaluation, spectra were pre-processed by using baselining, normalization and derivatization. Principal Components Analysis (PCA) was used to reduce the spectra to two PCs, which explained 73% of the total variance. Score plot of two PCs showed groupings of the samples according to their regions of origin. Furthermore, Partial Least Squares-Discriminant Analysis (PLSDA) was applied to the pre-processed data. The approach produced an external validation success rate of 100%. This study shows that FTIR analysis and chemometrics has discriminatory power to classify java tea based on its quality related to the region of origin.

  6. 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.

  7. West Java Snack Mapping based on Snack Types, Main Ingredients, and Processing Techniques

    NASA Astrophysics Data System (ADS)

    Nurani, A. S.; Subekti, S.; Ana

    2016-04-01

    The research was motivated by lack of literature on archipelago snack especially from West Java. It aims to explore the snack types, the processing techniques, and the main ingredients by planning a learning material on archipelago cake especially from West Java. The research methods used are descriptive observations and interviews. The samples were randomly chosen from all regions in West Java. The findings show the identification of traditional snack from West java including: 1. snack types which are similar in all regions as research sample namely: opak, rangginang, nagasari, aliagrem, cuhcur, keripik, semprong, wajit, dodol, kecimpring, combro, tape ketan, and surabi. The typical snack types involve burayot (Garut), simping kaum (Purwakarta), surabi hejo (Karawang), papais cisaat (Subang), Papais moyong, opak bakar (Kuningan), opak oded, ranggesing (Sumedang), gapit, tapel (Cirebon), gulampo, kue aci (Tasikmalaya), wajit cililin, gurilem (West Bandung), and borondong (Bandung District); 2. various processing techniques namely: steaming, boiling, frying, caramelizing, baking, grilling, roaster, sugaring; 3. various main ingredients namely rice, local glutinous rice, rice flour, glutinous rice flour, starch, wheat flour, hunkue flour, cassava, sweet potato, banana, nuts, and corn; 4. snack classification in West Java namely (1) traditional snack, (2) creation-snack, (3) modification-snack, (4) outside influence-snack.

  8. Spatial durbin error model for human development index in Province of Central Java.

    NASA Astrophysics Data System (ADS)

    Septiawan, A. R.; Handajani, S. S.; Martini, T. S.

    2018-05-01

    The Human Development Index (HDI) is an indicator used to measure success in building the quality of human life, explaining how people access development outcomes when earning income, health and education. Every year HDI in Central Java has improved to a better direction. In 2016, HDI in Central Java was 69.98 %, an increase of 0.49 % over the previous year. The objective of this study was to apply the spatial Durbin error model using angle weights queen contiguity to measure HDI in Central Java Province. Spatial Durbin error model is used because the model overcomes the spatial effect of errors and the effects of spatial depedency on the independent variable. Factors there use is life expectancy, mean years of schooling, expected years of schooling, and purchasing power parity. Based on the result of research, we get spatial Durbin error model for HDI in Central Java with influencing factors are life expectancy, mean years of schooling, expected years of schooling, and purchasing power parity.

  9. Collaborative Scheduling Using JMS in a Mixed Java and .NET Environment

    NASA Technical Reports Server (NTRS)

    Wang, Yeou-Fang; Wax, Allan; Lam, Ray; Baldwin, John; Borden, Chet

    2006-01-01

    A collaborative framework/environment was proto-typed to prove the feasibility of scheduling space flight missions on NASA's Deep Space Network (DSN) in a distributed fashion. In this environment, effective collaboration relies on efficient communications among all flight mission and DSN scheduling users. There-fore, messaging becomes critical to timely event notification and data synchronization. In the prototype, a rapid messaging system using Java Message Service (JMS) in a mixed Java and .NET environment is established. This scheme allows both Java and .NET applications to communicate with each other for data synchronization and schedule negotiation. The JMS approach we used is based on a centralized messaging scheme. With proper use of a high speed messaging system, all users in this collaborative framework can communicate with each other to generate a schedule collaboratively to meet DSN and projects tracking needs.

  10. Seismicity of the Earth 1900-2012 Java and vicinity

    USGS Publications Warehouse

    Jones, Eric S.; Hayes, Gavin P.; Bernardino, Melissa; Dannemann, Fransiska K.; Furlong, Kevin P.; Benz, Harley M.; Villaseñor, Antonio

    2014-01-01

    The Sunda convergent margin extends for 5,600 km from the Bay of Bengal and the Andaman Sea, both located northwest of the map area, towards the island of Sumba in the southeast, and then continues eastward as the Banda arc system. This tectonically active margin is a result of the India and Australia plates converging with and subducting beneath the Sunda plate at a rate of approximately 50 to 70 mm/yr. The main physiographic feature associated with this convergent margin is the Sunda-Java Trench, which stretches for 3,000 km parallel to the Java and Sumatra land masses and terminates at 120° E. The convergence of the Indo-Australia and Sunda plates produces two active volcanic arcs: Sunda, which extends from 105 to 122° E and Banda, which extends from 122 to 128° E. The Sunda arc results solely from relatively simple oceanic plate subduction, while the Banda arc represents the transition from oceanic subduction to continental collision, where a complex, broad deforming zone is found. Based on modern activity, the Banda arc can be divided into three distinct zones: an inactive section, the Wetar Zone, bound by two active segments, the Flores Zone in the west and the Damar Zone in the east. The lack of volcanism in the Wetar Zone is attributed to the collision of Australia with the Sunda plate. The absence of gap in volcanic activity is underlain by a gap in intermediate depth seismicity, which is in contrast to nearly continuous, deep seismicity below all three sections of the arc. The Flores Zone is characterized by down-dip compression in the subducted slab at intermediate depths and late Quaternary uplift of the forearc. These unusual features, along with GPS data interpretations indicate that the Flores Zone marks the transition between subduction of oceanic crust in the west and the collision of continental crust in the east. The Java section of the Sunda arc is considered relatively aseismic historically when compared to the highly seismically active

  11. An oceanic plateau subduction offshore Eastern Java

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  12. 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.

  13. Understanding resonance graphs using Easy Java Simulations (EJS) and why we use EJS

    NASA Astrophysics Data System (ADS)

    Wee, Loo Kang; Lee, Tat Leong; Chew, Charles; Wong, Darren; Tan, Samuel

    2015-03-01

    This paper reports a computer model simulation created using Easy Java Simulation (EJS) for learners to visualize how the steady-state amplitude of a driven oscillating system varies with the frequency of the periodic driving force. The simulation shows (N = 100) identical spring-mass systems being subjected to (1) a periodic driving force of equal amplitude but different driving frequencies, and (2) different amounts of damping. The simulation aims to create a visually intuitive way of understanding how the series of amplitude versus driving frequency graphs are obtained by showing how the displacement of the system changes over time as it transits from the transient to the steady state. A suggested ‘how to use’ the model is added to help educators and students in their teaching and learning, where we explain the theoretical steady-state equation time conditions when the model begins to allow data recording of maximum amplitudes to closely match the theoretical equation, and the steps to collect different runs of the degree of damping. We also discuss two of the design features in our computer model: displaying the instantaneous oscillation together with the achieved steady-state amplitudes, and the explicit world view overlay with scientific representation with different degrees of damping runs. Three advantages of using EJS include: (1) open source codes and creative commons attribution licenses for scaling up of interactively engaging educational practices; (2) the models made can run on almost any device, including Android and iOS; and (3) it allows the redefinition of physics educational practices through computer modeling.

  14. Identifying Intraplate Mechanism by B-Value Calculations in the South of Java Island

    NASA Astrophysics Data System (ADS)

    Bagus Suananda Y., Ida; Aufa, Irfan; Harlianti, Ulvienin

    2018-03-01

    Java is the most populous island in Indonesia with 50 million people live there. This island geologically formed at the Eurasia plate margin by the subduction of the Australian oceanic crust. At the south part of Java, beside the occurrence of 2-plate convergence earthquake (interplate), there are also the activities of the intraplate earthquake. Research for distinguish this 2 different earthquake type is necessary for estimating the behavior of the earthquake that may occur. The aim of this research is to map the b-value in the south of Java using earthquake data from 1963 until 2008. The research area are divided into clusters based on the epicenter mapping results with magnitude more than 4 and three different depth (0-30 km, 30-60 km, 60-100 km). This location clustering indicate group of earthquakes occurred by the same structure or mechanism. On some cluster in the south of Java, b-value obtained are between 0.8 and 1.25. This range of b-value indicates the region was intraplate earthquake zone, with 0.72-1.2 b-value range is the indication of intraplate earthquake zone. The final validation is to determine the mechanism of a segment done by correlating the epicenter and b-value plot with the available structural geology data. Based on this research, we discover that the earthquakes occur in Java not only the interplate earthquake, the intraplate earthquake also occurred here. By identifying the mechanism of a segment in the south of Java, earthquake characterization that may occur can be done for developing the accurate earthquake disaster mitigation system.

  15. SST cooling along coastal Java and Sumatra during positive Indian Ocean Dipole events

    NASA Astrophysics Data System (ADS)

    Delman, A. S.; McClean, J.; Sprintall, J.; Talley, L. D.; Bryan, F.; Johnson, B. K.; Carton, J.

    2016-02-01

    The evolution of positive Indian Ocean Dipole (pIOD) events is driven in part by anomalous SST cooling near the coasts of Java and Sumatra. However, the mechanisms and timeline of surface temperature changes near these two islands are distinct. Satellite data and mixed layer budgets in a forced ocean model simulation with 0.1° spatial resolution were used to characterize the dominant influences on SST in each region during pIOD events. Along the south coast of Java, where upwelling from southeasterly trade winds happens seasonally in June-September, strengthening/weakening of the trade winds has little effect on the interannual variability of SST. Instead, remotely-forced upwelling Kelvin waves are the primary mechanism for producing anomalous Java SST cooling in the early stages of a pIOD event. Other mechanisms that affect Java SST anomalies include inflows from the interior Indonesian Seas, mesoscale eddies, and air-sea heat fluxes; these influences can hasten the decay of cool Java SST anomalies and therefore may impact the strength and duration of pIOD events. Along the west coast of Sumatra, surface cooling is initially delayed by a deeper thermocline and a salinity-stratified barrier layer. Hence upwelling Kelvin waves do not substantially affect SST near Sumatra during the first 2-3 months of Java SST cooling; however, they do help drive surface cooling near Sumatra once the barrier layer has been sufficiently eroded by waters of decreasing temperature and increasing salinity. Upwelling Kelvin wave activity in the equatorial Indian Ocean starting in April is also shown to be a robust predictor of pIOD events later in the calendar year.

  16. A Standalone Vision Impairments Simulator for Java Swing Applications

    NASA Astrophysics Data System (ADS)

    Oikonomou, Theofanis; Votis, Konstantinos; Korn, Peter; Tzovaras, Dimitrios; Likothanasis, Spriridon

    A lot of work has been done lately in an attempt to assess accessibility. For the case of web rich-client applications several tools exist that simulate how a vision impaired or colour-blind person would perceive this content. In this work we propose a simulation tool for non-web JavaTM Swing applications. Developers and designers face a real challenge when creating software that has to cope with a lot of interaction situations, as well as specific directives for ensuring an accessible interaction. The proposed standalone tool will assist them to explore user-centered design and important accessibility issues for their JavaTM Swing implementations.

  17. Applications of Java and Vector Graphics to Astrophysical Visualization

    NASA Astrophysics Data System (ADS)

    Edirisinghe, D.; Budiardja, R.; Chae, K.; Edirisinghe, G.; Lingerfelt, E.; Guidry, M.

    2002-12-01

    We describe a series of projects utilizing the portability of Java programming coupled with the compact nature of vector graphics (SVG and SWF formats) for setup and control of calculations, local and collaborative visualization, and interactive 2D and 3D animation presentations in astrophysics. Through a set of examples, we demonstrate how such an approach can allow efficient and user-friendly control of calculations in compiled languages such as Fortran 90 or C++ through portable graphical interfaces written in Java, and how the output of such calculations can be packaged in vector-based animation having interactive controls and extremely high visual quality, but very low bandwidth requirements.

  18. ANEMOS: A computer code to estimate air concentrations and ground deposition rates for atmospheric nuclides emitted from multiple operating sources

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

    Miller, C.W.; Sjoreen, A.L.; Begovich, C.L.

    This code estimates concentrations in air and ground deposition rates for Atmospheric Nuclides Emitted from Multiple Operating Sources. ANEMOS is one component of an integrated Computerized Radiological Risk Investigation System (CRRIS) developed for the US Environmental Protection Agency (EPA) for use in performing radiological assessments and in developing radiation standards. The concentrations and deposition rates calculated by ANEMOS are used in subsequent portions of the CRRIS for estimating doses and risks to man. The calculations made in ANEMOS are based on the use of a straight-line Gaussian plume atmospheric dispersion model with both dry and wet deposition parameter options. Themore » code will accommodate a ground-level or elevated point and area source or windblown source. Adjustments may be made during the calculations for surface roughness, building wake effects, terrain height, wind speed at the height of release, the variation in plume rise as a function of downwind distance, and the in-growth and decay of daughter products in the plume as it travels downwind. ANEMOS can also accommodate multiple particle sizes and clearance classes, and it may be used to calculate the dose from a finite plume of gamma-ray-emitting radionuclides passing overhead. The output of this code is presented for 16 sectors of a circular grid. ANEMOS can calculate both the sector-average concentrations and deposition rates at a given set of downwind distances in each sector and the average of these quantities over an area within each sector bounded by two successive downwind distances. ANEMOS is designed to be used primarily for continuous, long-term radionuclide releases. This report describes the models used in the code, their computer implementation, the uncertainty associated with their use, and the use of ANEMOS in conjunction with other codes in the CRRIS. A listing of the code is included in Appendix C.« less

  19. Zika Virus, a Cause of Fever in Central Java, Indonesia

    DTIC Science & Technology

    1981-01-01

    ZIKA VIRUS , A CAUSE OF FEVER IN CENTRAL JAVA, INDONESIA J.G. Olson, T.G. Ksiazek, Suhandiman and Triwibowo REPORT NO. TR-879 NAMRU- DT1 &, AUG 0 9...75, No. 3, 1981 Zika virus , a cause of fever in Central Java, Indonesia J. G. OLSON’, T. G. KSIAZEK’, SUHANDIMAN 2 AND TRIwIBOWO 2 ’U.S. Naval...more days on admission. A physician member of the team recorded the Introduction patient’s age, sex and date of onset of symptoms and Zika virus ( ZIKA

  20. SU-E-T-212: Comparison of TG-43 Dosimetric Parameters of Low and High Energy Brachytherapy Sources Obtained by MCNP Code Versions of 4C, X and 5

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

    Zehtabian, M; Zaker, N; Sina, S

    2015-06-15

    Purpose: Different versions of MCNP code are widely used for dosimetry purposes. The purpose of this study is to compare different versions of the MCNP codes in dosimetric evaluation of different brachytherapy sources. Methods: The TG-43 parameters such as dose rate constant, radial dose function, and anisotropy function of different brachytherapy sources, i.e. Pd-103, I-125, Ir-192, and Cs-137 were calculated in water phantom. The results obtained by three versions of Monte Carlo codes (MCNP4C, MCNPX, MCNP5) were compared for low and high energy brachytherapy sources. Then the cross section library of MCNP4C code was changed to ENDF/B-VI release 8 whichmore » is used in MCNP5 and MCNPX codes. Finally, the TG-43 parameters obtained using the MCNP4C-revised code, were compared with other codes. Results: The results of these investigations indicate that for high energy sources, the differences in TG-43 parameters between the codes are less than 1% for Ir-192 and less than 0.5% for Cs-137. However for low energy sources like I-125 and Pd-103, large discrepancies are observed in the g(r) values obtained by MCNP4C and the two other codes. The differences between g(r) values calculated using MCNP4C and MCNP5 at the distance of 6cm were found to be about 17% and 28% for I-125 and Pd-103 respectively. The results obtained with MCNP4C-revised and MCNPX were similar. However, the maximum difference between the results obtained with the MCNP5 and MCNP4C-revised codes was 2% at 6cm. Conclusion: The results indicate that using MCNP4C code for dosimetry of low energy brachytherapy sources can cause large errors in the results. Therefore it is recommended not to use this code for low energy sources, unless its cross section library is changed. Since the results obtained with MCNP4C-revised and MCNPX were similar, it is concluded that the difference between MCNP4C and MCNPX is their cross section libraries.« less

  1. MPEG-compliant joint source/channel coding using discrete cosine transform and substream scheduling for visual communication over packet networks

    NASA Astrophysics Data System (ADS)

    Kim, Seong-Whan; Suthaharan, Shan; Lee, Heung-Kyu; Rao, K. R.

    2001-01-01

    Quality of Service (QoS)-guarantee in real-time communication for multimedia applications is significantly important. An architectural framework for multimedia networks based on substreams or flows is effectively exploited for combining source and channel coding for multimedia data. But the existing frame by frame approach which includes Moving Pictures Expert Group (MPEG) cannot be neglected because it is a standard. In this paper, first, we designed an MPEG transcoder which converts an MPEG coded stream into variable rate packet sequences to be used for our joint source/channel coding (JSCC) scheme. Second, we designed a classification scheme to partition the packet stream into multiple substreams which have their own QoS requirements. Finally, we designed a management (reservation and scheduling) scheme for substreams to support better perceptual video quality such as the bound of end-to-end jitter. We have shown that our JSCC scheme is better than two other two popular techniques by simulation and real video experiments on the TCP/IP environment.

  2. 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.

  3. The Particle Accelerator Simulation Code PyORBIT

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

    Gorlov, Timofey V; Holmes, Jeffrey A; Cousineau, Sarah M

    2015-01-01

    The particle accelerator simulation code PyORBIT is presented. The structure, implementation, history, parallel and simulation capabilities, and future development of the code are discussed. The PyORBIT code is a new implementation and extension of algorithms of the original ORBIT code that was developed for the Spallation Neutron Source accelerator at the Oak Ridge National Laboratory. The PyORBIT code has a two level structure. The upper level uses the Python programming language to control the flow of intensive calculations performed by the lower level code implemented in the C++ language. The parallel capabilities are based on MPI communications. The PyORBIT ismore » an open source code accessible to the public through the Google Open Source Projects Hosting service.« less

  4. Effect of the diffusion parameters on the observed γ-ray spectrum of sources and their contribution to the local all-electron spectrum: The EDGE code

    NASA Astrophysics Data System (ADS)

    López-Coto, R.; Hahn, J.; BenZvi, S.; Dingus, B.; Hinton, J.; Nisa, M. U.; Parsons, R. D.; Greus, F. Salesa; Zhang, H.; Zhou, H.

    2018-11-01

    The positron excess measured by PAMELA and AMS can only be explained if there is one or several sources injecting them. Moreover, at the highest energies, it requires the presence of nearby ( ∼ hundreds of parsecs) and middle age (maximum of ∼ hundreds of kyr) sources. Pulsars, as factories of electrons and positrons, are one of the proposed candidates to explain the origin of this excess. To calculate the contribution of these sources to the electron and positron flux at the Earth, we developed EDGE (Electron Diffusion and Gamma rays to the Earth), a code to treat the propagation of electrons and compute their diffusion from a central source with a flexible injection spectrum. Using this code, we can derive the source's gamma-ray spectrum, spatial extension, the all-electron density in space, the electron and positron flux reaching the Earth and the positron fraction measured at the Earth. We present in this paper the foundations of the code and study how different parameters affect the gamma-ray spectrum of a source and the electron flux measured at the Earth. We also studied the effect of several approximations usually performed in these studies. This code has been used to derive the results of the positron flux measured at the Earth in [1].

  5. Building interactive virtual environments for simulated training in medicine using VRML and Java/JavaScript.

    PubMed

    Korocsec, D; Holobar, A; Divjak, M; Zazula, D

    2005-12-01

    Medicine is a difficult thing to learn. Experimenting with real patients should not be the only option; simulation deserves a special attention here. Virtual Reality Modelling Language (VRML) as a tool for building virtual objects and scenes has a good record of educational applications in medicine, especially for static and animated visualisations of body parts and organs. However, to create computer simulations resembling situations in real environments the required level of interactivity and dynamics is difficult to achieve. In the present paper we describe some approaches and techniques which we used to push the limits of the current VRML technology further toward dynamic 3D representation of virtual environments (VEs). Our demonstration is based on the implementation of a virtual baby model, whose vital signs can be controlled from an external Java application. The main contributions of this work are: (a) outline and evaluation of the three-level VRML/Java implementation of the dynamic virtual environment, (b) proposal for a modified VRML Timesensor node, which greatly improves the overall control of system performance, and (c) architecture of the prototype distributed virtual environment for training in neonatal resuscitation comprising the interactive virtual newborn, active bedside monitor for vital signs and full 3D representation of the surgery room.

  6. Resurrecting Legacy Code Using Ontosoft Knowledge-Sharing and Digital Object Management to Revitalize and Reproduce Software for Groundwater Management Research

    NASA Astrophysics Data System (ADS)

    Kwon, N.; Gentle, J.; Pierce, S. A.

    2015-12-01

    Software code developed for research is often used for a relatively short period of time before it is abandoned, lost, or becomes outdated. This unintentional abandonment of code is a valid problem in the 21st century scientific process, hindering widespread reusability and increasing the effort needed to develop research software. Potentially important assets, these legacy codes may be resurrected and documented digitally for long-term reuse, often with modest effort. Furthermore, the revived code may be openly accessible in a public repository for researchers to reuse or improve. For this study, the research team has begun to revive the codebase for Groundwater Decision Support System (GWDSS), originally developed for participatory decision making to aid urban planning and groundwater management, though it may serve multiple use cases beyond those originally envisioned. GWDSS was designed as a java-based wrapper with loosely federated commercial and open source components. If successfully revitalized, GWDSS will be useful for both practical applications as a teaching tool and case study for groundwater management, as well as informing theoretical research. Using the knowledge-sharing approaches documented by the NSF-funded Ontosoft project, digital documentation of GWDSS is underway, from conception to development, deployment, characterization, integration, composition, and dissemination through open source communities and geosciences modeling frameworks. Information assets, documentation, and examples are shared using open platforms for data sharing and assigned digital object identifiers. Two instances of GWDSS version 3.0 are being created: 1) a virtual machine instance for the original case study to serve as a live demonstration of the decision support tool, assuring the original version is usable, and 2) an open version of the codebase, executable installation files, and developer guide available via an open repository, assuring the source for the

  7. Subduction erosion off central Java: transition from accretion to erosion manifested by wide-angle seismic studies

    NASA Astrophysics Data System (ADS)

    Wittwer, A.; Flueh, E.; Rabbel, W.; Wagner, D.

    2006-12-01

    In this study, offshore wide-angle data acquired by ocean bottom instruments of a combined onshore- offshore investigation of the tectonic framework of central Java will be presented. The joint interdisciplinary project MERAMEX (Merapi Amphibious Experiment) was carried out in order to characterize the subduction of the Indo-Australian plate beneath Eurasia. The interpretation of three wide-angle data profiles, modelled with forward raytracing, indicates that the subduction of the Roo Rise with its thickened oceanic crust strongly influences the subduction zone. The dip angle of the downgoing oceanic plate is 10° and its crustal thickness increases to the east from 8 km to 9 km between both dip profiles off central Java. Large scale forearc uplift is manifested in isolated forearc highs, reaching water depths of only 1000 m compared to 2000 m water depth off western Java, and results from oceanic basement relief subduction. A broad band of seamounts trends E-W at approximately 10°S. Its incipient subduction off central Java causes frontal erosion of the margin here and leads to mass wasting due to oversteepening of the upper trench wall. A suite of wide-angle profiles off southern Sumatra to central Java indicates a clear change in the tectonic environment between longitude 108°E and 109°E. The well-developed accretionary wedge off southern Sumatra and western Java changes into a small frontal prism with steep slope angles of the upper plate off central Java.

  8. 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.

  9. Source Code Stylometry Improvements in Python

    DTIC Science & Technology

    2017-12-14

    person can be identified via their handwriting or an author identified by their style or prose, programmers can be identified by their code...to say , picking 1 author out of a known complete set. However, expanded open-world classification and multiauthor classification have also been

  10. 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.

  11. Software Certification - Coding, Code, and Coders

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Holzmann, Gerard J.

    2011-01-01

    We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

  12. Land subsidence threats and its management in the North Coast of Java

    NASA Astrophysics Data System (ADS)

    Sarah, D.; Soebowo, E.

    2018-02-01

    Cities on the north coast of Java such as Jakarta, Semarang, Pekalongan, and Surabaya are vulnerable to environmental pressures such as sea level change and land subsidence. Land subsidence can be caused by natural and anthropogenic processes. Geologically, the north coastal plain of Java consists of unconsolidated Holocene alluvial deposit. The recent alluvial deposit is prone to compaction, and further aggravated by anthropogenic forces such as groundwater extraction and land development. Understanding the complex interaction of natural and manmade factors is essential to establish mitigation strategy. Although the impacts of land subsidence are widely felt, many do not realize that land subsidence is taking place. This paper presents a brief review of the land subsidence threats in the North coast of Java and proposes a recommendation for suitable management response.

  13. JPLEX: Java Simplex Implementation with Branch-and-Bound Search for Automated Test Assembly

    ERIC Educational Resources Information Center

    Park, Ryoungsun; Kim, Jiseon; Dodd, Barbara G.; Chung, Hyewon

    2011-01-01

    JPLEX, short for Java simPLEX, is an automated test assembly (ATA) program. It is a mixed integer linear programming (MILP) solver written in Java. It reads in a configuration file, solves the minimization problem, and produces an output file for postprocessing. It implements the simplex algorithm to create a fully relaxed solution and…

  14. 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

  15. Unexpected earthquake of June 25th, 2015 in Madiun, East Java

    NASA Astrophysics Data System (ADS)

    Nugraha, Andri Dian; Supendi, Pepen; Shiddiqi, Hasbi Ash; Widiyantoro, Sri

    2016-05-01

    An earthquake with magnitude 4.2 struck Madiun and its vicinity on June 25, 2015. According to Indonesian Meteorology, Climatology, and Geophysics Agency (BMKG), the earthquake occurred at 10:35:29 GMT+7 and was located in 7.73° S, 111.69 ° E, with a depth of 10 km. At least 57 houses suffered from light to medium damages. We reprocessed earthquake waveform data to obtain an accurate hypocenter location. We manually picked P- and S-waves arrival times from 12 seismic stations in the eastern part of Java. Earthquake location was determined by using Hypoellipse code that employs a single event determination method. Our inversion is able to resolve the fix-depth and shows that the earthquake occurred at 10:35:27.6 GMT+7 and was located in 7.6305° S, 111.7529 ° E with 14.81 km focus depth. Our location depicts a smaller travel time residual compared to that based on the BMKG result. Focal mechanism of the earthquake was determined by using HASH code. We used first arrival polarity of 9 seismic records with azimuthal gap less than 90°, and estimated take-off angles by using assumption of homogenous medium. Our focal mechanism solution shows a strike-slip mechanism with strike direction of 163o, which may be related to a strike-fault in Klangon, an area to the east of Madiun.

  16. 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

  17. Waveform identification and retracking analyses of Jason-2 altimeter satellite data for improving sea surface height estimation in Southern Java Island Waters and Java Sea, Indonesia

    NASA Astrophysics Data System (ADS)

    Nababan, Bisman; Hakim, Muhammad R.; Panjaitan, James P.

    2018-05-01

    Indonesian waters containing many small islands and shallow waters leads to a less accurate of sea surface height (SSH) estimation from satellite altimetry. Little efforts are also given for the validation of SSH estimation from the satellite in Indonesian waters. The purpose of this research was to identify and retrack waveforms of Jason-2 altimeter satellite data in southern Java island waters and Java Sea using several retrackers and performed improvement percentage analyses for new SSH estimation. The study used data of the Sensor Geophysical Data Record type D (SGDR-D) of Jason-2 satellite altimeter of the year 2010 in the southern Java island waters and 2012-2014 in Java Sea. Waveform retracking analyses were conducted using several retrackers (Offset Center of Gravity, Ice, Threshold, and Improved Threshold) and examined using a world reference undulation geoid of EGM08 and Oceanic retracker. Result showed that shape and pattern of waveforms were varied in all passes, seasons, and locations specifically along the coastal regions. In general, non-Brownish and complex waveforms were identified along coastal region specifically within the distance of 0-10 km from the shoreline. In contrary, generally Brownish waveforms were found in offshore. However, Brownish waveform can also be found within coastal region and non-Brownish waveforms within offshore region. The results were also showed that the four retrackers produced a better SSH estimation in coastal region. However, there was no dominant retracker to improve the accuracy of the SSH estimate.

  18. Interactive Learning with Java Applets: Using Interactive, Web-Based Java Applets to Present Science in a Concrete, Meaningful Manner

    ERIC Educational Resources Information Center

    Corder, Greg

    2005-01-01

    Science teachers face challenges that affect the quality of instruction. Tight budgets, limited resources, school schedules, and other obstacles limit students' opportunities to experience science that is visual and interactive. Incorporating web-based Java applets into science instruction offers a practical solution to these challenges. The…

  19. Hybrid concatenated codes and iterative decoding

    NASA Technical Reports Server (NTRS)

    Divsalar, Dariush (Inventor); Pollara, Fabrizio (Inventor)

    2000-01-01

    Several improved turbo code apparatuses and methods. The invention encompasses several classes: (1) A data source is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each encoder outputs a code element which may be transmitted or stored. A parallel decoder provides the ability to decode the code elements to derive the original source information d without use of a received data signal corresponding to d. The output may be coupled to a multilevel trellis-coded modulator (TCM). (2) A data source d is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each of the encoders outputs a code element. In addition, the original data source d is output from the encoder. All of the output elements are coupled to a TCM. (3) At least two data sources are applied to two or more encoders with an interleaver between each source and each of the second and subsequent encoders. The output may be coupled to a TCM. (4) At least two data sources are applied to two or more encoders with at least two interleavers between each source and each of the second and subsequent encoders. (5) At least one data source is applied to one or more serially linked encoders through at least one interleaver. The output may be coupled to a TCM. The invention includes a novel way of terminating a turbo coder.

  20. Descriptive Statistics and Cluster Analysis for Extreme Rainfall in Java Island

    NASA Astrophysics Data System (ADS)

    E Komalasari, K.; Pawitan, H.; Faqih, A.

    2017-03-01

    This study aims to describe regional pattern of extreme rainfall based on maximum daily rainfall for period 1983 to 2012 in Java Island. Descriptive statistics analysis was performed to obtain centralization, variation and distribution of maximum precipitation data. Mean and median are utilized to measure central tendency data while Inter Quartile Range (IQR) and standard deviation are utilized to measure variation of data. In addition, skewness and kurtosis used to obtain shape the distribution of rainfall data. Cluster analysis using squared euclidean distance and ward method is applied to perform regional grouping. Result of this study show that mean (average) of maximum daily rainfall in Java Region during period 1983-2012 is around 80-181mm with median between 75-160mm and standard deviation between 17 to 82. Cluster analysis produces four clusters and show that western area of Java tent to have a higher annual maxima of daily rainfall than northern area, and have more variety of annual maximum value.

  1. WWWinda Orchestrator: a mechanism for coordinating distributed flocks of Java Applets

    NASA Astrophysics Data System (ADS)

    Gutfreund, Yechezkal-Shimon; Nicol, John R.

    1997-01-01

    The WWWinda Orchestrator is a simple but powerful tool for coordinating distributed Java applets. Loosely derived from the Linda programming language developed by David Gelernter and Nicholas Carriero of Yale, WWWinda implements a distributed shared object space called TupleSpace where applets can post, read, or permanently store arbitrary Java objects. In this manner, applets can easily share information without being aware of the underlying communication mechanisms. WWWinda is a very useful for orchestrating flocks of distributed Java applets. Coordination event scan be posted to WWWinda TupleSpace and used to orchestrate the actions of remote applets. Applets can easily share information via the TupleSpace. The technology combines several functions in one simple metaphor: distributed web objects, remote messaging between applets, distributed synchronization mechanisms, object- oriented database, and a distributed event signaling mechanisms. WWWinda can be used a s platform for implementing shared VRML environments, shared groupware environments, controlling remote devices such as cameras, distributed Karaoke, distributed gaming, and shared audio and video experiences.

  2. Fast space-varying convolution using matrix source coding with applications to camera stray light reduction.

    PubMed

    Wei, Jianing; Bouman, Charles A; Allebach, Jan P

    2014-05-01

    Many imaging applications require the implementation of space-varying convolution for accurate restoration and reconstruction of images. Here, we use the term space-varying convolution to refer to linear operators whose impulse response has slow spatial variation. In addition, these space-varying convolution operators are often dense, so direct implementation of the convolution operator is typically computationally impractical. One such example is the problem of stray light reduction in digital cameras, which requires the implementation of a dense space-varying deconvolution operator. However, other inverse problems, such as iterative tomographic reconstruction, can also depend on the implementation of dense space-varying convolution. While space-invariant convolution can be efficiently implemented with the fast Fourier transform, this approach does not work for space-varying operators. So direct convolution is often the only option for implementing space-varying convolution. In this paper, we develop a general approach to the efficient implementation of space-varying convolution, and demonstrate its use in the application of stray light reduction. Our approach, which we call matrix source coding, is based on lossy source coding of the dense space-varying convolution matrix. Importantly, by coding the transformation matrix, we not only reduce the memory required to store it; we also dramatically reduce the computation required to implement matrix-vector products. Our algorithm is able to reduce computation by approximately factoring the dense space-varying convolution operator into a product of sparse transforms. Experimental results show that our method can dramatically reduce the computation required for stray light reduction while maintaining high accuracy.

  3. Phase II Evaluation of Clinical Coding Schemes

    PubMed Central

    Campbell, James R.; Carpenter, Paul; Sneiderman, Charles; Cohn, Simon; Chute, Christopher G.; Warren, Judith

    1997-01-01

    Abstract Objective: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). Methods: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for “parent” and “child” codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. Results: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p <.00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56; UMLS 3.17; READ 2.14, *p <.005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p <. 00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p

  4. Interactive Economics Instruction with Java and CGI.

    ERIC Educational Resources Information Center

    Gerdes, Geoffrey R.

    2000-01-01

    States that this Web site is based on the conviction that Web-based materials must contain interactive modules to achieve value beyond that obtained by conventional media. Discusses three applets that can be reached at the homepage of the Web site by selecting the Java applets link. (CMK)

  5. Playing jigsaw with large igneous provinces - a plate-tectonic reconstruction of Ontong Java Nui

    NASA Astrophysics Data System (ADS)

    Hochmuth, Katharina; Gohl, Karsten; Uenzelmann-Neben, Gabriele; Werner, Reinhard

    2015-04-01

    Ontong Java Nui is a Cretaceous large igneous province (LIP), which was rifted apart into various smaller plateaus shortly after its emplacement around 125 Ma in the central Pacific. It incorporated the Ontong Java Plateau, the Hikurangi Plateau and the Manihiki Plateau as well as multiple smaller fragments, which have been subducted. Its size has been estimated to be approximately 0.8% of the Earth's surface. A volcanic edifice of this size has potentially had a great impact on the environment such as its CO2 release. The break-up of the "Super"-LIP is poorly constrained, because the break-up and subsequent seafloor spreading occurred within the Cretaceous Quiet Period. The Manihiki Plateau is presumably the centerpiece of this "Super"-LIP and shows by its margins and internal fragmentation that its tectonic and volcanic activity is related to the break-up of Ontong Java Nui. By incorporating two new seismic refraction/wide-angle reflection lines across two of the main sub-plateaus of the Manihiki Plateau, we can classify the break-up modes of the individual margins of the Manihiki Plateau. The Western Plateaus experienced crustal stretching due to the westward motion of the Ontong Java Plateau. The High Plateau shows sharp strike-slip movements at its eastern boundary towards an earlier part of Ontong Java Nui, which is has been subducted, and a rifted margin with a strong volcanic overprint at its southern edges towards the Hikurangi Plateau. These observations allow us a re-examination of the conjugate margins of the Hikurangi Plateau and the Ontong Java Plateau. The repositioning of the different plateaus leads to the conclusion that Ontong Java Nui was larger (~1.2% of the Earth's surface at emplacement) than previously anticipated. We use these finding to improve the plate tectonic reconstruction of the Cretaceous Pacific and to illuminate the role of the LIPs within the plate tectonic circuit in the western and central Pacific.

  6. 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

  7. Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

    PubMed

    Campbell, J R; Carpenter, P; Sneiderman, C; Cohn, S; Chute, C G; Warren, J

    1997-01-01

    To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity

  8. Securing mobile code.

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

    Link, Hamilton E.; Schroeppel, Richard Crabtree; Neumann, William Douglas

    2004-10-01

    If software is designed so that the software can issue functions that will move that software from one computing platform to another, then the software is said to be 'mobile'. There are two general areas of security problems associated with mobile code. The 'secure host' problem involves protecting the host from malicious mobile code. The 'secure mobile code' problem, on the other hand, involves protecting the code from malicious hosts. This report focuses on the latter problem. We have found three distinct camps of opinions regarding how to secure mobile code. There are those who believe special distributed hardware ismore » necessary, those who believe special distributed software is necessary, and those who believe neither is necessary. We examine all three camps, with a focus on the third. In the distributed software camp we examine some commonly proposed techniques including Java, D'Agents and Flask. For the specialized hardware camp, we propose a cryptographic technique for 'tamper-proofing' code over a large portion of the software/hardware life cycle by careful modification of current architectures. This method culminates by decrypting/authenticating each instruction within a physically protected CPU, thereby protecting against subversion by malicious code. Our main focus is on the camp that believes that neither specialized software nor hardware is necessary. We concentrate on methods of code obfuscation to render an entire program or a data segment on which a program depends incomprehensible. The hope is to prevent or at least slow down reverse engineering efforts and to prevent goal-oriented attacks on the software and execution. The field of obfuscation is still in a state of development with the central problem being the lack of a basis for evaluating the protection schemes. We give a brief introduction to some of the main ideas in the field, followed by an in depth analysis of a technique called 'white-boxing'. We put forth some new attacks and

  9. 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.

  10. Monitoring 2015 drought in West Java using Normalized Difference Water Index (NDWI)

    NASA Astrophysics Data System (ADS)

    Febrina Amalo, Luisa; Ma’rufah, Ummu; Ayu Permatasari, Prita

    2018-05-01

    Drought is a slow developing phenomenon that accumulates over period and affecting various sectors. It is one of natural hazards that occurs each year, particularly in Indonesia over Australian Monsoon period. During drought event, vegetation’s cover can be affected by water stress. Normalized Difference Water Index (NDWI) is a method for water resource assessment and known to be strongly related to the plant water content. NDWI is produced from MODIS bands Near-infrared (NIR) and Short Wave Infrared (SWIR). This research aims to monitor drought using NDWI in West Java during El Niño 2015 and its impact on rainfall variability. The result showed rainfall was decreased significantly starting from May-June, then increased in November. According to NDWI, it also showed that mostly West Java Region affected by drought during May-November. Very strong drought occurred on September-November. On December, areal extent of drought was decreasing significantly because rainfall had increased during November. Generally, areal extent of drought in West Java was dominated by strong and moderate drought. It implied that El Niño 2015, give great impact on increasing drought and decreasing rainfall in West Java. NDWI can be detected drought occurrence as it have good correlation with rainfall spatially.

  11. Source Term Model for Steady Micro Jets in a Navier-Stokes Computer Code

    NASA Technical Reports Server (NTRS)

    Waithe, Kenrick A.

    2005-01-01

    A source term model for steady micro jets was implemented into a non-proprietary Navier-Stokes computer code, OVERFLOW. The source term models the mass flow and momentum created by a steady blowing micro jet. The model is obtained by adding the momentum and mass flow created by the jet to the Navier-Stokes equations. The model was tested by comparing with data from numerical simulations of a single, steady micro jet on a flat plate in two and three dimensions. The source term model predicted the velocity distribution well compared to the two-dimensional plate using a steady mass flow boundary condition, which was used to simulate a steady micro jet. The model was also compared to two three-dimensional flat plate cases using a steady mass flow boundary condition to simulate a steady micro jet. The three-dimensional comparison included a case with a grid generated to capture the circular shape of the jet and a case without a grid generated for the micro jet. The case without the jet grid mimics the application of the source term. The source term model compared well with both of the three-dimensional cases. Comparisons of velocity distribution were made before and after the jet and Mach and vorticity contours were examined. The source term model allows a researcher to quickly investigate different locations of individual or several steady micro jets. The researcher is able to conduct a preliminary investigation with minimal grid generation and computational time.

  12. Strategies for teaching object-oriented concepts with Java

    NASA Astrophysics Data System (ADS)

    Sicilia, Miguel-Ángel

    2006-03-01

    A considerable amount of experiences in teaching object-oriented concepts using the Java language have been reported to date, some of which describe language pitfalls and concrete learning difficulties. In this paper, a number of additional issues that have been experienced as difficult for students to master, along with approaches intended to overcome them, are addressed. Concretely, practical issues regarding associations, interfaces, genericity and exceptions are described. These issues suggest that more emphasis is required on presenting Java programs as derivations of conceptual models, in order to guarantee that a thorough design of the object structure actually precedes implementation issues. In addition, common student misunderstandings about the uses of interfaces and exceptions point to the necessity of introducing both specific design philosophies and also a clear distinction between design-for-reuse and more specific implementation issues.

  13. The simulation of 3D structure of groundwater system based on Java/Java3D

    NASA Astrophysics Data System (ADS)

    Yang, Xiaodong; Cui, Weihong; Wang, Peifa; Huang, Yongqi

    2007-06-01

    With the singular development of Internet technique and 3DGIS as well as VR and the imminence demand of 3D visualization from Groundwater information management field, how to display, roam, anatomize and analyze of 3D structure of Groundwater system on Internet have become a research hotspot in hydrogeology field. We simulated the 3D Groundwater resource structure of Taiyuan basin and implemented displaying, roaming, anatomizing and analyzing functions on Internet by Java 3D.

  14. Improving the interactivity and functionality of Web-based radiology teaching files with the Java programming language.

    PubMed

    Eng, J

    1997-01-01

    Java is a programming language that runs on a "virtual machine" built into World Wide Web (WWW)-browsing programs on multiple hardware platforms. Web pages were developed with Java to enable Web-browsing programs to overlay transparent graphics and text on displayed images so that the user could control the display of labels and annotations on the images, a key feature not available with standard Web pages. This feature was extended to include the presentation of normal radiologic anatomy. Java programming was also used to make Web browsers compatible with the Digital Imaging and Communications in Medicine (DICOM) file format. By enhancing the functionality of Web pages, Java technology should provide greater incentive for using a Web-based approach in the development of radiology teaching material.

  15. Visualized kinematics code for two-body nuclear reactions

    NASA Astrophysics Data System (ADS)

    Lee, E. J.; Chae, K. Y.

    2016-05-01

    The one or few nucleon transfer reaction has been a great tool for investigating the single-particle properties of a nucleus. Both stable and exotic beams are utilized to study transfer reactions in normal and inverse kinematics, respectively. Because many energy levels of the heavy recoil from the two-body nuclear reaction can be populated by using a single beam energy, identifying each populated state, which is not often trivial owing to high level-density of the nucleus, is essential. For identification of the energy levels, a visualized kinematics code called VISKIN has been developed by utilizing the Java programming language. The development procedure, usage, and application of the VISKIN is reported.

  16. An Investigation of Factors Related to Self-Efficacy for Java Programming among Engineering Students

    ERIC Educational Resources Information Center

    Askar, Petek; Davenport, David

    2009-01-01

    The purpose of this study was to examine the factors related to self-efficacy for Java programming among first year engineering students. An instrument assessing Java programming self-efficacy was developed from the computer programming self-efficacy scale of Ramalingam & Wiedenbeck. The instrument was administered at the beginning of the…

  17. Exo-Transmit: An Open-Source Code for Calculating Transmission Spectra for Exoplanet Atmospheres of Varied Composition

    NASA Astrophysics Data System (ADS)

    Kempton, Eliza M.-R.; Lupu, Roxana; Owusu-Asare, Albert; Slough, Patrick; Cale, Bryson

    2017-04-01

    We present Exo-Transmit, a software package to calculate exoplanet transmission spectra for planets of varied composition. The code is designed to generate spectra of planets with a wide range of atmospheric composition, temperature, surface gravity, and size, and is therefore applicable to exoplanets ranging in mass and size from hot Jupiters down to rocky super-Earths. Spectra can be generated with or without clouds or hazes with options to (1) include an optically thick cloud deck at a user-specified atmospheric pressure or (2) to augment the nominal Rayleigh scattering by a user-specified factor. The Exo-Transmit code is written in C and is extremely easy to use. Typically the user will only need to edit parameters in a single user input file in order to run the code for a planet of their choosing. Exo-Transmit is available publicly on Github with open-source licensing at https://github.com/elizakempton/Exo_Transmit.

  18. Volcanoes in Central Java, Indonesia

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The Indonesian island of Java (8.0S, 112.0) has over 35 active volcanoes, some of which are the most explosive in the world, and form an east/west line of peaks the length of the island. Five are in this image and at least one is thought to be currently active. The plume flowing north from Welirang (just east of the central cloud mass) is believed to be steam emissions. Also, the lack of vegetation at the peak indicates volcanic activity.

  19. Ambient Noise Tomography of central Java, with Transdimensional Bayesian Inversion

    NASA Astrophysics Data System (ADS)

    Zulhan, Zulfakriza; Saygin, Erdinc; Cummins, Phil; Widiyantoro, Sri; Nugraha, Andri Dian; Luehr, Birger-G.; Bodin, Thomas

    2014-05-01

    Delineating the crustal structure of central Java is crucial for understanding its complex tectonic setting. However, seismic imaging of the strong heterogeneity typical of such a tectonically active region can be challenging, particularly in the upper crust where velocity contrasts are strongest and steep body wave ray-paths provide poor resolution. We have applied ambient noise cross correlation of pair stations in central Java, Indonesia by using the MERapi Amphibious EXperiment (MERAMEX) dataset. The data were collected between May to October 2004. We used 120 of 134 temporary seismic stations for about 150 days of observation, which covered central Java. More than 5000 Rayleigh wave Green's function were extracted by cross-correlating the noise simultaneously recorded at available station pairs. We applied a fully nonlinear 2D Bayesian inversion technique to the retrieved travel times. Features in the derived tomographic images correlate well with previous studies, and some shallow structures that were not evident in previous studies are clearly imaged with Ambient Noise Tomography. The Kendeng Basin and several active volcanoes appear with very low group velocities, and anomalies with relatively high velocities can be interpreted in terms of crustal sutures and/or surface geological features.

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  1. Java-based browsing, visualization and processing of heterogeneous medical data from remote repositories.

    PubMed

    Masseroli, M; Bonacina, S; Pinciroli, F

    2004-01-01

    The actual development of distributed information technologies and Java programming enables employing them also in the medical arena to support the retrieval, integration and evaluation of heterogeneous data and multimodal images in a web browser environment. With this aim, we used them to implement a client-server architecture based on software agents. The client side is a Java applet running in a web browser and providing a friendly medical user interface to browse and visualize different patient and medical test data, integrating them properly. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. Based on the Java Advanced Imaging API, processing and analysis tools were developed to support the evaluation of remotely retrieved bioimages through the quantification of their features in different regions of interest. The Java platform-independence allows the centralized management of the implemented prototype and its deployment to each site where an intranet or internet connection is available. Giving healthcare providers effective support for comprehensively browsing, visualizing and evaluating medical images and records located in different remote repositories, the developed prototype can represent an important aid in providing more efficient diagnoses and medical treatments.

  2. Rickettsia felis in Xenopsylla cheopis, Java, Indonesia

    PubMed Central

    Jiang, Ju; Soeatmadji, Djoko W.; Henry, Katherine M.; Ratiwayanto, Sutanti; Bangs, Michael J.

    2006-01-01

    Rickettsia typhi and R. felis, etiologic agents of murine typhus and fleaborne spotted fever, respectively, were detected in Oriental rat fleas (Xenopsylla cheopis) collected from rodents and shrews in Java, Indonesia. We describe the first evidence of R. felis in Indonesia and naturally occurring R. felis in Oriental rat fleas. PMID:16965716

  3. Verification of Java Programs using Symbolic Execution and Invariant Generation

    NASA Technical Reports Server (NTRS)

    Pasareanu, Corina; Visser, Willem

    2004-01-01

    Software verification is recognized as an important and difficult problem. We present a norel framework, based on symbolic execution, for the automated verification of software. The framework uses annotations in the form of method specifications an3 loop invariants. We present a novel iterative technique that uses invariant strengthening and approximation for discovering these loop invariants automatically. The technique handles different types of data (e.g. boolean and numeric constraints, dynamically allocated structures and arrays) and it allows for checking universally quantified formulas. Our framework is built on top of the Java PathFinder model checking toolset and it was used for the verification of several non-trivial Java programs.

  4. Java across Different Curricula, Courses and Countries Using a Common Pool of Teaching Material

    ERIC Educational Resources Information Center

    Ivanovic, Mirjana; Budimac, Zoran; Mishev, Anastas; Bothe, Klaus; Jurca, Ioan

    2013-01-01

    Under the auspices of a DAAD funded educational project, a subproject devoted to different aspects of teaching the Java programming language started several years ago. The initial intention of the subproject was to attract members of the subproject to prepare some teaching materials for teaching essentials of the Java programming language. During…

  5. 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.

  6. Mobile, hybrid Compton/coded aperture imaging for detection, identification and localization of gamma-ray sources at stand-off distances

    NASA Astrophysics Data System (ADS)

    Tornga, Shawn R.

    The Stand-off Radiation Detection System (SORDS) program is an Advanced Technology Demonstration (ATD) project through the Department of Homeland Security's Domestic Nuclear Detection Office (DNDO) with the goal of detection, identification and localization of weak radiological sources in the presence of large dynamic backgrounds. The Raytheon-SORDS Tri-Modal Imager (TMI) is a mobile truck-based, hybrid gamma-ray imaging system able to quickly detect, identify and localize, radiation sources at standoff distances through improved sensitivity while minimizing the false alarm rate. Reconstruction of gamma-ray sources is performed using a combination of two imaging modalities; coded aperture and Compton scatter imaging. The TMI consists of 35 sodium iodide (NaI) crystals 5x5x2 in3 each, arranged in a random coded aperture mask array (CA), followed by 30 position sensitive NaI bars each 24x2.5x3 in3 called the detection array (DA). The CA array acts as both a coded aperture mask and scattering detector for Compton events. The large-area DA array acts as a collection detector for both Compton scattered events and coded aperture events. In this thesis, developed coded aperture, Compton and hybrid imaging algorithms will be described along with their performance. It will be shown that multiple imaging modalities can be fused to improve detection sensitivity over a broader energy range than either alone. Since the TMI is a moving system, peripheral data, such as a Global Positioning System (GPS) and Inertial Navigation System (INS) must also be incorporated. A method of adapting static imaging algorithms to a moving platform has been developed. Also, algorithms were developed in parallel with detector hardware, through the use of extensive simulations performed with the Geometry and Tracking Toolkit v4 (GEANT4). Simulations have been well validated against measured data. Results of image reconstruction algorithms at various speeds and distances will be presented as well as

  7. A Java API for working with PubChem datasets.

    PubMed

    Southern, Mark R; Griffin, Patrick R

    2011-03-01

    PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

  8. Java-based PACS and reporting system for nuclear medicine

    NASA Astrophysics Data System (ADS)

    Slomka, Piotr J.; Elliott, Edward; Driedger, Albert A.

    2000-05-01

    In medical imaging practice, images and reports often need be reviewed and edited from many locations. We have designed and implemented a Java-based Remote Viewing and Reporting System (JaRRViS) for a nuclear medicine department, which is deployed as a web service, at the fraction of the cost dedicated PACS systems. The system can be extended to other imaging modalities. JaRRViS interfaces to the clinical patient databases of imaging workstations. Specialized nuclear medicine applets support interactive displays of data such as 3-D gated SPECT with all the necessary options such as cine, filtering, dynamic lookup tables, and reorientation. The reporting module is implemented as a separate applet using Java Foundation Classes (JFC) Swing Editor Kit and allows composition of multimedia reports after selection and annotation of appropriate images. The reports are stored on the server in the HTML format. JaRRViS uses Java Servlets for the preparation and storage of final reports. The http links to the reports or to the patient's raw images with applets can be obtained from JaRRViS by any Hospital Information System (HIS) via standard queries. Such links can be sent via e-mail or included as text fields in any HIS database, providing direct access to the patient reports and images via standard web browsers.

  9. 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.

  10. Source Term Model for Vortex Generator Vanes in a Navier-Stokes Computer Code

    NASA Technical Reports Server (NTRS)

    Waithe, Kenrick A.

    2004-01-01

    A source term model for an array of vortex generators was implemented into a non-proprietary Navier-Stokes computer code, OVERFLOW. The source term models the side force created by a vortex generator vane. The model is obtained by introducing a side force to the momentum and energy equations that can adjust its strength automatically based on the local flow. The model was tested and calibrated by comparing data from numerical simulations and experiments of a single low profile vortex generator vane on a flat plate. In addition, the model was compared to experimental data of an S-duct with 22 co-rotating, low profile vortex generators. The source term model allowed a grid reduction of about seventy percent when compared with the numerical simulations performed on a fully gridded vortex generator on a flat plate without adversely affecting the development and capture of the vortex created. The source term model was able to predict the shape and size of the stream-wise vorticity and velocity contours very well when compared with both numerical simulations and experimental data. The peak vorticity and its location were also predicted very well when compared to numerical simulations and experimental data. The circulation predicted by the source term model matches the prediction of the numerical simulation. The source term model predicted the engine fan face distortion and total pressure recovery of the S-duct with 22 co-rotating vortex generators very well. The source term model allows a researcher to quickly investigate different locations of individual or a row of vortex generators. The researcher is able to conduct a preliminary investigation with minimal grid generation and computational time.

  11. Universal Noiseless Coding Subroutines

    NASA Technical Reports Server (NTRS)

    Schlutsmeyer, A. P.; Rice, R. F.

    1986-01-01

    Software package consists of FORTRAN subroutines that perform universal noiseless coding and decoding of integer and binary data strings. Purpose of this type of coding to achieve data compression in sense that coded data represents original data perfectly (noiselessly) while taking fewer bits to do so. Routines universal because they apply to virtually any "real-world" data source.

  12. The NASA Langley Research Center 0.3-meter transonic cryogenic tunnel microcomputer controller source code

    NASA Technical Reports Server (NTRS)

    Kilgore, W. Allen; Balakrishna, S.

    1991-01-01

    The 0.3 m Transonic Cryogenic Tunnel (TCT) microcomputer based controller has been operating for several thousand hours in a safe and efficient manner. A complete listing is provided of the source codes for the tunnel controller and tunnel simulator. Included also is a listing of all the variables used in these programs. Several changes made to the controller are described. These changes are to improve the controller ease of use and safety.

  13. PARAVT: Parallel Voronoi tessellation code

    NASA Astrophysics Data System (ADS)

    González, R. E.

    2016-10-01

    In this study, we present a new open source code for massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition takes into account consistent boundary computation between tasks, and includes periodic conditions. In addition, the code computes neighbors list, Voronoi density, Voronoi cell volume, density gradient for each particle, and densities on a regular grid. Code implementation and user guide are publicly available at https://github.com/regonzar/paravt.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  15. The spirit of democracy in the implementation of public information policy at the provincial government of West Java

    NASA Astrophysics Data System (ADS)

    Sjoraida, D. F.; Asmawi, A.; Anwar, R. K.

    2018-03-01

    This article analyses the implementation of Law Number 14/2008 on Public Information Disclosure on the Provincial Government of West Java. This descriptive-qualitative study presents a discussion of the spirit of democracy in the implementation of the abovem-entioned policy in West Java Province. With the theory of policy implementation and democratization, data obtains that the element of democratic spirit in the implementation of public information policy in the government of West Java is quite thick. Therefore, there must be a massification of the implementation of the law in West Java, especially its socialization to districts/cities and society in general. It was found that the democratization of the West Java Provincial Government in implementing the Act has been well received in the community. However, the lack of publicity about this Law can reduce the strength of moral messages that exist in the law to the public.

  16. Relationships between anopheline mosquitoes and topography in West Timor and Java, Indonesia.

    PubMed

    Ndoen, Ermi; Wild, Clyde; Dale, Pat; Sipe, Neil; Dale, Mike

    2010-08-26

    Malaria is a serious health issue in Indonesia. Mosquito control is one aspect of an integrated malaria management programme. To focus resources on priority areas, information is needed about the vectors and their habitats. This research aimed to identify the relationship between anopheline mosquitoes and topography in West Timor and Java. Study areas were selected in three topographic types in West Timor and Java. These were: coastal plain, hilly (rice field) and highland. Adult mosquitoes were captured landing on humans identified to species level and counted. Eleven species were recorded, four of which were significant for malaria transmission: Anopheles aconitus, Anopheles barbirostris, Anopheles subpictus and Anopheles sundaicus. Each species occupied different topographies, but only five were significantly associated: Anopheles annularis, Anopheles vagus and Anopheles subpictus (Java only) with hilly rice fields; Anopheles barbirostris, Anopheles maculatus and Anopheles subpictus (West Timor only) with coastal areas. Information on significant malaria vectors associated with specific topography is useful for planning the mosquito control aspect of malaria management.

  17. 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.

  18. Transparent ICD and DRG coding using information technology: linking and associating information sources with the eXtensible Markup Language.

    PubMed

    Hoelzer, Simon; Schweiger, Ralf K; Dudeck, Joachim

    2003-01-01

    With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or "semantically associated" parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach.

  19. Transparent ICD and DRG Coding Using Information Technology: Linking and Associating Information Sources with the eXtensible Markup Language

    PubMed Central

    Hoelzer, Simon; Schweiger, Ralf K.; Dudeck, Joachim

    2003-01-01

    With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or “semantically associated” parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach. PMID:12807813

  20. Shuttle Data Center File-Processing Tool in Java

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Miller, Walter H.

    2006-01-01

    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.

  1. JGromacs: a Java package for analyzing protein simulations.

    PubMed

    Münz, Márton; Biggin, Philip C

    2012-01-23

    In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

  2. 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.

  3. Application discussion of source coding standard in voyage data recorder

    NASA Astrophysics Data System (ADS)

    Zong, Yonggang; Zhao, Xiandong

    2018-04-01

    This paper analyzes the disadvantages of the audio and video compression coding technology used by Voyage Data Recorder, and combines the improvement of performance of audio and video acquisition equipment. The thinking of improving the audio and video compression coding technology of the voyage data recorder is proposed, and the feasibility of adopting the new compression coding technology is analyzed from economy and technology two aspects.

  4. MetaJC++: A flexible and automatic program transformation technique using meta framework

    NASA Astrophysics Data System (ADS)

    Beevi, Nadera S.; Reghu, M.; Chitraprasad, D.; Vinodchandra, S. S.

    2014-09-01

    Compiler is a tool to translate abstract code containing natural language terms to machine code. Meta compilers are available to compile more than one languages. We have developed a meta framework intends to combine two dissimilar programming languages, namely C++ and Java to provide a flexible object oriented programming platform for the user. Suitable constructs from both the languages have been combined, thereby forming a new and stronger Meta-Language. The framework is developed using the compiler writing tools, Flex and Yacc to design the front end of the compiler. The lexer and parser have been developed to accommodate the complete keyword set and syntax set of both the languages. Two intermediate representations have been used in between the translation of the source program to machine code. Abstract Syntax Tree has been used as a high level intermediate representation that preserves the hierarchical properties of the source program. A new machine-independent stack-based byte-code has also been devised to act as a low level intermediate representation. The byte-code is essentially organised into an output class file that can be used to produce an interpreted output. The results especially in the spheres of providing C++ concepts in Java have given an insight regarding the potential strong features of the resultant meta-language.

  5. Cognitive characteristics of learning Java, an object-oriented programming language

    NASA Astrophysics Data System (ADS)

    White, Garry Lynn

    Industry and Academia are moving from procedural programming languages (e.g., COBOL) to object-oriented programming languages, such as Java for the Internet. Past studies in the cognitive aspects of programming have focused primarily on procedural programming languages. Some of the languages used have been Pascal, C, Basic, FORTAN, and COBOL. Object-oriented programming (OOP) represents a new paradigm for computing. Industry is finding that programmers are having difficulty shifting to this new programming paradigm. This instruction in OOP is currently starting in colleges and universities across the country. What are the cognitive aspects for this new OOP language Java? When is a student developmentally ready to handle the cognitive characteristics of the OOP language Java? Which cognitive teaching style is best for this OOP language Java? Questions such as the aforementioned are the focus of this research Such research is needed to improve understanding of the learning process and identify students' difficulties with OOP methods. This can enhance academic teaching and industry training (Scholtz, 1993; Sheetz, 1997; Rosson, 1990). Cognitive development as measured by the Propositional Logic Test, cognitive style as measured by the Hemispheric Mode Indicator, and physical hemispheric dominance as measured by a self-report survey were obtained from thirty-six university students studying Java programming. Findings reveal that physical hemispheric dominance is unrelated to cognitive and programming language variables. However, both procedural and object oriented programming require Piaget's formal operation cognitive level as indicated by the Propositional Logic Test. This is consistent with prior research A new finding is that object oriented programming also requires formal operation cognitive level. Another new finding is that object oriented programming appears to be unrelated to hemispheric cognitive style as indicated by the Hemispheric Mode Indicator (HMI

  6. Providing the Persistent Data Storage in a Software Engineering Environment Using Java/COBRA and a DBMS

    NASA Technical Reports Server (NTRS)

    Dhaliwal, Swarn S.

    1997-01-01

    An investigation was undertaken to build the software foundation for the WHERE (Web-based Hyper-text Environment for Requirements Engineering) project. The TCM (Toolkit for Conceptual Modeling) was chosen as the foundation software for the WHERE project which aims to provide an environment for facilitating collaboration among geographically distributed people involved in the Requirements Engineering process. The TCM is a collection of diagram and table editors and has been implemented in the C++ programming language. The C++ implementation of the TCM was translated into Java in order to allow the editors to be used for building various functionality of the WHERE project; the WHERE project intends to use the Web as its communication back- bone. One of the limitations of the translated software (TcmJava), which militated against its use in the WHERE project, was persistent data management mechanisms which it inherited from the original TCM; it was designed to be used in standalone applications. Before TcmJava editors could be used as a part of the multi-user, geographically distributed applications of the WHERE project, a persistent storage mechanism must be built which would allow data communication over the Internet, using the capabilities of the Web. An approach involving features of Java, CORBA (Common Object Request Broker), the Web, a middle-ware (Java Relational Binding (JRB)), and a database server was used to build the persistent data management infrastructure for the WHERE project. The developed infrastructure allows a TcmJava editor to be downloaded and run from a network host by using a JDK 1.1 (Java Developer's Kit) compatible Web-browser. The aforementioned editor establishes connection with a server by using the ORB (Object Request Broker) software and stores/retrieves data in/from the server. The server consists of a CORBA object or objects depending upon whether the data is to be made persistent on a single server or multiple servers. The CORBA

  7. A progressive data compression scheme based upon adaptive transform coding: Mixture block coding of natural images

    NASA Technical Reports Server (NTRS)

    Rost, Martin C.; Sayood, Khalid

    1991-01-01

    A method for efficiently coding natural images using a vector-quantized variable-blocksized transform source coder is presented. The method, mixture block coding (MBC), incorporates variable-rate coding by using a mixture of discrete cosine transform (DCT) source coders. Which coders are selected to code any given image region is made through a threshold driven distortion criterion. In this paper, MBC is used in two different applications. The base method is concerned with single-pass low-rate image data compression. The second is a natural extension of the base method which allows for low-rate progressive transmission (PT). Since the base method adapts easily to progressive coding, it offers the aesthetic advantage of progressive coding without incorporating extensive channel overhead. Image compression rates of approximately 0.5 bit/pel are demonstrated for both monochrome and color images.

  8. Source Listings for Computer Code SPIRALI Incompressible, Turbulent Spiral Grooved Cylindrical and Face Seals

    NASA Technical Reports Server (NTRS)

    Walowit, Jed A.; Shapiro, Wibur

    2005-01-01

    This is the source listing of the computer code SPIRALI which predicts the performance characteristics of incompressible cylindrical and face seals with or without the inclusion of spiral grooves. Performance characteristics include load capacity (for face seals), leakage flow, power requirements and dynamic characteristics in the form of stiffness, damping and apparent mass coefficients in 4 degrees of freedom for cylindrical seals and 3 degrees of freedom for face seals. These performance characteristics are computed as functions of seal and groove geometry, load or film thickness, running and disturbance speeds, fluid viscosity, and boundary pressures.

  9. 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.

  10. High Resolution Hypocenter Relocation for Events in Central Java, Indonesia using Double-Difference Technique

    NASA Astrophysics Data System (ADS)

    Sahara, D. P.; Widiyantoro, S.; Nugraha, A. D.; Sule, R.; Luehr, B. G.

    2010-12-01

    Seismic and volcanic activities in Central Java are highly related to the subduction of the Indo-Australian plate. In the MERapi AMphibious Experiments (MERAMEX), a network consisting of 169 seismographic stations was installed onshore and offshore in central Java and recorded 282 events during the operation. In this study, we present the results of relative hypocenters relocation by using Double Difference (DD) method to image the subduction beneath the volcanic chain in central Java. The DD method is an iterative procedure using Least Square optimization to determine high-resolution hypocenter locations over large distances. This relocation method uses absolute travel-time measurements and/or cross-correlation of P- and S-wave differential travel-time measurements. The preliminary results of our study showed that the algorithm could collapse the diffused event locations obtained from previous study into a sharp image of seismicity structure and reduce the residual travel time errors significantly (7 - 60%). As a result, narrow regions of a double seismic zone which correlated with the subducting slab can be determined more accurately. The dip angle of the slab increases gradually from almost horizontal beneath offshore to very steep (65-80 degrees) beneath the northern part of central Java. The aseismic gap at depths of 140 km - 185 km is also depicted clearly. The next step of the ongoing research is to provide detailed quantitative constraints on the structures of the mantle wedge and crust beneath central Java and to show the ascending paths of fluids and partially molten materials below the volcanic arc by applying Double-Difference Tomography method (TomoDD).

  11. Modelling of land use change in Indramayu District, West Java Province

    NASA Astrophysics Data System (ADS)

    Handayani, L. D. W.; Tejaningrum, M. A.; Damrah, F.

    2017-01-01

    Indramayu District into a strategic area for a stopover and overseas from East Java area because Indramayu District passed the north coast main lane, which is the first as the economic lifeblood of the Java Island. Indramayu District is part of mainstream economic Java pathways so that physical development of the area and population density as well as community activities grew by leaps and bounds. Growth acceleration raised the level of land use change. Land use change and population activities in coastal area would reduce the carrying capacity and impact on environmental quality. This research aim to analyse landuse change of years 2000 and 2011 in Indramayu District. Using this land use change map, we can predict the condition of landuse change of year 2022 in Indramayu District. Cellular Automata Markov (Markov CA) Method is used to create a spatial model of land use changes. The results of this study are predictive of land use in 2022 and the suitability with Spatial Plan (RTRW). A settlement increase predicted to continue in the future the designation of the land according to the spatial plan should be maintained.

  12. Promoting innovative business in the fishery sector in West Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Nurhayati, A.; Aisah, I.; Supriatna, A. K.

    2018-04-01

    West Java represents an important fisheries production center in Indonesia, owing to the abundant capture and aquaculture resources. However, the intrinsic characteristics of fish products such as perishable, voluminous, and seasonal currently prevent fisheries from having brought significant economic contribution to the province. In line with it, this research was aimed to analyze and identify leverage factors that will lead to fishery-based innovative business in West Java. Data used in this research were primary and secondary ones, which were collected through surveys involving 30 respondents representing fish processors and the same number representing consumers. A Focus Group Discussion (FGD) was also carried out to verify the collected data. Analytical tools adopted in this research were fishery triangle product model. Based on the analyses, it was found factors influencing the success of a fishery innovative business in West Java, Indonesia were consecutively: the existence of derivative products, product processing innovativeness, product price competitiveness, market place, and promotion. Based on the fishery trianggle product model, it was found that fish onboard handling, post-harvest handling, and procesing was in the development stage and therefore these production nodes need a particularly high attention.

  13. RIES - Rijnland Internet Election System: A Cursory Study of Published Source Code

    NASA Astrophysics Data System (ADS)

    Gonggrijp, Rop; Hengeveld, Willem-Jan; Hotting, Eelco; Schmidt, Sebastian; Weidemann, Frederik

    The Rijnland Internet Election System (RIES) is a system designed for voting in public elections over the internet. A rather cursory scan of the source code to RIES showed a significant lack of security-awareness among the programmers which - among other things - appears to have left RIES vulnerable to near-trivial attacks. If it had not been for independent studies finding problems, RIES would have been used in the 2008 Water Board elections, possibly handling a million votes or more. While RIES was more extensively studied to find cryptographic shortcomings, our work shows that more down-to-earth secure design practices can be at least as important, and the aspects need to be examined much sooner than right before an election.

  14. Monitoring the UPS and Downs of Sumatra and Java with D-Insar Time-Series

    NASA Astrophysics Data System (ADS)

    Chaussard, E.; Amelung, F.

    2010-12-01

    We performed, for the first time, a global D-InSAR survey of the Indonesian islands of Sumatra and Java to define locations where deformation is occurring. The goals of this study are 1) to create an inventory of actively deforming volcanic centers and 2) monitor all types of ground motion. This work provides ground deformation data for previously unmonitored areas and can assist the Indonesian authorities to improve hazards assessment. The D-InSAR survey covers an area of about 500 000 km2 and 3000 km long on the islands of Sumatra, Java and Bali. We used ALOS data from 45 tracks and more than 1500 granules obtained from the Alaska Satellite Facility (ASF) through the US Government Research Consortium (USGRC). We completed more than 1000 interferograms spanning a period from the end of 2006 to the beginning of 2009. L-band SAR images enable deformation mapping at global scales even in highly vegetated areas where C-band signal experiences loss of coherence. To identify locations where ground deformations are occurring, we used multiple SAR acquisitions of the same area and performed time series analysis using the Small BAseline Subset (SBAS) method. Interferograms with a maximum spatial baseline of 3000 m were phase-unwrapped and subsequently inverted for the phase with respect to the first acquisition. Temporal coherence of each pixel is computed on the set of interferograms in order to select only pixels with high temporal coherence. The compiled InSAR velocity map reveals the background level of activity of the 84 volcanic centers constituting the Sumatra, Java and Bali volcanic arcs. We identified possible uplift at 6 volcanic centers: Agung (Bali), Lamongan (Java), Lawu (Java), Slamet (Java), Kerinci (Sumatra) and Sinabung (Sumatra). Moreover, we identified subsidence in 5 major cities and 1 coastal area. Subsidence rates range from 6 cm/yr in Medan, the largest city of Sumatra, to more than 15 cm/yr in Jakarta. These major subsidence areas are probably due

  15. Distriblets: Java-Based Distributed Computing on the Web.

    ERIC Educational Resources Information Center

    Finkel, David; Wills, Craig E.; Brennan, Brian; Brennan, Chris

    1999-01-01

    Describes a system for using the World Wide Web to distribute computational tasks to multiple hosts on the Web that is written in Java programming language. Describes the programs written to carry out the load distribution, the structure of a "distriblet" class, and experiences in using this system. (Author/LRW)

  16. 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

  17. 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.

  18. The analysis of export commodity competitiveness in Central Java Province at period 2011-2015

    NASA Astrophysics Data System (ADS)

    Elysi, M. G.; Darsono; Riptanti, E. W.

    2018-03-01

    This study aims to determine the competitiveness of furniture export in Central Java Province Indonesia in terms of comparative and competitive advantages and to formulate the strategies to enhance the competitiveness of furniture export in Central Java Province. Descriptive analytic method was used for this research. Data used in this research are primary and secondary data. Data were analyzed using RCA (Revealed Comparative Advantage), TSI (Trade Specialization Index) and SOAR (Strength, Opportunity, Aspiration, Result). The results showed that furniture commodity in Central Java Province had strong comparative competitiveness with the value of RCA>1 and had strong competitiveness with positive index values in the range of 0 to 1. Based on SOAR analysis, strategy measures can be formulated, namely maintaining the existing and expanding targeted markets, improving product designs (innovations) and improving raw materials efficiency.

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

    PubMed

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

    2015-03-01

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

  20. Geographically Weighted Regression Model with Kernel Bisquare and Tricube Weighted Function on Poverty Percentage Data in Central Java Province

    NASA Astrophysics Data System (ADS)

    Nugroho, N. F. T. A.; Slamet, I.

    2018-05-01

    Poverty is a socio-economic condition of a person or group of people who can not fulfil their basic need to maintain and develop a dignified life. This problem still cannot be solved completely in Central Java Province. Currently, the percentage of poverty in Central Java is 13.32% which is higher than the national poverty rate which is 11.13%. In this research, data of percentage of poor people in Central Java Province has been analyzed through geographically weighted regression (GWR). The aim of this research is therefore to model poverty percentage data in Central Java Province using GWR with weighted function of kernel bisquare, and tricube. As the results, we obtained GWR model with bisquare and tricube kernel weighted function on poverty percentage data in Central Java province. From the GWR model, there are three categories of region which are influenced by different of significance factors.

  1. Effects of a Case-Based Reasoning System on Student Performance in a Java Programming Course

    ERIC Educational Resources Information Center

    Schmidt, Cecil

    2007-01-01

    The purpose of this study was to determine if a case-based reasoning tool would improve a student's understanding of the complex concepts in a Java programming course. Subjects for the study were randomly assigned from two sections of an introductory Java programming course. Posttests were used to measure the effects of the case-based reasoning…

  2. 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.

  3. Extraction of essential oil from baby Java orange (Citrus sinensis) solid waste using water and steam distillation

    NASA Astrophysics Data System (ADS)

    Dewi, I. A.; Prastyo, A. M.; Wijana, S.

    2018-03-01

    Baby java orange (Citrus sinensis) is commonly consumed as juice. Processing of baby java orange leaves organic waste which consist of the mesocarp, exocarp, seed, and wall of the orange. Therefore, it is necessary to process baby java orange waste to be valuable products. The purpose of this study was to provide added value to unutilized baby java orange waste, and to find out the pretreatment of time-delay process that maximize the yield of essential oil produced. Essential oil processing can be done by water and steam distillation. The study used randomized block design with one factor namely distillation time-delay process by air drying consisted of 4 levels i.e. the distillation delay for 2, 4, 6, and 8 days. The best treatment was determined based on the yield. The best essential oil from baby java orange waste was obtained from the treatment of distillation delay-process of 8 days. This pretreatment generated yield value of 0.63% with moisture content of 24.21%. By estimating the price of essential oil showed that this effort not only reduced the bulky organic waste but also provided potential economical value.

  4. LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions.

    PubMed

    Chen, Jinbo; Scholz, Uwe; Zhou, Ruonan; Lange, Matthias

    2018-03-01

    is 0.90. The software is either available as tool set to build and train dedicated query suggestion services or as already trained general purpose RESTful web service. The service uses open interfaces to be seamless embeddable into database frontends. The JAVA implementation uses highly optimized data structures and streamlined code to provide fast and scalable response for web service calls. The source code of LAILAPS-QSM is available under GNU General Public License version 2 in Bitbucket GIT repository: https://bitbucket.org/ipk_bit_team/bioescorte-suggestion.

  5. Coding Issues in Grounded Theory

    ERIC Educational Resources Information Center

    Moghaddam, Alireza

    2006-01-01

    This paper discusses grounded theory as one of the qualitative research designs. It describes how grounded theory generates from data. Three phases of grounded theory--open coding, axial coding, and selective coding--are discussed, along with some of the issues which are the source of debate among grounded theorists, especially between its…

  6. Strategies for Teaching Object-Oriented Concepts with Java

    ERIC Educational Resources Information Center

    Sicilia, Miguel-Angel

    2006-01-01

    A considerable amount of experiences in teaching object-oriented concepts using the Java language have been reported to date, some of which describe language pitfalls and concrete learning difficulties. In this paper, a number of additional issues that have been experienced as difficult for students to master, along with approaches intended to…

  7. 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.

  8. 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.

  9. 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.

  10. A Java API for working with PubChem datasets

    PubMed Central

    Southern, Mark R.; Griffin, Patrick R.

    2011-01-01

    Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability: http://code.google.com/p/pubchemdb Contact: southern@scripps.edu PMID:21216779

  11. Acoustic Scattering by Three-Dimensional Stators and Rotors Using the SOURCE3D Code. Volume 2; Scattering Plots

    NASA Technical Reports Server (NTRS)

    Meyer, Harold D.

    1999-01-01

    This second volume of Acoustic Scattering by Three-Dimensional Stators and Rotors Using the SOURCE3D Code provides the scattering plots referenced by Volume 1. There are 648 plots. Half are for the 8750 rpm "high speed" operating condition and the other half are for the 7031 rpm "mid speed" operating condition.

  12. DNA sequence chromatogram browsing using JAVA and CORBA.

    PubMed

    Parsons, J D; Buehler, E; Hillier, L

    1999-03-01

    DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.

  13. Handle with care: the impact of using Java applets in Web-based studies on dropout and sample composition.

    PubMed

    Stieger, Stefan; Göritz, Anja S; Voracek, Martin

    2011-05-01

    In Web-based studies, Web browsers are used to display online questionnaires. If an online questionnaire relies on non-standard technologies (e.g., Java applets), it is often necessary to install a particular browser plug-in. This can lead to technically induced dropout because some participants lack the technological know-how or the willingness to install the plug-in. In two thematically identical online studies conducted across two time points in two different participant pools (N = 1,527 and 805), we analyzed whether using a Java applet produces dropout and distortion of demographics in the final sample. Dropout was significantly higher on the Java applet questionnaire page than on the preceding and subsequent questionnaire pages. Age-specific effects were found only in one sample (i.e., dropouts were older), whereas sex-specific effects were found in both samples (i.e., women dropped out more frequently than men on the Java applet page). These results additionally support the recommendation that using additional technologies (e.g., Java applets) can be dangerous in producing a sample that is biased toward both younger and male respondents.

  14. Predicting Attack-Prone Components with Source Code Static Analyzers

    DTIC Science & Technology

    2009-05-01

    models to determine if additional metrics are required to increase the accuracy of the model: non-security SCSA warnings, code churn and size, the count...code churn and size, the count of faults found manually during development, and the measure of coupling between components. The dependent variable...is the count of vulnerabilities reported by testing and those found in the field. We evaluated our model on three commercial telecommunications

  15. An Assessment of Some Design Constraints on Heat Production of a 3D Conceptual EGS Model Using an Open-Source Geothermal Reservoir Simulation Code

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

    Yidong Xia; Mitch Plummer; Robert Podgorney

    2016-02-01

    Performance of heat production process over a 30-year period is assessed in a conceptual EGS model with a geothermal gradient of 65K per km depth in the reservoir. Water is circulated through a pair of parallel wells connected by a set of single large wing fractures. The results indicate that the desirable output electric power rate and lifespan could be obtained under suitable material properties and system parameters. A sensitivity analysis on some design constraints and operation parameters indicates that 1) the fracture horizontal spacing has profound effect on the long-term performance of heat production, 2) the downward deviation anglemore » for the parallel doublet wells may help overcome the difficulty of vertical drilling to reach a favorable production temperature, and 3) the thermal energy production rate and lifespan has close dependence on water mass flow rate. The results also indicate that the heat production can be improved when the horizontal fracture spacing, well deviation angle, and production flow rate are under reasonable conditions. To conduct the reservoir modeling and simulations, an open-source, finite element based, fully implicit, fully coupled hydrothermal code, namely FALCON, has been developed and used in this work. Compared with most other existing codes that are either closed-source or commercially available in this area, this new open-source code has demonstrated a code development strategy that aims to provide an unparalleled easiness for user-customization and multi-physics coupling. Test results have shown that the FALCON code is able to complete the long-term tests efficiently and accurately, thanks to the state-of-the-art nonlinear and linear solver algorithms implemented in the code.« less

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

    PubMed

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

    2015-12-12

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

  17. Fractionation of Java Citronella Oil and Citronellal Purification by Batch Vacuum Fractional Distillation

    NASA Astrophysics Data System (ADS)

    Eden, W. T.; Alighiri, D.; Cahyono, E.; Supardi, K. I.; Wijayati, N.

    2018-04-01

    The aim of this work was to assess the performance of a vacuum fractionating column for the fractionation of Java Citronella Oil (Cymbopogon winterianus) and citronellal purification during batch mode operation at vacuum -76 cmHg and reflux ratios 5:1. Based on GC-MS analysis of Java Citronella Oil is known that citronellal, citronellol, and geraniol has yielded 21,59%; 7,43%; and 34,27%, respectively. Fractional distillation under reduced pressure and continued redistilled are needed to isolate the component of Java Citronella Oil. Redistilled can improve the purity, then distillate collected while the temperature changed. In the first distillate yielded citronellal with a purity of 75.67%. The first distillate obtained residue rhodinol product will then be carried back to separation into citronellol and geraniol. The purity of citronellol reached 80,65% purity, whereas geraniol reached 76.63% purity. Citronellal Purification resulting citronellal to 95.10% purity and p-menthane-3,8-diol reached 75.95% purity.

  18. A Review on Spectral Amplitude Coding Optical Code Division Multiple Access

    NASA Astrophysics Data System (ADS)

    Kaur, Navpreet; Goyal, Rakesh; Rani, Monika

    2017-06-01

    This manuscript deals with analysis of Spectral Amplitude Coding Optical Code Division Multiple Access (SACOCDMA) system. The major noise source in optical CDMA is co-channel interference from other users known as multiple access interference (MAI). The system performance in terms of bit error rate (BER) degrades as a result of increased MAI. It is perceived that number of users and type of codes used for optical system directly decide the performance of system. MAI can be restricted by efficient designing of optical codes and implementing them with unique architecture to accommodate more number of users. Hence, it is a necessity to design a technique like spectral direct detection (SDD) technique with modified double weight code, which can provide better cardinality and good correlation property.

  19. Assume-Guarantee Verification of Source Code with Design-Level Assumptions

    NASA Technical Reports Server (NTRS)

    Giannakopoulou, Dimitra; Pasareanu, Corina S.; Cobleigh, Jamieson M.

    2004-01-01

    Model checking is an automated technique that can be used to determine whether a system satisfies certain required properties. To address the 'state explosion' problem associated with this technique, we propose to integrate assume-guarantee verification at different phases of system development. During design, developers build abstract behavioral models of the system components and use them to establish key properties of the system. To increase the scalability of model checking at this level, we have developed techniques that automatically decompose the verification task by generating component assumptions for the properties to hold. The design-level artifacts are subsequently used to guide the implementation of the system, but also to enable more efficient reasoning at the source code-level. In particular we propose to use design-level assumptions to similarly decompose the verification of the actual system implementation. We demonstrate our approach on a significant NASA application, where design-level models were used to identify; and correct a safety property violation, and design-level assumptions allowed us to check successfully that the property was presented by the implementation.

  20. Geological structure analysis in Central Java using travel time tomography technique of S waves

    NASA Astrophysics Data System (ADS)

    Palupi, I. R.; Raharjo, W.; Nurdian, S. W.; Giamboro, W. S.; Santoso, A.

    2016-11-01

    Java is one of the islands in Indonesia that is prone to the earthquakes, in south of Java, there is the Australian Plate move to the Java island and press with perpendicular direction. This plate movement formed subduction zone and cause earthquakes. The earthquake is the release of energy due to the sudden movement of the plates. When an earthquake occurs, the energy is released and record by seismometers in the waveform. The first wave recorded is called the P waves (primary) and the next wave is called S waves (secondary). Both of these waves have different characteristics in terms of propagation and direction of movement. S wave is composed of waves of Rayleigh and Love waves, with each direction of movement of the vertical and horizontal, subsurface imaging by using S wave tomography technique can describe the type of the S wave through the medium. The variation of wave velocity under Central Java (esearch area) is ranging from -10% to 10% at the depth of 20, 30 and 40 km, the velocity decrease with the depth increase. Moho discontinuity is lies in the depth of 32 km under the crust, it is indicates there is strong heterogenity in Moho.