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.

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.

Distributed Planning in a Mixed-Initiative Environment

DTIC Science & Technology

2008-06-01

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

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.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

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.

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

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

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

The effect of green supply chain management implementation to marketing performance through company competitiveness (study on paper industry in West Java)

NASA Astrophysics Data System (ADS)

Hijuzaman, O.; Rahayu, A.; Kusnendi

2018-05-01

The purpose of this study was to determine and analyze the effect of direct and indirect implementation of Green Supply-Chain Management (GSCM) on the Performance Marketing and Competitiveness Mediation Paper Company in West Java province. Object This research is the paper company that existed in West Java Province, which amounts to 30 companies as well as a sample of research, while variables studied are Variable Green Supply- Chain Management, Company Competitiveness Variable and Variable of Paper Marketing Industry Performance in West Java Province. The method used SEM with Variance Based or Component Based with Software used is SmartPLS 3.0. On this research are identified that no effect of Competitiveness on Marketing Performance in Paper Companies in West Java Province.

3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.

A web-based 3D geological information visualization system

NASA Astrophysics Data System (ADS)

Song, Renbo; Jiang, Nan

2013-03-01

Construction of 3D geological visualization system has attracted much more concern in GIS, computer modeling, simulation and visualization fields. It not only can effectively help geological interpretation and analysis work, but also can it can help leveling up geosciences professional education. In this paper, an applet-based method was introduced for developing a web-based 3D geological information visualization system. The main aims of this paper are to explore a rapid and low-cost development method for constructing a web-based 3D geological system. First, the borehole data stored in Excel spreadsheets was extracted and then stored in SQLSERVER database of a web server. Second, the JDBC data access component was utilized for providing the capability of access the database. Third, the user interface was implemented with applet component embedded in JSP page and the 3D viewing and querying functions were implemented with PickCanvas of Java3D. Last, the borehole data acquired from geological survey were used for test the system, and the test results has shown that related methods of this paper have a certain application values.

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

Daniela Ushizima, Wes Bethel

Quant-CT is currently a plugin to ImageJ, designed as a Java-class that provides control mechanism for the user to choose volumes of interest within porous material, followed by the selection of image subsamples for automated tuning of parameters for filters and classifiers, and finally measurement of material geometry, porosity, and visualization. Denoising is mandatory before any image interpretation, and we implemented a new 3D java code that performs bilateral filtering of data. Segmentation of the dense material is essential before any quantifications about geological sample structure, and we invented new schemes to deal with over segmentation when using statistical regionmore » merging algorithm to pull out grains that compose imaged material. It make uses of ImageJ API and other standard and thirty-party APIs. Quant-CT conception started in 2011 under Scidac-e sponsor, and details of the first prototype were documented in publications below. While it is used right now for microtomography images, it can potentially be used by anybody with 3D image data obtained by experiment or produced by simulation.« less

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.

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.

[The dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modeling language (VRML)].

PubMed

Yu, Zhengyang; Zheng, Shusen; Chen, Huaiqing; Wang, Jianjun; Xiong, Qingwen; Jing, Wanjun; Zeng, Yu

2006-10-01

This research studies the process of dynamic concision and 3D reconstruction from medical body data using VRML and JavaScript language, focuses on how to realize the dynamic concision of 3D medical model built with VRML. The 2D medical digital images firstly are modified and manipulated by 2D image software. Then, based on these images, 3D mould is built with VRML and JavaScript language. After programming in JavaScript to control 3D model, the function of dynamic concision realized by Script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be formed in high quality near to those got in traditional methods. By this way, with the function of dynamic concision, VRML browser can offer better windows of man-computer interaction in real time environment than before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and has a promising prospect in the fields of medical image.

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.

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.

Visualization Development of the Ballistic Threat Geospatial Optimization

DTIC Science & Technology

2015-07-01

topographic globes, Keyhole Markup Language (KML), and Collada files. World Wind gives the user the ability to import 3-D models and navigate...present. After the first person view window is closed , the images stored in memory are then converted to a QuickTime movie (.MOV). The video will be...processing unit HPC high-performance computing JOGL Java implementation of OpenGL KML Keyhole Markup Language NASA National Aeronautics and Space

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.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-12-21

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-10-01

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies - Three.js, D3.js and PHP - as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

Large-Scale Dynamic Observation Planning for Unmanned Surface Vessels

DTIC Science & Technology

2007-06-01

programming language. In addition, the useful development software NetBeans IDE is free and makes the use of Java very user-friendly. 92...3. We implemented the greedy and 3PAA algorithms in Java using the NetBeans IDE version 5.5. 4. The test datasets were generated in MATLAB. 5

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

PubMed Central

Moore, Eider B; Poliakov, Andrew V; Lincoln, Peter; Brinkley, James F

2007-01-01

Background Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. Results We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: . Conclusion MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine. PMID:17937818

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.

PubMed

Moore, Eider B; Poliakov, Andrew V; Lincoln, Peter; Brinkley, James F

2007-10-15

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer. MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

Internet-based distributed collaborative environment for engineering education and design

NASA Astrophysics Data System (ADS)

Sun, Qiuli

2001-07-01

This research investigates the use of the Internet for engineering education, design, and analysis through the presentation of a Virtual City environment. The main focus of this research was to provide an infrastructure for engineering education, test the concept of distributed collaborative design and analysis, develop and implement the Virtual City environment, and assess the environment's effectiveness in the real world. A three-tier architecture was adopted in the development of the prototype, which contains an online database server, a Web server as well as multi-user servers, and client browsers. The environment is composed of five components, a 3D virtual world, multiple Internet-based multimedia modules, an online database, a collaborative geometric modeling module, and a collaborative analysis module. The environment was designed using multiple Intenet-based technologies, such as Shockwave, Java, Java 3D, VRML, Perl, ASP, SQL, and a database. These various technologies together formed the basis of the environment and were programmed to communicate smoothly with each other. Three assessments were conducted over a period of three semesters. The Virtual City is open to the public at www.vcity.ou.edu. The online database was designed to manage the changeable data related to the environment. The virtual world was used to implement 3D visualization and tie the multimedia modules together. Students are allowed to build segments of the 3D virtual world upon completion of appropriate undergraduate courses in civil engineering. The end result is a complete virtual world that contains designs from all of their coursework and is viewable on the Internet. The environment is a content-rich educational system, which can be used to teach multiple engineering topics with the help of 3D visualization, animations, and simulations. The concept of collaborative design and analysis using the Internet was investigated and implemented. Geographically dispersed users can build the same geometric model simultaneously over the Internet and communicate with each other through a chat room. They can also conduct finite element analysis collaboratively on the same object over the Internet. They can mesh the same object, apply and edit the same boundary conditions and forces, obtain the same analysis results, and then discuss the results through the Internet.

Bootstrapped Learning Analysis and Curriculum Development Environment (BLADE)

DTIC Science & Technology

2012-02-01

framework  Development of the automated teacher   The software development aspect of the BL program was conducted primarily in the Java programming...parameters are analogous to Java class data members or to fields in a C structure. Here is an example composite IL object from Blocks World, an...2 and 3, alternative methods of implementing generators were developed, first in Java , later in Ruby. Both of these alternatives lowered the

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

Shimoide, Alan; Lin, Luping; Hong, Tracie-Lynne; Yoon, Ilmi; Aragon, Sergio R.

2005-01-01

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

Shimoide, Alan; Lin, Luping; Hong, Tracie-Lynne; Yoon, Ilmi; Aragon, Sergio R.

2004-12-01

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

Molecular characterization of Salmonella Paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis

USDA-ARS?s Scientific Manuscript database

Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are human pathogens frequently isolated from poultry. As a step towards implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance (COIPARS), this study characterized molecular patt...

Spatial Modeling Tools for Cell Biology

DTIC Science & Technology

2006-10-01

multiphysics modeling expertise. A graphical user interface (GUI) for CoBi, JCoBi, was written in Java and interactive 3D graphics. CoBi has been...tools (C++ and Java ) to simulate complex cell and organ biology problems. CoBi has been designed to interact with the other Bio-SPICE software...fall of 2002. VisIt supports C++, Python and Java interfaces. The C++ and Java interfaces make it possible to provide alternate user interfaces for

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

PubMed

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

2010-08-15

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

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

Wu, C

Purpose: To implement a novel, automatic, institutional customizable DVH quantities evaluation and PDF report tool on Philips Pinnacle treatment planning system (TPS) Methods: An add-on program (P3DVHStats) is developed by us to enable automatic DVH quantities evaluation (including both volume and dose based quantities, such as V98, V100, D2), and automatic PDF format report generation, for EMR convenience. The implementation is based on a combination of Philips Pinnacle scripting tool and Java language pre-installed on each Pinnacle Sun Solaris workstation. A single Pinnacle script provide user a convenient access to the program when needed. The activated script will first exportmore » DVH data for user selected ROIs from current Pinnacle plan trial; a Java program then provides a simple GUI interface, utilizes the data to compute any user requested DVH quantities, compare with preset institutional DVH planning goals; if accepted by users, the program will also generate a PDF report of the results and export it from Pinnacle to EMR import folder via FTP. Results: The program was tested thoroughly and has been released for clinical use at our institution (Pinnacle Enterprise server with both thin clients and P3PC access), for all dosimetry and physics staff, with excellent feedback. It used to take a few minutes to use MS-Excel worksheet to calculate these DVH quantities for IMRT/VMAT plans, and manually save them as PDF report; with the new program, it literally takes a few mouse clicks in less than 30 seconds to complete the same tasks. Conclusion: A Pinnacle scripting and Java language based program is successfully implemented, customized to our institutional needs. It is shown to dramatically reduce time and effort needed for DVH quantities computing and EMR reporting.« less

A Sketching Interface for Freeform 3D Modeling

NASA Astrophysics Data System (ADS)

Igarashi, Takeo

This chapter introduces Teddy, a sketch-based modeling system to quickly and easily design freeform models such as stuffed animals and other rotund objects. The user draws several 2D freeform strokes interactively on the screen and the system automatically constructs plausible 3D polygonal surfaces. Our system supports several modeling operations, including the operation to construct a 3D polygonal surface from a 2D silhouette drawn by the user: it inflates the region surrounded by the silhouette making a wide area fat, and a narrow area thin. Teddy, our prototype system, is implemented as a Java program, and the mesh construction is done in real-time on a standard PC. Our informal user study showed that a first-time user masters the operations within 10 minutes, and can construct interesting 3D models within minutes. We also report the result of a case study where a high school teacher taught various 3D concepts in geography using the system.

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.

Interactive Visualization of National Airspace Data in 4D (IV4D)

DTIC Science & Technology

2010-08-01

Research Laboratory) JView graphics engine. All of the software, IV4D/Viewer/JView, is written in Java and is platform independent, meaning that it...both parts. 11 3.3.1.1 Airspace Volumes Once appropriate CSV or ACES XML airspace boundary files are selected from a standard Java File Chooser...persistence mechanism, Hibernate , was replaced with JDBC specific code and, over time, quite a bit of JDBC support code was added to the Viewer and to

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.

Factors to Consider When Implementing Automated Software Testing

DTIC Science & Technology

2016-11-10

programming, e.g., Java or Visual Basic.  Subject Matter Experts (SME) with firm grasp of application being automated. 2. Additional costs for setup (e.g...Abilities (KSA) required (e.g., Test and Evaluation). 2. Analyze programming skills needed (e.g., Java , C, C++, Visual Basic). 3. Compose team – testers

Plasma Interactions With Spacecraft (I)

DTIC Science & Technology

2009-04-01

with the Windows, Red hat LINUX, and MacOS X environments. We wrote N2kScriptRunner, a C++ code that runs a Nascap-2k script outside of the Java ...console-based and with a Java interface), a stand alone program that reads and writes Nascap-2k database files. This program has proved invaluable...surface currents for DSX and prototyped it in Java . A description of the algorithm and the prototype implementation is in Section 3. 1.5. DSX

Algorithms for Large-Scale Astronomical Problems

DTIC Science & Technology

2013-08-01

implemented as a succession of Hadoop MapReduce jobs and sequential programs written in Java . The sampling and splitting stages are implemented as...one MapReduce job, the partitioning and clustering phases make up another job. The merging stage is implemented as a stand-alone Java program. The...Merging. The merging stage is implemented as a sequential Java program that reads the files with the shell information, which were generated by

Direct volumetric rendering based on point primitives in OpenGL.

PubMed

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

2006-01-01

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

Performance analysis of algorithms for retrieval of magnetic resonance images for interactive teleradiology

NASA Astrophysics Data System (ADS)

Atkins, M. Stella; Hwang, Robert; Tang, Simon

2001-05-01

We have implemented a prototype system consisting of a Java- based image viewer and a web server extension component for transmitting Magnetic Resonance Images (MRI) to an image viewer, to test the performance of different image retrieval techniques. We used full-resolution images, and images compressed/decompressed using the Set Partitioning in Hierarchical Trees (SPIHT) image compression algorithm. We examined the SPIHT decompression algorithm using both non- progressive and progressive transmission, focusing on the running times of the algorithm, client memory usage and garbage collection. We also compared the Java implementation with a native C++ implementation of the non- progressive SPIHT decompression variant. Our performance measurements showed that for uncompressed image retrieval using a 10Mbps Ethernet, a film of 16 MR images can be retrieved and displayed almost within interactive times. The native C++ code implementation of the client-side decoder is twice as fast as the Java decoder. If the network bandwidth is low, the high communication time for retrieving uncompressed images may be reduced by use of SPIHT-compressed images, although the image quality is then degraded. To provide diagnostic quality images, we also investigated the retrieval of up to 3 images on a MR film at full-resolution, using progressive SPIHT decompression. The Java-based implementation of progressive decompression performed badly, mainly due to the memory requirements for maintaining the image states, and the high cost of execution of the Java garbage collector. Hence, in systems where the bandwidth is high, such as found in a hospital intranet, SPIHT image compression does not provide advantages for image retrieval performance.

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.

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

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

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

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

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

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

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).

Visualization of Documents and Concepts in Neuroinformatics with the 3D-SE Viewer

PubMed Central

Naud, Antoine; Usui, Shiro; Ueda, Naonori; Taniguchi, Tatsuki

2007-01-01

A new interactive visualization tool is proposed for mining text data from various fields of neuroscience. Applications to several text datasets are presented to demonstrate the capability of the proposed interactive tool to visualize complex relationships between pairs of lexical entities (with some semantic contents) such as terms, keywords, posters, or papers' abstracts. Implemented as a Java applet, this tool is based on the spherical embedding (SE) algorithm, which was designed for the visualization of bipartite graphs. Items such as words and documents are linked on the basis of occurrence relationships, which can be represented in a bipartite graph. These items are visualized by embedding the vertices of the bipartite graph on spheres in a three-dimensional (3-D) space. The main advantage of the proposed visualization tool is that 3-D layouts can convey more information than planar or linear displays of items or graphs. Different kinds of information extracted from texts, such as keywords, indexing terms, or topics are visualized, allowing interactive browsing of various fields of research featured by keywords, topics, or research teams. A typical use of the 3D-SE viewer is quick browsing of topics displayed on a sphere, then selecting one or several item(s) displays links to related terms on another sphere representing, e.g., documents or abstracts, and provides direct online access to the document source in a database, such as the Visiome Platform or the SfN Annual Meeting. Developed as a Java applet, it operates as a tool on top of existing resources. PMID:18974802

Visualization of Documents and Concepts in Neuroinformatics with the 3D-SE Viewer.

PubMed

Naud, Antoine; Usui, Shiro; Ueda, Naonori; Taniguchi, Tatsuki

2007-01-01

A new interactive visualization tool is proposed for mining text data from various fields of neuroscience. Applications to several text datasets are presented to demonstrate the capability of the proposed interactive tool to visualize complex relationships between pairs of lexical entities (with some semantic contents) such as terms, keywords, posters, or papers' abstracts. Implemented as a Java applet, this tool is based on the spherical embedding (SE) algorithm, which was designed for the visualization of bipartite graphs. Items such as words and documents are linked on the basis of occurrence relationships, which can be represented in a bipartite graph. These items are visualized by embedding the vertices of the bipartite graph on spheres in a three-dimensional (3-D) space. The main advantage of the proposed visualization tool is that 3-D layouts can convey more information than planar or linear displays of items or graphs. Different kinds of information extracted from texts, such as keywords, indexing terms, or topics are visualized, allowing interactive browsing of various fields of research featured by keywords, topics, or research teams. A typical use of the 3D-SE viewer is quick browsing of topics displayed on a sphere, then selecting one or several item(s) displays links to related terms on another sphere representing, e.g., documents or abstracts, and provides direct online access to the document source in a database, such as the Visiome Platform or the SfN Annual Meeting. Developed as a Java applet, it operates as a tool on top of existing resources.

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.

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…

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.

XMM-Newton Mobile Web Application

NASA Astrophysics Data System (ADS)

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

2013-10-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

FlaME: Flash Molecular Editor - a 2D structure input tool for the web

PubMed Central

2011-01-01

Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions. PMID:21284863

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

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

NASA Technical Reports Server (NTRS)

Sabey, Nickolas J.

2014-01-01

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

Digitizing Consumption Across the Operational Spectrum

DTIC Science & Technology

2014-09-01

Figure 14.  Java -implemented Dictionary and Query: Result ............................................22  Figure 15.  Global Database Architecture...format. Figure 14 is an illustration of the query submitted in Java and the result which would be shown using the data shown in Figure 13. Figure...13. NoSQL (key, value) Dictionary Example 22 Figure 14. Java -implemented Dictionary and Query: Result While a

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

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

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

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

Design and Implementation of a Three-Tiered Web-Based Inventory Ordering and Tracking System Prototype Using CORBA and Java

DTIC Science & Technology

2000-03-01

languages yet still be able to access the legacy relational databases that businesses have huge investments in. JDBC is a low-level API designed for...consider the return of investment . The system requirements, discussed in Chapter II, are the main source of input to developing the relational...1996. Inprise, Gatekeeper Guide, Inprise Corporation, 1999. Kroenke, D., Database Processing Fundementals , Design, and Implementation, Sixth Edition

QSPIN: A High Level Java API for Quantum Computing Experimentation

NASA Technical Reports Server (NTRS)

Barth, Tim

2017-01-01

QSPIN is a high level Java language API for experimentation in QC models used in the calculation of Ising spin glass ground states and related quadratic unconstrained binary optimization (QUBO) problems. The Java API is intended to facilitate research in advanced QC algorithms such as hybrid quantum-classical solvers, automatic selection of constraint and optimization parameters, and techniques for the correction and mitigation of model and solution errors. QSPIN includes high level solver objects tailored to the D-Wave quantum annealing architecture that implement hybrid quantum-classical algorithms [Booth et al.] for solving large problems on small quantum devices, elimination of variables via roof duality, and classical computing optimization methods such as GPU accelerated simulated annealing and tabu search for comparison. A test suite of documented NP-complete applications ranging from graph coloring, covering, and partitioning to integer programming and scheduling are provided to demonstrate current capabilities.

TeCo3D: a 3D telecooperation application based on VRML and Java

NASA Astrophysics Data System (ADS)

Mauve, Martin

1998-12-01

In this paper we present a method for sharing collaboration- unaware VRML content, e.g. 3D models which were not specifically developed for use in a distributed environment. This functionality is an essential requirement for the inclusion of arbitrary VRML content, as generated by standard CAD or animation software, into teleconferencing sessions. We have developed a 3D TeleCooperation (TeCo3D) prototype to demonstrate the feasibility of our approach. The basic services provided by the prototype are the distribution of cooperation unaware VRML content, the sharing of user interactions, and the joint viewing of the content. In order to achieve maximum portability, the prototype was developed completely in Java. This paper presents general aspects of sharing VRML content as well as the concepts, the architecture and the services of the TeCo3D prototype. Our approach relies on existing VRML browsers as the VRML presentation and execution engines while reliable multicast is used as the means of communication to provide for scalability.

Effectiveness of Ministry of Internal Affairs Regulation Number 15 Year 2008 about Mainstreaming Gender on Basic Education Level in the East Java, Indonesia

ERIC Educational Resources Information Center

Handayani, Trisakti; Widodo, Wahyu

2016-01-01

General purpose of this research are: assessing the implementation of Permendagri no. 15 year 2008 about Gender Mainstreaming on Basic Education Levels in the East Java Province, analyze the problem of the implementation of Permendagri no. 15 year 2008 about Gender Mainstreaming on Basic Education Levels in the East Java Province and analyze the…

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…

Science Opportunity Analyzer (SOA): Science Planning Made Simple

NASA Technical Reports Server (NTRS)

Streiffert, Barbara A.; Polanskey, Carol A.

2004-01-01

.For the first time at JPL, the Cassini mission to Saturn is using distributed science operations for developing their experiments. Remote scientists needed the ability to: a) Identify observation opportunities; b) Create accurate, detailed designs for their observations; c) Verify that their designs meet their objectives; d) Check their observations against project flight rules and constraints; e) Communicate their observations to other scientists. Many existing tools provide one or more of these functions, but Science Opportunity Analyzer (SOA) has been built to unify these tasks into a single application. Accurate: Utilizes JPL Navigation and Ancillary Information Facility (NAIF) SPICE* software tool kit - Provides high fidelity modeling. - Facilitates rapid adaptation to other flight projects. Portable: Available in Unix, Windows and Linux. Adaptable: Designed to be a multi-mission tool so it can be readily adapted to other flight projects. Implemented in Java, Java 3D and other innovative technologies. Conclusion: SOA is easy to use. It only requires 6 simple steps. SOA's ability to show the same accurate information in multiple ways (multiple visualization formats, data plots, listings and file output) is essential to meet the needs of a diverse, distributed science operations environment.

Debris Dispersion Model Using Java 3D

NASA Technical Reports Server (NTRS)

Thirumalainambi, Rajkumar; Bardina, Jorge

2004-01-01

This paper describes web based simulation of Shuttle launch operations and debris dispersion. Java 3D graphics provides geometric and visual content with suitable mathematical model and behaviors of Shuttle launch. Because the model is so heterogeneous and interrelated with various factors, 3D graphics combined with physical models provides mechanisms to understand the complexity of launch and range operations. The main focus in the modeling and simulation covers orbital dynamics and range safety. Range safety areas include destruct limit lines, telemetry and tracking and population risk near range. If there is an explosion of Shuttle during launch, debris dispersion is explained. The shuttle launch and range operations in this paper are discussed based on the operations from Kennedy Space Center, Florida, USA.

DSSR-enhanced visualization of nucleic acid structures in Jmol.

PubMed

Hanson, Robert M; Lu, Xiang-Jun

2017-07-03

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A web-based instruction module for interpretation of craniofacial cone beam CT anatomy.

PubMed

Hassan, B A; Jacobs, R; Scarfe, W C; Al-Rawi, W T

2007-09-01

To develop a web-based module for learner instruction in the interpretation and recognition of osseous anatomy on craniofacial cone-beam CT (CBCT) images. Volumetric datasets from three CBCT systems were acquired (i-CAT, NewTom 3G and AccuiTomo FPD) for various subjects using equipment-specific scanning protocols. The datasets were processed using multiple software to provide two-dimensional (2D) multiplanar reformatted (MPR) images (e.g. sagittal, coronal and axial) and three-dimensional (3D) visual representations (e.g. maximum intensity projection, minimum intensity projection, ray sum, surface and volume rendering). Distinct didactic modules which illustrate the principles of CBCT systems, guided navigation of the volumetric dataset, and anatomic correlation of 3D models and 2D MPR graphics were developed using a hybrid combination of web authoring and image analysis techniques. Interactive web multimedia instruction was facilitated by the use of dynamic highlighting and labelling, and rendered video illustrations, supplemented with didactic textual material. HTML coding and Java scripting were heavily implemented for the blending of the educational modules. An interactive, multimedia educational tool for visualizing the morphology and interrelationships of osseous craniofacial anatomy, as depicted on CBCT MPR and 3D images, was designed and implemented. The present design of a web-based instruction module may assist radiologists and clinicians in learning how to recognize and interpret the craniofacial anatomy of CBCT based images more efficiently.

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

PubMed

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

2014-01-01

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

The ENSDF Java Package

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

Sonzogni, A.A.

2005-05-24

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

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.

Development of a 3D WebGIS System for Retrieving and Visualizing CityGML Data Based on their Geometric and Semantic Characteristics by Using Free and Open Source Technology

NASA Astrophysics Data System (ADS)

Pispidikis, I.; Dimopoulou, E.

2016-10-01

CityGML is considered as an optimal standard for representing 3D city models. However, international experience has shown that visualization of the latter is quite difficult to be implemented on the web, due to the large size of data and the complexity of CityGML. As a result, in the context of this paper, a 3D WebGIS application is developed in order to successfully retrieve and visualize CityGML data in accordance with their respective geometric and semantic characteristics. Furthermore, the available web technologies and the architecture of WebGIS systems are investigated, as provided by international experience, in order to be utilized in the most appropriate way for the purposes of this paper. Specifically, a PostgreSQL/ PostGIS Database is used, in compliance with the 3DCityDB schema. At Server tier, Apache HTTP Server and GeoServer are utilized, while a Server Side programming language PHP is used. At Client tier, which implemented the interface of the application, the following technologies were used: JQuery, AJAX, JavaScript, HTML5, WebGL and Ol3-Cesium. Finally, it is worth mentioning that the application's primary objectives are a user-friendly interface and a fully open source development.

Portable parallel portfolio optimization in the Aurora Financial Management System

NASA Astrophysics Data System (ADS)

Laure, Erwin; Moritsch, Hans

2001-07-01

Financial planning problems are formulated as large scale, stochastic, multiperiod, tree structured optimization problems. An efficient technique for solving this kind of problems is the nested Benders decomposition method. In this paper we present a parallel, portable, asynchronous implementation of this technique. To achieve our portability goals we elected the programming language Java for our implementation and used a high level Java based framework, called OpusJava, for expressing the parallelism potential as well as synchronization constraints. Our implementation is embedded within a modular decision support tool for portfolio and asset liability management, the Aurora Financial Management System.

GeoBuilder: a geometric algorithm visualization and debugging system for 2D and 3D geometric computing.

PubMed

Wei, Jyh-Da; Tsai, Ming-Hung; Lee, Gen-Cher; Huang, Jeng-Hung; Lee, Der-Tsai

2009-01-01

Algorithm visualization is a unique research topic that integrates engineering skills such as computer graphics, system programming, database management, computer networks, etc., to facilitate algorithmic researchers in testing their ideas, demonstrating new findings, and teaching algorithm design in the classroom. Within the broad applications of algorithm visualization, there still remain performance issues that deserve further research, e.g., system portability, collaboration capability, and animation effect in 3D environments. Using modern technologies of Java programming, we develop an algorithm visualization and debugging system, dubbed GeoBuilder, for geometric computing. The GeoBuilder system features Java's promising portability, engagement of collaboration in algorithm development, and automatic camera positioning for tracking 3D geometric objects. In this paper, we describe the design of the GeoBuilder system and demonstrate its applications.

Next Generation Transport Phenomenology Model

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

An Interface Transformation Strategy for AF-IPPS

DTIC Science & Technology

2012-12-01

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

The D3 Middleware Architecture

NASA Technical Reports Server (NTRS)

Walton, Joan; Filman, Robert E.; Korsmeyer, David J.; Lee, Diana D.; Mak, Ron; Patel, Tarang

2002-01-01

DARWIN is a NASA developed, Internet-based system for enabling aerospace researchers to securely and remotely access and collaborate on the analysis of aerospace vehicle design data, primarily the results of wind-tunnel testing and numeric (e.g., computational fluid-dynamics) model executions. DARWIN captures, stores and indexes data; manages derived knowledge (such as visualizations across multiple datasets); and provides an environment for designers to collaborate in the analysis of test results. DARWIN is an interesting application because it supports high-volumes of data. integrates multiple modalities of data display (e.g., images and data visualizations), and provides non-trivial access control mechanisms. DARWIN enables collaboration by allowing not only sharing visualizations of data, but also commentary about and views of data. Here we provide an overview of the architecture of D3, the third generation of DARWIN. Earlier versions of DARWIN were characterized by browser-based interfaces and a hodge-podge of server technologies: CGI scripts, applets, PERL, and so forth. But browsers proved difficult to control, and a proliferation of computational mechanisms proved inefficient and difficult to maintain. D3 substitutes a pure-Java approach for that medley: A Java client communicates (though RMI over HTTPS) with a Java-based application server. Code on the server accesses information from JDBC databases, distributed LDAP security services, and a collaborative information system. D3 is a three tier-architecture, but unlike 'E-commerce' applications, the data usage pattern suggests different strategies than traditional Enterprise Java Beans - we need to move volumes of related data together, considerable processing happens on the client, and the 'business logic' on the server-side is primarily data integration and collaboration. With D3, we are extending DARWIN to handle other data domains and to be a distributed system, where a single login allows a user transparent access to test results from multiple servers and authority domains.

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.

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

DTIC Science & Technology

2007-12-01

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

Component Composition for Embedded Systems Using Semantic Aspect-Oriented Programming

DTIC Science & Technology

2004-10-01

real - time systems for the defense community. Our research focused on Real-Time Java implementation and analysis techniques. Real-Time Java is important for the defense community because it holds out the promise of enabling developers to apply COTS Java technology to specialized military embedded systems. It also promises to allow the defense community to utilize a large Java-literate workforce for building defense systems. Our research has delivered several techniques that may make Real-Time Java a better platform for developing embedded

Using a Java Web-based Graphical User Interface to access the SOHO Data Arch ive

NASA Astrophysics Data System (ADS)

Scholl, I.; Girard, Y.; Bykowski, A.

This paper presents the architecture of a Java web-based graphical interface dedicated to the access of the SOHO Data archive. This application allows local and remote users to search in the SOHO data catalog and retrieve the SOHO data files from the archive. It has been developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France), which is one of the European Archives for the SOHO data. This development is part of a joint effort between ESA, NASA and IAS in order to implement long term archive systems for the SOHO data. The software architecture is built as a client-server application using Java language and SQL above a set of components such as an HTTP server, a JDBC gateway, a RDBMS server, a data server and a Web browser. Since HTML pages and CGI scripts are not powerful enough to allow user interaction during a multi-instrument catalog search, this type of requirement enforces the choice of Java as the main language. We also discuss performance issues, security problems and portability on different Web browsers and operating syste ms.

Telescope Automation and Remote Observing System (TAROS)

NASA Astrophysics Data System (ADS)

Wilson, G.; Czezowski, A.; Hovey, G. R.; Jarnyk, M. A.; Nielsen, J.; Roberts, B.; Sebo, K.; Smith, D.; Vaccarella, A.; Young, P.

2005-12-01

TAROS is a system that will allow for the Australian National University telescopes at a remote location to be operated automatically or interactively with authenticated control via the internet. TAROS is operated by a Java front-end GUI and employs the use of several Java technologies - such as Java Message Service (JMS) for communication between the telescope and the remote observer, Java Native Interface to integrate existing data acquisition software written in C++ (CICADA) with new Java programs and the JSky collection of Java GUI components for parts of the remote observer client. In this poster the design and implementation of TAROS is described.

CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules.

PubMed

Aguirre-Valderrama, Alonso; Dobado, José A

2008-12-01

Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.

Distributed Planning in a Mixed-Initiative Environment: Collaborative Technologies for Network Centric Operations

DTIC Science & Technology

2008-10-01

Agents in the DEEP architecture extend and use the Java Agent Development (JADE) framework. DEEP requires a distributed multi-agent system and a...framework to help simplify the implementation of this system. JADE was chosen because it is fully implemented in Java , and supports these requirements

Summary of Synoptic Meteorological Observations. Indonesian Coastal Marine Areas. Volume 2. Area 8 - West Borneo, Area 9 - Karimata Strait, Area 10 - Southwest Java Sea, Area 11 - South Central Java, Area 12 - Southeast Java, Area 13 - Southeast Java Sea, Area 14 - Northeast Java Sea

DTIC Science & Technology

1975-04-01

5 ’ :00 0 1’.20 2. 219 39 : .:0 :00 .0 A.. AP99 120 , ~ ~ ~ ~ ~ -y- ,M -.7yT ,, T , . , .,77M III II P~ kID : (¢E(’Ll) 9•3-977AREA 0009 KARIMATA STRAIT...TYPE OTHER WEATHER PHENOMENA kNO 01D RAIN PAIN VAIL RAIG SNOW OTHER HAI. PORN AT PCPN PAST ?HOR FOG FOG WO SMOKE SPRAY NO SHoR PON FRZN 06 TIME HOUR LTNG...NAONO DIR RAIN RAIN ORIL RCZG SNOW OTHER HAIL PCORN A? FCN PAST THOR OTOH HAZE SPRy NOUST SI ? R G PUG W SMOK SPRAY No PHft PCN PRN OPTM OR LTNG Wa PORN

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

Shallow Depth Study Using Gravity & Magnetics Data in Central Java - Yogyakarta

NASA Astrophysics Data System (ADS)

Fawzy Ismullah M, Muhammad; Altin Massinai, Muhammad; Maria

2018-03-01

Gravity and magnetics measurements carried out in Karangsambung - Bayat - Wonosari track, Central Java - Yogyakarta region as much as 34 points for subsurface identification. Modeling and interpretation using both data at 3 sections. Section A lies on Karangsambung area and reach to 1900 m. Section A showed formation of 0.000001 - 0.0014 nT and 2.00 - 2.80 g/cm3 like alluvium, basalt and tuff. Section B lies on Wates - Yogyakarta area and reach to 1700 m. Section B showed formation of (-0.01) - 0.02 nT and 2.40 - 3.00 g/cm3 like andesite intrusive and Merapi volcano sediments. Section C lies on Bayat - Wonosari area and reach to 2000 m. Section C showed formation of 0.00016 - 0.0005 nT and 2.30 - 3.14 g/cm3 like limestone, tuff and diorite intrusive. Based on modeling results from 2D structure inversion method can identify the formation of sediments from volcano activity on Karangsambung - Bayat - Wonosari track, Central Java - Yogyakarta region. The method of this study shows potential application for identify the formation of volcano activity from 2D structure.

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.

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 ability to associate services with actions. Several Java technologies have been incorporated into JAS, including Swing, Internal Frames, Java Beans, XML, JavaScript, JavaHelp, and Jini. Additional information is contained in the original extended abstract.

Generating Animated Displays of Spacecraft Orbits

NASA Technical Reports Server (NTRS)

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

2005-01-01

Tool for Interactive Plotting, Sonification, and 3D Orbit Display (TIPSOD) is a computer program for generating interactive, animated, four-dimensional (space and time) displays of spacecraft orbits. TIPSOD utilizes the programming interface of the Satellite Situation Center Web (SSCWeb) services to communicate with the SSC logic and database by use of the open protocols of the Internet. TIPSOD is implemented in Java 3D and effects an extension of the preexisting SSCWeb two-dimensional static graphical displays of orbits. Orbits can be displayed in any or all of the following seven reference systems: true-of-date (an inertial system), J2000 (another inertial system), geographic, geomagnetic, geocentric solar ecliptic, geocentric solar magnetospheric, and solar magnetic. In addition to orbits, TIPSOD computes and displays Sibeck's magnetopause and Fairfield's bow-shock surfaces. TIPSOD can be used by the scientific community as a means of projection or interpretation. It also has potential as an educational tool.

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

Web Based Nasal Surgical Simulator Using VRML and Java.

PubMed

Yuan-Yuan, Zhao; Guo-Hong, Zhou; De-Rong, Ye

2005-01-01

This paper describes a nasal surgical simulator that we have designed and implemented to run on the WWW using VRML and Java. In this paper we concentrate on implementation details such as collision detection and the usage of our simulator. At last, we discuss the advantage and disadvantave of the simulator.

CPU Performance Counter-Based Problem Diagnosis for Software Systems

DTIC Science & Technology

2009-09-01

application servers and implementation techniques), this thesis only used the Enterprise Java Bean (EJB) SessionBean version of RUBiS. The PHP and Servlet ...collection statistics at the Java Virtual Machine (JVM) level can be reused for any Java application. Other examples of gray-box instrumentation include path...used gray-box approaches. For example, PinPoint [11, 14] and [29] use request tracing to diagnose Java exceptions, endless calls, and null calls in

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…

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.

Sockeye: A 3D Environment for Comparative Genomics

PubMed Central

Montgomery, Stephen B.; Astakhova, Tamara; Bilenky, Mikhail; Birney, Ewan; Fu, Tony; Hassel, Maik; Melsopp, Craig; Rak, Marcin; Robertson, A. Gordon; Sleumer, Monica; Siddiqui, Asim S.; Jones, Steven J.M.

2004-01-01

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization. PMID:15123592

Virtual reality on the web: the potentials of different methodologies and visualization techniques for scientific research and medical education.

PubMed

Kling-Petersen, T; Pascher, R; Rydmark, M

1999-01-01

Academic and medical imaging are increasingly using computer based 3D reconstruction and/or visualization. Three-dimensional interactive models play a major role in areas such as preclinical medical education, clinical visualization and medical research. While 3D is comparably easy to do on a high end workstations, distribution and use of interactive 3D graphics necessitate the use of personal computers and the web. Several new techniques have been demonstrated providing interactive 3D via a web browser thereby allowing a limited version of VR to be experienced by a larger majority of students, medical practitioners and researchers. These techniques include QuickTimeVR2 (QTVR), VRML2, QuickDraw3D, OpenGL and Java3D. In order to test the usability of the different techniques, Mednet have initiated a number of projects designed to evaluate the potentials of 3D techniques for scientific reporting, clinical visualization and medical education. These include datasets created by manual tracing followed by triangulation, smoothing and 3D visualization, MRI or high-resolution laserscanning. Preliminary results indicate that both VRML and QTVR fulfills most of the requirements of web based, interactive 3D visualization, whereas QuickDraw3D is too limited. Presently, the JAVA 3D has not yet reached a level where in depth testing is possible. The use of high-resolution laserscanning is an important addition to 3D digitization.

PSPVDC: An Adaptation of the PSP that Incorporates Verified Design by Contract

DTIC Science & Technology

2013-05-01

characteristics mentioned above, including the following: • Java Modeling Language (JML) implements DbC in Java . VDbC can then be carried out using tools like...Extended Static Checking (ESC/ Java ) [Cok 2005] or TACO [Galeotti 2010]. • Perfect Developer [Crocker 2003] is a specification and modeling language...These are written in the language employed in the environment (e.g., as Java Boolean expressions, if JML is used) which we call the carrier lan

Towards Formalizing the Java Security Architecture of JDK 1.2

DTIC Science & Technology

1998-01-01

and Richard E. Newman for their contributions to this paper. References 1. Balfanz , D. and Gong, L.: Experience with Secure Multi-Processing in Java...Privacy, IEEE Computer Society, Oakland, California, Pages 122-136, 1992. 18. Wallach, D. S., Balfanz , D., Dean, D., and Felton, E. W.: Extensible

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.

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

PubMed Central

2014-01-01

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

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…

Advances in the spatially distributed ages-w model: parallel computation, java connection framework (JCF) integration, and streamflow/nitrogen dynamics assessment

USDA-ARS?s Scientific Manuscript database

AgroEcoSystem-Watershed (AgES-W) is a modular, Java-based spatially distributed model which implements hydrologic and water quality (H/WQ) simulation components under the Java Connection Framework (JCF) and the Object Modeling System (OMS) environmental modeling framework. AgES-W is implicitly scala...

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

Gosling, James

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 designmore » 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.« less

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

Ballard, Sanford; Hipp, James; Kraus, Brian

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

Implementation of partnership management model of SMK (Vocational High School) with existing industries in mechanical engineering expertise in Central Java

NASA Astrophysics Data System (ADS)

Sumbodo, Wirawan; Pardjono, Samsudi, Rahadjo, Winarno Dwi

2018-03-01

This study aims to determine the existing conditions of implementation of partnership management model of SMK with the industry on the mechanical engineering expertise in Central Java. The method used is descriptive analysis. The research result shows that the implementation of partnership management model of SMK based on new existing industry produces ready graduates of 62.5% which belongs to low category, although the partnership program of SMK with the industry is done well with the average score of 3.17. As many as 37.5% of SMK graduates of Mechanical Engineering Expertise Program choose to continue their studies or to be an entrepreneur. It is expected that the partnership model of SMK with the industry can be developed into a reference for government policy in developing SMK that is able to produce graduates who are ready to work according to the needs of partner industry.

3D Visualisation and Artistic Imagery to Enhance Interest in "Hidden Environments"--New Approaches to Soil Science

ERIC Educational Resources Information Center

Gilford, J.; Falconer, R. E.; Wade, R.; Scott-Brown, K. C.

2014-01-01

Interactive Virtual Environments (VEs) have the potential to increase student interest in soil science. Accordingly a bespoke "soil atlas" was created using Java3D as an interactive 3D VE, to show soil information in the context of (and as affected by) the over-lying landscape. To display the below-ground soil characteristics, four sets…

Mass Estimation and Its Applications

DTIC Science & Technology

2012-02-23

parameters); e.g., the rect- angular kernel function has fixed width or fixed per unit size. But the rectangular function used in mass has no parameter...MassTER is implemented in JAVA , and we use DBSCAN in WEKA [13] and a version of DENCLUE implemented in R (www.r-project.org) in our empirical evaluation...Proceedings of SIGKDD, 2010, 989-998. [13] I.H. Witten and E. Frank, Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations

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.

Client-Server Connection Status Monitoring Using Ajax Push Technology

NASA Technical Reports Server (NTRS)

Lamongie, Julien R.

2008-01-01

This paper describes how simple client-server connection status monitoring can be implemented using Ajax (Asynchronous JavaScript and XML), JSF (Java Server Faces) and ICEfaces technologies. This functionality is required for NASA LCS (Launch Control System) displays used in the firing room for the Constellation project. Two separate implementations based on two distinct approaches are detailed and analyzed.

Teachers' Experience in Implementing Cooperative Learning in the Classrooms (Phenomenological Research at Junior High School Classrooms in Ponorogo, East Java, Indonesia)

ERIC Educational Resources Information Center

Harjali

2017-01-01

This study aimed to investigate the teachers' perception toward the implementation of cooperative learning in the classroom. The research applied a qualitative phenomenological design that used a purposeful sample of six teachers at Junior High School Classrooms in Ponorogo, East Java, Indonesia. Data collected via in-depth interviews, participant…

Device-Enabled Authorization in the Grey System

DTIC Science & Technology

2005-02-01

proof checker. Journal of Automated Reasoning 31(3-4):231–260, 2003. [7] D. Balfanz , D. Dean, and M. Spreitzer. A security infrastructure for...distributed Java applications. In Proceedings of the 21st IEEE Symposium on Security and Privacy, May 2002. [8] D. Balfanz and E. Felten. Hand-held computers

Anatomy of the western Java plate interface from depth-migrated seismic images

NASA Astrophysics Data System (ADS)

Kopp, H.; Hindle, D.; Klaeschen, D.; Oncken, O.; Reichert, C.; Scholl, D.

2009-11-01

Newly pre-stack depth-migrated seismic images resolve the structural details of the western Java forearc and plate interface. The structural segmentation of the forearc into discrete mechanical domains correlates with distinct deformation styles. Approximately 2/3 of the trench sediment fill is detached and incorporated into frontal prism imbricates, while the floor sequence is underthrust beneath the décollement. Western Java, however, differs markedly from margins such as Nankai or Barbados, where a uniform, continuous décollement reflector has been imaged. In our study area, the plate interface reveals a spatially irregular, nonlinear pattern characterized by the morphological relief of subducted seamounts and thicker than average patches of underthrust sediment. The underthrust sediment is associated with a low velocity zone as determined from wide-angle data. Active underplating is not resolved, but likely contributes to the uplift of the large bivergent wedge that constitutes the forearc high. Our profile is located 100 km west of the 2006 Java tsunami earthquake. The heterogeneous décollement zone regulates the friction behavior of the shallow subduction environment where the earthquake occurred. The alternating pattern of enhanced frictional contact zones associated with oceanic basement relief and weak material patches of underthrust sediment influences seismic coupling and possibly contributed to the heterogeneous slip distribution. Our seismic images resolve a steeply dipping splay fault, which originates at the décollement and terminates at the sea floor and which potentially contributes to tsunami generation during co-seismic activity.

Anatomy of the western Java plate interface from depth-migrated seismic images

USGS Publications Warehouse

Kopp, H.; Hindle, D.; Klaeschen, D.; Oncken, O.; Reichert, C.; Scholl, D.

2009-01-01

Newly pre-stack depth-migrated seismic images resolve the structural details of the western Java forearc and plate interface. The structural segmentation of the forearc into discrete mechanical domains correlates with distinct deformation styles. Approximately 2/3 of the trench sediment fill is detached and incorporated into frontal prism imbricates, while the floor sequence is underthrust beneath the d??collement. Western Java, however, differs markedly from margins such as Nankai or Barbados, where a uniform, continuous d??collement reflector has been imaged. In our study area, the plate interface reveals a spatially irregular, nonlinear pattern characterized by the morphological relief of subducted seamounts and thicker than average patches of underthrust sediment. The underthrust sediment is associated with a low velocity zone as determined from wide-angle data. Active underplating is not resolved, but likely contributes to the uplift of the large bivergent wedge that constitutes the forearc high. Our profile is located 100 km west of the 2006 Java tsunami earthquake. The heterogeneous d??collement zone regulates the friction behavior of the shallow subduction environment where the earthquake occurred. The alternating pattern of enhanced frictional contact zones associated with oceanic basement relief and weak material patches of underthrust sediment influences seismic coupling and possibly contributed to the heterogeneous slip distribution. Our seismic images resolve a steeply dipping splay fault, which originates at the d??collement and terminates at the sea floor and which potentially contributes to tsunami generation during co-seismic activity. ?? 2009 Elsevier B.V.

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.

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).

PubMed

Beaver, John E; Bourne, Philip E; Ponomarenko, Julia V

2007-02-21

Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools. The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site http://www.immuneepitope.org through the quick link 'Browse Records by 3D Structure.' The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required.

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

PubMed

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

2017-11-06

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

An Object-Oriented View of Backend Databases in a Mobile Environment for Navy and Marine Corps Applications

DTIC Science & Technology

2006-09-01

Each of these layers will be described in more detail to include relevant technologies ( Java , PDA, Hibernate , and PostgreSQL) used to implement...Logic Layer -Object-Relational Mapper ( Hibernate ) Data 35 capable in order to interface with Java applications. Based on meeting the selection...further discussed. Query List Application Logic Layer HibernateApache - Java Servlet - Hibernate Interface -OR Mapper -RDBMS Interface

Benchmark Intelligent Agent Systems for Distributed Battle Tracking

DTIC Science & Technology

2008-06-20

services in the military and other domains, each entity in the benchmark system exposes a standard set of Web services. Jess ( Java Expert Shell...System) is a rule engine for the Java platform and is an interpreter for the Jess rule language. It is used here to implement policies that maintain...battle tracking system (DBTS), maintaining distributed situation awareness. The Java Agent DEvelopment (JADE) framework is a software framework

Improving energy efficiency in handheld biometric applications

NASA Astrophysics Data System (ADS)

Hoyle, David C.; Gale, John W.; Schultz, Robert C.; Rakvic, Ryan N.; Ives, Robert W.

2012-06-01

With improved smartphone and tablet technology, it is becoming increasingly feasible to implement powerful biometric recognition algorithms on portable devices. Typical iris recognition algorithms, such as Ridge Energy Direction (RED), utilize two-dimensional convolution in their implementation. This paper explores the energy consumption implications of 12 different methods of implementing two-dimensional convolution on a portable device. Typically, convolution is implemented using floating point operations. If a given algorithm implemented integer convolution vice floating point convolution, it could drastically reduce the energy consumed by the processor. The 12 methods compared include 4 major categories: Integer C, Integer Java, Floating Point C, and Floating Point Java. Each major category is further divided into 3 implementations: variable size looped convolution, static size looped convolution, and unrolled looped convolution. All testing was performed using the HTC Thunderbolt with energy measured directly using a Tektronix TDS5104B Digital Phosphor oscilloscope. Results indicate that energy savings as high as 75% are possible by using Integer C versus Floating Point C. Considering the relative proportion of processing time that convolution is responsible for in a typical algorithm, the savings in energy would likely result in significantly greater time between battery charges.

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

Cognitive/emotional models for human behavior representation in 3D avatar simulations

NASA Astrophysics Data System (ADS)

Peterson, James K.

2004-08-01

Simplified models of human cognition and emotional response are presented which are based on models of auditory/ visual polymodal fusion. At the core of these models is a computational model of Area 37 of the temporal cortex which is based on new isocortex models presented recently by Grossberg. These models are trained using carefully chosen auditory (musical sequences), visual (paintings) and higher level abstract (meta level) data obtained from studies of how optimization strategies are chosen in response to outside managerial inputs. The software modules developed are then used as inputs to character generation codes in standard 3D virtual world simulations. The auditory and visual training data also enable the development of simple music and painting composition generators which significantly enhance one's ability to validate the cognitive model. The cognitive models are handled as interacting software agents implemented as CORBA objects to allow the use of multiple language coding choices (C++, Java, Python etc) and efficient use of legacy code.

Comparative case study between D3 and highcharts on lustre data visualization

NASA Astrophysics Data System (ADS)

ElTayeby, Omar; John, Dwayne; Patel, Pragnesh; Simmerman, Scott

2013-12-01

One of the challenging tasks in visual analytics is to target clustered time-series data sets, since it is important for data analysts to discover patterns changing over time while keeping their focus on particular subsets. In order to leverage the humans ability to quickly visually perceive these patterns, multivariate features should be implemented according to the attributes available. However, a comparative case study has been done using JavaScript libraries to demonstrate the differences in capabilities of using them. A web-based application to monitor the Lustre file system for the systems administrators and the operation teams has been developed using D3 and Highcharts. Lustre file systems are responsible of managing Remote Procedure Calls (RPCs) which include input output (I/O) requests between clients and Object Storage Targets (OSTs). The objective of this application is to provide time-series visuals of these calls and storage patterns of users on Kraken, a University of Tennessee High Performance Computing (HPC) resource in Oak Ridge National Laboratory (ORNL).

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

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

GeoTess: A generalized Earth model software utility

DOE PAGES

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

2016-03-23

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

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.

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).

User interface using a 3D model for video surveillance

NASA Astrophysics Data System (ADS)

Hata, Toshihiko; Boh, Satoru; Tsukada, Akihiro; Ozaki, Minoru

1998-02-01

These days fewer people, who must carry out their tasks quickly and precisely, are required in industrial surveillance and monitoring applications such as plant control or building security. Utilizing multimedia technology is a good approach to meet this need, and we previously developed Media Controller, which is designed for the applications and provides realtime recording and retrieval of digital video data in a distributed environment. In this paper, we propose a user interface for such a distributed video surveillance system in which 3D models of buildings and facilities are connected to the surveillance video. A novel method of synchronizing camera field data with each frame of a video stream is considered. This method records and reads the camera field data similarity to the video data and transmits it synchronously with the video stream. This enables the user interface to have such useful functions as comprehending the camera field immediately and providing clues when visibility is poor, for not only live video but also playback video. We have also implemented and evaluated the display function which makes surveillance video and 3D model work together using Media Controller with Java and Virtual Reality Modeling Language employed for multi-purpose and intranet use of 3D model.

ReSEARCH: A Requirements Search Engine: Progress Report 2

DTIC Science & Technology

2008-09-01

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

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

PubMed Central

Martin, Andrew C. R.

2014-01-01

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

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

PubMed

Martin, Andrew C R

2014-01-01

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

Java Radar Analysis Tool

NASA Technical Reports Server (NTRS)

Zaczek, Mariusz P.

2005-01-01

Java Radar Analysis Tool (JRAT) is a computer program for analyzing two-dimensional (2D) scatter plots derived from radar returns showing pieces of the disintegrating Space Shuttle Columbia. JRAT can also be applied to similar plots representing radar returns showing aviation accidents, and to scatter plots in general. The 2D scatter plots include overhead map views and side altitude views. The superposition of points in these views makes searching difficult. JRAT enables three-dimensional (3D) viewing: by use of a mouse and keyboard, the user can rotate to any desired viewing angle. The 3D view can include overlaid trajectories and search footprints to enhance situational awareness in searching for pieces. JRAT also enables playback: time-tagged radar-return data can be displayed in time order and an animated 3D model can be moved through the scene to show the locations of the Columbia (or other vehicle) at the times of the corresponding radar events. The combination of overlays and playback enables the user to correlate a radar return with a position of the vehicle to determine whether the return is valid. JRAT can optionally filter single radar returns, enabling the user to selectively hide or highlight a desired radar return.

Java RMI Software Technology for the Payload Planning System of the International Space Station

NASA Technical Reports Server (NTRS)

Bryant, Barrett R.

1999-01-01

The Payload Planning System is for experiment planning on the International Space Station. The planning process has a number of different aspects which need to be stored in a database which is then used to generate reports on the planning process in a variety of formats. This process is currently structured as a 3-tier client/server software architecture comprised of a Java applet at the front end, a Java server in the middle, and an Oracle database in the third tier. This system presently uses CGI, the Common Gateway Interface, to communicate between the user-interface and server tiers and Active Data Objects (ADO) to communicate between the server and database tiers. This project investigated other methods and tools for performing the communications between the three tiers of the current system so that both the system performance and software development time could be improved. We specifically found that for the hardware and software platforms that PPS is required to run on, the best solution is to use Java Remote Method Invocation (RMI) for communication between the client and server and SQLJ (Structured Query Language for Java) for server interaction with the database. Prototype implementations showed that RMI combined with SQLJ significantly improved performance and also greatly facilitated construction of the communication software.

Java simulations of embedded control systems.

PubMed

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

2010-01-01

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

Java Simulations of Embedded Control Systems

PubMed Central

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

2010-01-01

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

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 object providing the persistent data server is implemented using the Java progranu-ning language. It uses the JRB to store/retrieve data in/from a relational database server. The persistent data management system provides transaction and user management facilities which allow multi-user, distributed access to the stored data in a secure manner.

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

PubMed

Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

2012-02-15

We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

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.

Intraspecific variability of Steinernema feltiae strains from Cemoro Lawang, eastern Java, Indonesia.

PubMed

Addis, T; Mulawarman, M; Waeyenberge, L; Moens, M; Viaene, N; Ehlers, R U

2010-01-01

Four strains of Steinernema feltiae from Eastern Java, Indonesia were characterized based on morphometric, morphological and molecular data. In addition, their virulence against last instar Tenebrio molitor and heat tolerance was tested. Infective juvenile have a mean body length ranging from 749 to 792 microm. The maximum sequence difference among the four strains was 7 bp (8.8%) in the ITS and 2 bp (0.3%) in D2D3 regions of the rDNA. All the strains are not reproductively isolated and can reproduce with European strain S. feltiae Owiplant. The lowest LC50 was observed for strain SCM (373) and the highest for S. feltiae strain Owiplant (458) IJs/40 T. molitor. All four strains showed relatively better mean heat tolerance when compared with S. feltiae Owiplant, both in adapted and non-adapted heat tolerance experiments.

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.

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.

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.

A browser-based event display for the CMS Experiment at the LHC using WebGL

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

Modern web browsers are powerful and sophisticated applications that support an ever-wider range of uses. One such use is rendering high-quality, GPU-accelerated, interactive 2D and 3D graphics in an HTML canvas. This can be done via WebGL, a JavaScript API based on OpenGL ES. Applications delivered via the browser have several distinct benefits for the developer and user. For example, they can be implemented using well-known and well-developed technologies, while distribution and use via a browser allows for rapid prototyping and deployment and ease of installation. In addition, delivery of applications via the browser allows for easy use on mobile, touch-enabled devices such as phones and tablets. iSpy WebGL is an application for visualization of events detected and reconstructed by the CMS Experiment at the Large Hadron Collider at CERN. The first event display developed for an LHC experiment to use WebGL, iSpy WebGL is a client-side application written in JavaScript, HTML, and CSS and uses the WebGL API three.js. iSpy WebGL is used for monitoring of CMS detector performance, for production of images and animations of CMS collisions events for the public, as a virtual reality application using Google Cardboard, and asa tool available for public education and outreach such as in the CERN Open Data Portal and the CMS masterclasses. We describe here its design, development, and usage as well as future plans.

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

PubMed

Earley, Clarke W

2013-11-18

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

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

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

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.

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.

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.

Dynamic Data-Driven Prognostics and Condition Monitoring of On-board Electronics

DTIC Science & Technology

2012-08-27

of functionality and accessibility; it is an open language unlike Java or Visual meaning that it is also free. It is also one of the most popular...and C# are able to run without the use of a virtual machine like Java . 4.2.1.5 Implementation For building of an OSA-CBM system, the primer...documentation [7] recommends the following steps: 1. Choose a middleware technology (DCOM, CORBA, Web Services, Java RMI, etc.). 2. Transform OSA-CBM UML

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.

Auxiliary Library Explorer (ALEX) Development

DTIC Science & Technology

2016-02-01

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

Towards 100,000 CPU Cycle-Scavenging by Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We examine a web-centric design using standard tools such as web servers, web browsers, PHP, and mySQL. We also consider the applicability of Information Power Grid tools such as the Globus (no relation to the author) Toolkit. We intend to implement this architecture with JavaGenes running on at least two cycle-scavengers: Condor and United Devices. JavaGenes, a genetic algorithm code written in Java, will be used to evolve multi-species reactive molecular force field parameters.

Shared virtual environments for telerehabilitation.

PubMed

Popescu, George V; Burdea, Grigore; Boian, Rares

2002-01-01

Current VR telerehabilitation systems use offline remote monitoring from the clinic and patient-therapist videoconferencing. Such "store and forward" and video-based systems cannot implement medical services involving patient therapist direct interaction. Real-time telerehabilitation applications (including remote therapy) can be developed using a shared Virtual Environment (VE) architecture. We developed a two-user shared VE for hand telerehabilitation. Each site has a telerehabilitation workstation with a videocamera and a Rutgers Master II (RMII) force feedback glove. Each user can control a virtual hand and interact hapticly with virtual objects. Simulated physical interactions between therapist and patient are implemented using hand force feedback. The therapist's graphic interface contains several virtual panels, which allow control over the rehabilitation process. These controls start a videoconferencing session, collect patient data, or apply therapy. Several experimental telerehabilitation scenarios were successfully tested on a LAN. A Web-based approach to "real-time" patient telemonitoring--the monitoring portal for hand telerehabilitation--was also developed. The therapist interface is implemented as a Java3D applet that monitors patient hand movement. The monitoring portal gives real-time performance on off-the-shelf desktop workstations.

Using Runtime Analysis to Guide Model Checking of Java Programs

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Norvig, Peter (Technical Monitor)

2001-01-01

This paper describes how two runtime analysis algorithms, an existing data race detection algorithm and a new deadlock detection algorithm, have been implemented to analyze Java programs. Runtime analysis is based on the idea of executing the program once. and observing the generated run to extract various kinds of information. This information can then be used to predict whether other different runs may violate some properties of interest, in addition of course to demonstrate whether the generated run itself violates such properties. These runtime analyses can be performed stand-alone to generate a set of warnings. It is furthermore demonstrated how these warnings can be used to guide a model checker, thereby reducing the search space. The described techniques have been implemented in the b e grown Java model checker called PathFinder.

ArgoEcoSystem-watershed (AgES-W) model evaluation for streamflow and nitrogen/sediment dynamics on a midwest agricultural watershed

USDA-ARS?s Scientific Manuscript database

AgroEcoSystem-Watershed (AgES-W) is a modular, Java-based spatially distributed model which implements hydrologic/water quality simulation components under the Object Modeling System Version 3 (OMS3). The AgES-W model was previously evaluated for streamflow and recently has been enhanced with the ad...

Review of Software Platforms for Agent Based Models

DTIC Science & Technology

2008-04-01

EINSTein 4.3.2 Battlefield Python (optional, for batch runs) MANA 4.3.3 Battlefield N/A MASON 4.3.4 General Java NetLogo 4.3.5 General Logo-variant...through the use of relatively simple Python scripts. It also has built-in functions for parameter sweeps, and can plot the resulting fitness landscape ac...Nonetheless its ease of use, and support for automatic drawing of agents in 2D or 3D2 makes this a suitable platform for beginner programmers. 2Only in the

A remote patient monitoring system using a Java-enabled 3G mobile phone.

PubMed

Zhang, Pu; Kogure, Yuichi; Matsuoka, Hiroki; Akutagawa, Masatake; Kinouchi, Yohsuke; Zhang, Qinyu

2007-01-01

Telemedicine systems have become an important supporting for the medical staffs. As the development of the mobile phones, it is possible to apply the mobile phones to be a part of telemedicine systems. We developed an innovative Remote Patient Monitoring System using a Java-enabled 3G mobile phone. By using this system, doctors can monitor the vital biosignals of patients in ICU/CCU, such as ECG, RESP, SpO2, EtCO2 and so on by using the real-time waveform and data monitoring and list trend data monitoring functions of installed Java jiglet application on the mobile phone. Futhermore, doctors can check the patients' information by using the patient information checking function. The 3G mobile phone used has the ability to implement the application as the same time as being used to mak a voice call. Therefore, the doctor can get more and more information both from the browsing the screen of the mobile phone and the communicating with the medical staffs who are beside the patients and the monitors. The system can be conducted to evaluate the diagnostic accuracy, efficiency, and safety of telediagnosis.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

PubMed

Markiewicz, Tomasz

2011-03-30

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8 GHz 4 GB RAM server with 768x576 pixel size, 1.28 Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server - 3.5 seconds, at remote analysis - 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

PubMed Central

2011-01-01

Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. Methods In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8GHz 4GB RAM server with 768x576 pixel size, 1.28Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server – 3.5 seconds, at remote analysis – 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. Conclusions The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system. PMID:21489188

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.

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.

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.

Design Virtual Reality Scene Roam for Tour Animations Base on VRML and Java

NASA Astrophysics Data System (ADS)

Cao, Zaihui; hu, Zhongyan

Virtual reality has been involved in a wide range of academic and commercial applications. It can give users a natural feeling of the environment by creating realistic virtual worlds. Implementing a virtual tour through a model of a tourist area on the web has become fashionable. In this paper, we present a web-based application that allows a user to, walk through, see, and interact with a fully three-dimensional model of the tourist area. Issues regarding navigation and disorientation areaddressed and we suggest a combination of the metro map and an intuitive navigation system. Finally we present a prototype which implements our ideas. The application of VR techniques integrates the visualization and animation of the three dimensional modelling to landscape analysis. The use of the VRML format produces the possibility to obtain some views of the 3D model and to explore it in real time. It is an important goal for the spatial information sciences.

SITEHOUND-web: a server for ligand binding site identification in protein structures.

PubMed

Hernandez, Marylens; Ghersi, Dario; Sanchez, Roberto

2009-07-01

SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of the protein structure and the putative sites using the Jmol java applet. Various downloadable data files are also provided for offline data analysis.

Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System

PubMed Central

Warren, Wayne; Brinkley, James F.

2005-01-01

Few biomedical subjects of study are as resource-intensive to teach as gross anatomy. Medical education stands to benefit greatly from applications which deliver virtual representations of human anatomical structures. While many applications have been created to achieve this goal, their utility to the student is limited because of a lack of interactivity or customizability by expert authors. Here we describe the first version of the Biolucida system, which allows an expert anatomist author to create knowledge-based, customized, and fully interactive scenes and lessons for students of human macroscopic anatomy. Implemented in Java and VRML, Biolucida allows the sharing of these instructional 3D environments over the internet. The system simplifies the process of authoring immersive content while preserving its flexibility and expressivity. PMID:16779148

Knowledge-based, interactive, custom anatomical scene creation for medical education: the Biolucida system.

PubMed

Warren, Wayne; Brinkley, James F

2005-01-01

Few biomedical subjects of study are as resource-intensive to teach as gross anatomy. Medical education stands to benefit greatly from applications which deliver virtual representations of human anatomical structures. While many applications have been created to achieve this goal, their utility to the student is limited because of a lack of interactivity or customizability by expert authors. Here we describe the first version of the Biolucida system, which allows an expert anatomist author to create knowledge-based, customized, and fully interactive scenes and lessons for students of human macroscopic anatomy. Implemented in Java and VRML, Biolucida allows the sharing of these instructional 3D environments over the internet. The system simplifies the process of authoring immersive content while preserving its flexibility and expressivity.

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.

Geographic information systems for mapping the National Exam Result of Junior High School in 2014 at West Java Province

NASA Astrophysics Data System (ADS)

Setiawan Abdullah, Atje; Nurani Ruchjana, Budi; Rejito, Juli; Rosadi, Rudi; Candra Permana, Fahmi

2017-10-01

National Exam level of schooling is implemented by the Ministry of Education and Culture for the development of education in Indonesia. The national examinations are centrally evaluated by the National Education Standards Agency, and the expected implementation of the national exams can describe the successful implementation of education at the district, municipal, provincial, or national level. In this study, we evaluate, analyze, and explore the implementation of the national exam database of the results of the Junior High School in 2014, with the Junior High School (SMP/MTs) as the smallest unit of analysis at the district level. The method used in this study is a data mining approach using the methodology of Knowledge Discovery in Databases (KDD) using descriptive analysis and spatial mapping of national examinations. The results of the classification of the data mining process to national exams of Junior High School in 2014 using data 6,878 SMP/MTs in West Java showed that 81.01 % were at moderate levels. While the results of the spatial mapping for SMP/MTs in West Java can be explained 36,99 % at the unfavorable level. The evaluation results visualization in graphic is done using ArcGIS to provide position information quality of education in municipal, provincial or national level. The results of this study can be used by management to make decision to improve educational services based on the national exam database in West Java. Keywords: KDD, spatial mapping, national exam.

Matching spatial with ontological brain regions using Java tools for visualization, database access, and integrated data analysis.

PubMed

Bezgin, Gleb; Reid, Andrew T; Schubert, Dirk; Kötter, Rolf

2009-01-01

Brain atlases are widely used in experimental neuroscience as tools for locating and targeting specific brain structures. Delineated structures in a given atlas, however, are often difficult to interpret and to interface with database systems that supply additional information using hierarchically organized vocabularies (ontologies). Here we discuss the concept of volume-to-ontology mapping in the context of macroscopical brain structures. We present Java tools with which we have implemented this concept for retrieval of mapping and connectivity data on the macaque brain from the CoCoMac database in connection with an electronic version of "The Rhesus Monkey Brain in Stereotaxic Coordinates" authored by George Paxinos and colleagues. The software, including our manually drawn monkey brain template, can be downloaded freely under the GNU General Public License. It adds value to the printed atlas and has a wider (neuro-)informatics application since it can read appropriately annotated data from delineated sections of other species and organs, and turn them into 3D registered stacks. The tools provide additional features, including visualization and analysis of connectivity data, volume and centre-of-mass estimates, and graphical manipulation of entire structures, which are potentially useful for a range of research and teaching applications.

A Web-based, secure, light weight clinical multimedia data capture and display system.

PubMed Central

Wang, S. S.; Starren, J.

2000-01-01

Computer-based patient records are traditionally composed of textual data. Integration of multimedia data has been historically slow. Multimedia data such as image, audio, and video have been traditionally more difficult to handle. An implementation of a clinical system for multimedia data is discussed. The system implementation uses Java, Secure Socket Layer (SSL), and Oracle 8i. The system is on top of the Internet so it is architectural independent, cross-platform, cross-vendor, and secure. Design and implementations issues are discussed. Images Figure 2 Figure 3 PMID:11080014

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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.

Telemedicine with integrated data security in ATM-based networks

NASA Astrophysics Data System (ADS)

Thiel, Andreas; Bernarding, Johannes; Kurth, Ralf; Wenzel, Rudiger; Villringer, Arno; Tolxdorff, Thomas

1997-05-01

Telemedical services rely on the digital transfer of large amounts of data in a short time. The acceptance of these services requires therefore new hard- and software concepts. The fast exchange of data is well performed within a high- speed ATM-based network. The fast access to the data from different platforms imposes more difficult problems, which may be divided into those relating to standardized data formats and those relating to different levels of data security across nations. For a standardized access to the formats and those relating to different levels of data security across nations. For a standardized access to the image data, a DICOM 3.0 server was implemented.IMages were converted into the DICOM 3.0 standard if necessary. The access to the server is provided by an implementation of DICOM in JAVA allowing access to the data from different platforms. Data protection measures to ensure the secure transfer of sensitive patient data are not yet solved within the DICOM concept. We investigated different schemes to protect data using the DICOM/JAVA modality with as little impact on data transfer speed as possible.

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.

Runtime Support for Type-Safe Dynamic Java Classes

DTIC Science & Technology

2000-01-01

Section 4.3. For each dynamic class C, we create a proxy class, Cproxy, and an implementation class, Cimp . In order to wrap method calls, Cproxy...wrapper method (W) and a reference to the associated method body (M). W explicitly invokes M, which points to the corresponding method body in Cimp ...When C’s implementation Cimp is switched, M is updated to point to the corresponding method object in the new C imp. Cproxy also contains a reference

JCell--a Java-based framework for inferring regulatory networks from time series data.

PubMed

Spieth, C; Supper, J; Streichert, F; Speer, N; Zell, A

2006-08-15

JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

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.

Technical implementation of an Internet address database with online maintenance module.

PubMed

Mischke, K L; Bollmann, F; Ehmer, U

2002-01-01

The article describes the technical implementation and management of the Internet address database of the center for ZMK (University of Münster, Dental School) Münster, which is integrated in the "ZMK-Web" website. The editorially maintained system guarantees its topicality primarily due to the electronically organized division of work with the aid of an online maintenance module programmed in JavaScript/PHP, as well as a database-related feedback function for the visitor to the website through configuration-independent direct mail windows programmed in JavaScript/PHP.

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 .

JGromacs: A Java Package for Analyzing Protein Simulations

PubMed Central

2011-01-01

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. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

JAva GUi for Applied Research (JAGUAR) v 3.0

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

JAGUAR is a Java software tool for automatically rendering a graphical user interface (GUI) from a structured input specification. It is designed as a plug-in to the Eclipse workbench to enable users to create, edit, and externally execute analysis application input decks and then view the results. JAGUAR serves as a GUI for Sandia's DAKOTA software toolkit for optimization and uncertainty quantification. It will include problem (input deck)set-up, option specification, analysis execution, and results visualization. Through the use of wizards, templates, and views, JAGUAR helps uses navigate the complexity of DAKOTA's complete input specification. JAGUAR is implemented in Java, leveragingmore » Eclipse extension points and Eclipse user interface. JAGUAR parses a DAKOTA NIDR input specification and presents the user with linked graphical and plain text representations of problem set-up and option specification for DAKOTA studies. After the data has been input by the user, JAGUAR generates one or more input files for DAKOTA, executes DAKOTA, and captures and interprets the results« less

A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns.

PubMed

Gerth, Victor E; Vize, Peter D

2005-04-01

The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT.

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

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

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

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.

Hypocenter Determination Using a Non-Linear Method for Events in West Java, Indonesia: A Preliminary Result

NASA Astrophysics Data System (ADS)

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

2017-04-01

West Java, part of the Sunda Arc, has relatively high seismicity due to subduction activity and faulting. The first step of tomography study in order to infer the geometry of the structure beneath West Java is to conduct precise earthquake hypocenter determination. In this study, we used earthquake waveform data taken from the regional Meteorological, Climatological, Geophysical Agency (BMKG) network from South Sumatra to central Java. We have repicked P and S arrival times from about 800 events in the period from April 2009 to December 2015. We selected the events which have azimuthal gap < 210° and phase more than 8. The non-linear method employed in this study used the oct-tree sampling algorithm from NonLinLoc program to determine the earthquake hypocenters. The hypocenter location results give better clustering earthquakes which are correlated well with geological structure in the study region. We also compared our results with BMKG catalog data and found that the average hypocenter location difference is about 12 km in latitude direction, 9.5 km in longitude direction, and the average focal depth difference is about 19.5 km. For future studies, we will conduct tomographic imaging to invert 3-D seismic velocity structure beneath the western part of Java.

The dynamic of tuberculosis case finding in the era of the public–private mix strategy for tuberculosis control in Central Java, Indonesia

PubMed Central

Reviono, Reviono; Setianingsih, Wahyu; Damayanti, Kusmadewi Eka; Ekasari, Ratna

2017-01-01

ABSTRACT Background: The public–private mix (PPM) strategy has strengthened tuberculosis care and control in many countries. Indonesia, a country with a high tuberculosis burden, has a low tuberculosis case detection rate (CDR), despite PPM implementation in 2003. The PPM in Indonesia involves primary healthcare centers, hospitals, and specialized chest clinics. The long-term impact of the strategy is unknown. Objective: We aimed to explore the case detection achievements of the tuberculosis program since PPM implementation in Central Java in 2003. Methods: This retrospective cohort study covered the period 1 January 2000 to 31 December 2014. The data from tuberculosis patients treated in all health facilities in Central Java implementing directly observed treatment short-course, recorded via a standardized form, were analyzed after being validated by the Office of Health of Central Java Province. We evaluated the CDR, case notification rate, and total number of cases, using linear regression to analyze the temporal trends of those indicators in the phases of PPM implementation. Results: The CDR increased during the initial phase (2000–2005), decreased during the mid-phase (2006–2009), and increased slightly during the late phase (2010–2014), ranging from 13 to 61.72. These trends were observed despite a steady increase in the number of participating healthcare facilities. The regression analysis showed that the CDR of referral institutions contributed the most to the total CDR of Central Java Province. Many of the smear-negative tuberculosis cases recorded at primary healthcare centers may have been smear positive; this probable misclassification could have been partially avoided if more specific and sensitive diagnostic tools were available. Conclusions: The CDR remains below the national target (70%). Early awareness of a negative trend in certain program indicators is important to ensure program sustainability. Careful observation of the indicator pattern will secure the long-term success of the program. PMID:28766465

The dynamic of tuberculosis case finding in the era of the public-private mix strategy for tuberculosis control in Central Java, Indonesia.

PubMed

Reviono, Reviono; Setianingsih, Wahyu; Damayanti, Kusmadewi Eka; Ekasari, Ratna

2017-01-01

The public-private mix (PPM) strategy has strengthened tuberculosis care and control in many countries. Indonesia, a country with a high tuberculosis burden, has a low tuberculosis case detection rate (CDR), despite PPM implementation in 2003. The PPM in Indonesia involves primary healthcare centers, hospitals, and specialized chest clinics. The long-term impact of the strategy is unknown.  We aimed to explore the case detection achievements of the tuberculosis program since PPM implementation in Central Java in 2003. This retrospective cohort study covered the period 1 January 2000 to 31 December 2014. The data from tuberculosis patients treated in all health facilities in Central Java implementing directly observed treatment short-course, recorded via a standardized form, were analyzed after being validated by the Office of Health of Central Java Province. We evaluated the CDR, case notification rate, and total number of cases, using linear regression to analyze the temporal trends of those indicators in the phases of PPM implementation. The CDR increased during the initial phase (2000-2005), decreased during the mid-phase (2006-2009), and increased slightly during the late phase (2010-2014), ranging from 13 to 61.72. These trends were observed despite a steady increase in the number of participating healthcare facilities. The regression analysis showed that the CDR of referral institutions contributed the most to the total CDR of Central Java Province. Many of the smear-negative tuberculosis cases recorded at primary healthcare centers may have been smear positive; this probable misclassification could have been partially avoided if more specific and sensitive diagnostic tools were available. The CDR remains below the national target (70%). Early awareness of a negative trend in certain program indicators is important to ensure program sustainability. Careful observation of the indicator pattern will secure the long-term success of the program.

Success Factors for Adoption of Real-Time Java

DTIC Science & Technology

2010-04-01

use Java in an effective way in order to achieve objectives If d ’t l t ti f bj ti d d ’t lt i t l i 9© 2010 Atego. All rights reserved. you on p an o...order to effectively use object-oriented programming practices. Te ps d’execution des algos 400 450 500 550 600 650 700 n m s TacticalPicture...find all garbage, nor to defragment the available free pool Common operations may have surprising effects (e.g. entering a mutual exclusion region

Project Golden Gate: towards real-time Java in space missions

NASA Technical Reports Server (NTRS)

Dvorak, Daniel; Bollella, Greg; Canham, Tim; Carson, Vanessa; Champlin, Virgil; Giovannoni, Brian; Indictor, Mark; Meyer, Kenny; Murray, Alex; Reinholtz, Kirk

2004-01-01

This paper describes the problem domain and our experimentation with the first commercial implementation of the Real Time Specification for Java. The two main issues explored in this report are: (1) the effect of RTSJ's non-heap memory on the programming model, and (2) performance benchmarking of RTSJ/Linux relative to C++/VxWorks.

Shark: Fast Data Analysis Using Coarse-grained Distributed Memory

DTIC Science & Technology

2013-05-01

Schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 7.1.1 Java Objects...often MySQL or Derby) with a namespace for tables, table metadata, and par- tition information. Table data is stored in an HDFS directory, while a...saving time and space for large data sets. This is achieved with support for custom SerDe (serialization/deserialization) java interface implementations

Towards a Decision Support Tool for 3d Visualisation: Application to Selectivity Purpose of Single Object in a 3d City Scene

NASA Astrophysics Data System (ADS)

Neuville, R.; Pouliot, J.; Poux, F.; Hallot, P.; De Rudder, L.; Billen, R.

2017-10-01

This paper deals with the establishment of a comprehensive methodological framework that defines 3D visualisation rules and its application in a decision support tool. Whilst the use of 3D models grows in many application fields, their visualisation remains challenging from the point of view of mapping and rendering aspects to be applied to suitability support the decision making process. Indeed, there exists a great number of 3D visualisation techniques but as far as we know, a decision support tool that facilitates the production of an efficient 3D visualisation is still missing. This is why a comprehensive methodological framework is proposed in order to build decision tables for specific data, tasks and contexts. Based on the second-order logic formalism, we define a set of functions and propositions among and between two collections of entities: on one hand static retinal variables (hue, size, shape…) and 3D environment parameters (directional lighting, shadow, haze…) and on the other hand their effect(s) regarding specific visual tasks. It enables to define 3D visualisation rules according to four categories: consequence, compatibility, potential incompatibility and incompatibility. In this paper, the application of the methodological framework is demonstrated for an urban visualisation at high density considering a specific set of entities. On the basis of our analysis and the results of many studies conducted in the 3D semiotics, which refers to the study of symbols and how they relay information, the truth values of propositions are determined. 3D visualisation rules are then extracted for the considered context and set of entities and are presented into a decision table with a colour coding. Finally, the decision table is implemented into a plugin developed with three.js, a cross-browser JavaScript library. The plugin consists of a sidebar and warning windows that help the designer in the use of a set of static retinal variables and 3D environment parameters.

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.

Changing On Diurnal Cycle Of Rainfall In Northern Coastal Of West Java

NASA Astrophysics Data System (ADS)

Yulihastin, E.; Hadi, T. W.; Ningsih, N. S.

2017-12-01

The floods event in the north of Java was largely due to persistent of rainfall that occurred in the morning which indicated of deviation of diurnal pattern of rainfall. The shift of the phase of diurnal rainfall cycle using TRMM satellite hourly data of 3B41RT on the rainy period of 2000-2016 exhibits over land from Late Afternoon-Early Midnight (LA-EM) to morning. The peak of the cycle changes from diurnal to semidiurnal with a peak occurring in LA-EM and morning. Location of rainfall which usually occurs in the oceans shifted into near coastal area. The classification of diurnal rainfall cycles based on composite analysis shows four types: Normal (N) Type (45.6%) with one peak rainfall occurring in the afternoon until night, Diurnal (D) Type (26%) with one peak and phase opposite to normal type, Semidiurnal (SD) Type (6.5 %) with two peaks and the main peak occurring in the afternoon until night, Third Diurnal (TD) Type (21.7%) with three peaks and the main peak occurs in the morning. The classification was confirmed using the objective method of Empirical Mode Decomposition (EMD) and obtained three IMFs representing three diurnal cycle modes of Type TD (67.8%) with the main rain peak taking place in the afternoon, Type D with rain peak occurring in the early hours (18.9%), and SD type (9.9%) with the first peak occurred in the afternoon. For D Type, the results also prove that the diurnal cycle with significant deviations in amplitude occurred in February 2002, 2004, 2008, 2014, wich is the maximum rainfall occurs in the EM. It also seems that in those years, rainfall intensity is concentrated on the northern coast of West Java while in the Java Sea rainfall was minimum.

A kickball game for ankle rehabilitation by JAVA, JNI, and VRML

NASA Astrophysics Data System (ADS)

Choi, Hyungjeen; Ryu, Jeha; Lee, Chansu

2004-03-01

This paper presents development of a virtual environment that can be applied to the ankle rehabilitation procedure. We developed a virtual football stadium to intrigue a patient, where two degree of freedom (DOF) plate-shaped object is oriented to kick a ball falling from the sky in accordance with the data from the ankle's dorisflexion/plantarflexion and inversion/eversion motion on the moving platform of the K-Platform. This Kickball Game is implemented by Virtual Reality Modeling Language (VRML). To control virtual objects, data from the K-Platform are transmitted through the communication module implemented in C++. Java, Java Native Interface (JNI) and VRML plug-in are combined together so as to interface the communication module with the virtual environment by VRML. This game may be applied to the Active Range of Motion (AROM) exercise procedure that is one of the ankle rehabilitation procedures.

Simulating Candidate Missions for a Novel Glider Unmanned Underwater Vehicle

DTIC Science & Technology

2007-03-01

MOTIVATION ................................................................................................2 D . OBJECTIVES...7 D . PROGRAMMING CONSTRUCTS.............................................................10 1. JAVA...21 D . DISKIT

Guest Editor's introduction: Selected papers from the 4th USENIX Conference on Object-Oriented Technologies and Systems

NASA Astrophysics Data System (ADS)

Sventek, Joe

1998-12-01

Hewlett-Packard Laboratories, 1501 Page Mill Road, Palo Alto, CA 94304, USA Introduction The USENIX Conference on Object-Oriented Technologies and Systems (COOTS) is held annually in the late spring. The conference evolved from a set of C++ workshops that were held under the auspices of USENIX, the first of which met in 1989. Given the growing diverse interest in object-oriented technologies, the C++ focus of the workshop eventually became too narrow, with the result that the scope was widened in 1995 to include object-oriented technologies and systems. COOTS is intended to showcase advanced R&D efforts in object-oriented technologies and software systems. The conference emphasizes experimental research and experience gained by using object-oriented techniques and languages to build complex software systems that meet real-world needs. COOTS solicits papers in the following general areas: application of, and experiences with, object-oriented technologies in particular domains (e.g. financial, medical, telecommunication); the architecture and implementation of distributed object systems (e.g. CORBA, DCOM, RMI); object-oriented programming and specification languages; object-oriented design and analysis. The 4th meeting of COOTS was held 27 - 30 April 1998 at the El Dorado Hotel, Santa Fe, New Mexico, USA. Several tutorials were given. The technical program proper consisted of a single track of six sessions, with three paper presentations per session. A keynote address and a provocative panel session rounded out the technical program. The program committee reviewed 56 papers, selecting the best 18 for presentation in the technical sessions. While we solicit papers across the spectrum of applications of object-oriented technologies, this year there was a predominance of distributed, object-oriented papers. The accepted papers reflected this asymmetry, with 15 papers on distributed objects and 3 papers on object-oriented languages. The papers in this special issue are the six best distributed object papers (in the opinion of the program committee). They represent the diversity of research in this particular area, and should give the reader a good idea of the types of papers presented at COOTS as well as the calibre of the work so presented. The papers The paper by Jain, Widoff and Schmidt explores the suitability of Java for writing performance-sensitive distributed applications. Despite the popularity of Java, there are many concerns about its efficiency; in particular, networking and computation performance are key concerns when considering the use of Java to develop performance-sensitive distributed applications. This paper makes three contributions to the study of Java for these applications: it describes an architecture using Java and the Web to develop MedJava, which is a distributed electronic medical imaging system with stringent networking and computation requirements; it presents benchmarks of MedJava image processing and compares the results to the performance of xv, which is an equivalent image processing application written in C; it presents performance benchmarks using Java as a transport interface to exchange large medical images over high-speed ATM networks. The paper by Little and Shrivastava covers the integration of several important topics: transactions, distributed systems, Java, the Internet and security. The usefulness of this paper lies in the synthesis of an effective solution applying work in different areas of computing to the Java environment. Securing applications constructed from distributed objects is important if these applications are to be used in mission-critical situations. Delegation is one aspect of distributed system security that is necessary for such applications. The paper by Nagaratnam and Lea describes a secure delegation model for Java-based, distributed object environments. The paper by Frølund and Koistinen addresses the topical issue of providing a common way for describing Quality-of-Service (QoS) features in distributed, object-oriented systems. They present a general QoS language, QML, that can be used to capture QoS properties as part of a design. They also show how to extend UML to support QML concepts. The paper by Szymaszek, Uszok and Zielinski discusses the important issue of efficient implementation and usage of fine-grained objects in CORBA-based applications. Fine-grained objects can have serious ramifications on overall application performance and scalability, and the paper suggests that such objects should not be treated as first-class CORBA objects, proposing instead the use of collections and smart proxies for efficient implementation. The paper by Milojicic, LaForge and Chauhan describes a mobile objects and agents infrastructure. Their particular research has focused on communication support across agent migration and extensive resource control. The paper also discusses issues regarding interoperation between agent systems. Acknowledgments The editor wishes to thank all of the authors, reviewers and publishers. Without their excellent work, and the contribution of their valuable time, this special issue would not have been possible.

The Spatially-Distributed Agroecosystem-Watershed (Ages-W) Hydrologic/Water Quality (H/WQ) model for assessment of conservation effects

USDA-ARS?s Scientific Manuscript database

AgroEcoSystem-Watershed (AgES-W) is a modular, Java-based spatially distributed model which implements hydrologic/water quality (H/WQ) simulation components under the Object Modeling System (OMS3) environmental modeling framework. AgES-W has recently been enhanced with the addition of nitrogen (N) a...

Implementing a Java Based GUI for RICH Detector Analysis

NASA Astrophysics Data System (ADS)

Lendacky, Andrew; Voloshin, Andrew; Benmokhtar, Fatiha

2016-09-01

The CLAS12 detector at Thomas Jefferson National Accelerator Facility (TJNAF) is undergoing an upgrade. One of the improvements is the addition of a Ring Imaging Cherenkov (RICH) detector to improve particle identification in the 3-8 GeV/c momentum range. Approximately 400 multi anode photomultiplier tubes (MAPMTs) are going to be used to detect Cherenkov Radiation in the single photoelectron spectra (SPS). The SPS of each pixel of all MAPMTs have been fitted to a mathematical model of roughly 45 parameters for 4 HVs, 3 OD. Out of those parameters, 9 can be used to evaluate the PMTs performance and placement in the detector. To help analyze data when the RICH is operational, a GUI application was written in Java using Swing and detector packages from TJNAF. To store and retrieve the data, a MySQL database program was written in Java using the JDBC package. Using the database, the GUI pulls the values and produces histograms and graphs for a selected PMT at a specific HV and OD. The GUI will allow researchers to easily view a PMT's performance and efficiency to help with data analysis and ring reconstruction when the RICH is finished.

Evaluating the Response of Polyvinyl Toluene Scintillators used in Portal Detectors

DTIC Science & Technology

2008-03-01

For the example shell script , the working directory is located at d:\\g4work. The Java development kit (jdk) is located at c:/ Java /jdk1.7.0. “JAIDA...Interval . . . . . . . . . . . . . . . . . . . . . . 64 SLAC Stanford Linear Accelerator . . . . . . . . . . . . . . . . . 84 jdk Java development...Em0, Em13, Em14 Stopping power, particle range ... Em0, Em1, Em5, Em11, Em12 Final state : energy spectra, angular distributions Em14 Energy loss

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

DTIC Science & Technology

2014-03-27

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

Challenges to the implementation of the integrated management of childhood illness (IMCI) at community health centres in West Java province, Indonesia.

PubMed

Titaley, C R; Jusril, H; Ariawan, I; Soeharno, N; Setiawan, T; Weber, M W

2014-01-01

The integrated management of childhood illness (IMCI) is a comprehensive approach to child health, which has been adopted in Indonesia since 1997. This study aims to provide an overview of IMCI implementation at community health centres (puskesmas) in West Java province, Indonesia. Data were derived from a cross-sectional study conducted in 10 districts of West Java province, from November to December 2012. Semi-structured interviews were used to obtain information from staff at 80 puskesmas, including the heads (80 informants), pharmacy staff (79 informants) and midwives/nurses trained in IMCI (148 informants), using semi-structured interviews. Quantitative data were analysed using frequency tabulations and qualitative data were analysed by identifying themes that emerged in informants' responses. Almost all (N = 79) puskesmas implemented the IMCI strategy; however, only 64% applied it to all visiting children. Several barriers to IMCI implementation were identified, including shortage of health workers trained in IMCI (only 43% of puskesmas had all health workers in the child care unit trained in IMCI and 40% of puskesmas conducted on-the-job training). Only 19% of puskesmas had all the essential drugs and equipment for IMCI. Nearly all health workers acknowledged the importance of IMCI in their routine services and very few did not perceive its benefits. Lack of supervision from district health office staff and low community awareness regarding the importance of IMCI were reported. Complaints received from patients'families were generally related to the long duration of treatment and no administration of medication after physical examination. Interventions aiming to create local regulations endorsing IMCI implementation; promoting monitoring and supervision; encouraging on-the-job training for health workers; and strengthening training programmes, counselling and other promotional activities are important for promoting IMCI implementation in West Java province, and are also likely to be useful elsewhere in the country.

FMT (Flight Software Memory Tracker) For Cassini Spacecraft-Software Engineering Using JAVA

NASA Technical Reports Server (NTRS)

Kan, Edwin P.; Uffelman, Hal; Wax, Allan H.

1997-01-01

The software engineering design of the Flight Software Memory Tracker (FMT) Tool is discussed in this paper. FMT is a ground analysis software set, consisting of utilities and procedures, designed to track the flight software, i.e., images of memory load and updatable parameters of the computers on-board Cassini spacecraft. FMT is implemented in Java.

A WebGIS-based system for analyzing and visualizing air quality data for Shanghai Municipality

NASA Astrophysics Data System (ADS)

Wang, Manyi; Liu, Chaoshun; Gao, Wei

2014-10-01

An online visual analytical system based on Java Web and WebGIS for air quality data for Shanghai Municipality was designed and implemented to quantitatively analyze and qualitatively visualize air quality data. By analyzing the architecture of WebGIS and Java Web, we firstly designed the overall scheme for system architecture, then put forward the software and hardware environment and also determined the main function modules for the system. The visual system was ultimately established with the DIV + CSS layout method combined with JSP, JavaScript, and some other computer programming languages based on the Java programming environment. Moreover, Struts, Spring, and Hibernate frameworks (SSH) were integrated in the system for the purpose of easy maintenance and expansion. To provide mapping service and spatial analysis functions, we selected ArcGIS for Server as the GIS server. We also used Oracle database and ESRI file geodatabase to store spatial data and non-spatial data in order to ensure the data security. In addition, the response data from the Web server are resampled to implement rapid visualization through the browser. The experimental successes indicate that this system can quickly respond to user's requests, and efficiently return the accurate processing results.

THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

The new THttpServer class in ROOT implements HTTP server for arbitrary ROOT applications. It is based on Civetweb embeddable HTTP server and provides direct access to all objects registered for the server. Objects data could be provided in different formats: binary, XML, GIF/PNG, and JSON. A generic user interface for THttpServer has been implemented with HTML/JavaScript based on JavaScript ROOT development. With any modern web browser one could list, display, and monitor objects available on the server. THttpServer is used in Go4 framework to provide HTTP interface to the online analysis.

Windows Memory Forensic Data Visualization

DTIC Science & Technology

2014-06-12

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

Automatic visualization of 3D geometry contained in online databases

NASA Astrophysics Data System (ADS)

Zhang, Jie; John, Nigel W.

2003-04-01

In this paper, the application of the Virtual Reality Modeling Language (VRML) for efficient database visualization is analyzed. With the help of JAVA programming, three examples of automatic visualization from a database containing 3-D Geometry are given. The first example is used to create basic geometries. The second example is used to create cylinders with a defined start point and end point. The third example is used to processs data from an old copper mine complex in Cheshire, United Kingdom. Interactive 3-D visualization of all geometric data in an online database is achieved with JSP technology.

Using Cesium for 3D Thematic Visualisations on the Web

NASA Astrophysics Data System (ADS)

Gede, Mátyás

2018-05-01

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

EUMIS - an open portal framework for interoperable marine environmental services

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

FacetModeller: Software for manual creation, manipulation and analysis of 3D surface-based models

NASA Astrophysics Data System (ADS)

Lelièvre, Peter G.; Carter-McAuslan, Angela E.; Dunham, Michael W.; Jones, Drew J.; Nalepa, Mariella; Squires, Chelsea L.; Tycholiz, Cassandra J.; Vallée, Marc A.; Farquharson, Colin G.

2018-01-01

The creation of 3D models is commonplace in many disciplines. Models are often built from a collection of tessellated surfaces. To apply numerical methods to such models it is often necessary to generate a mesh of space-filling elements that conforms to the model surfaces. While there are meshing algorithms that can do so, they place restrictive requirements on the surface-based models that are rarely met by existing 3D model building software. Hence, we have developed a Java application named FacetModeller, designed for efficient manual creation, modification and analysis of 3D surface-based models destined for use in numerical modelling.

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

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.

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/.

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.

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.

Modeling Airport Ground Operations using Discrete Event Simulation (DES) and X3D Visualization

DTIC Science & Technology

2008-03-01

scenes. It is written in open-source Java and XML using the Netbeans platform, which gave the features of being suitable as standalone applications...and as a plug-in module for the Netbeans integrated development environment (IDE). X3D Graphics is the tool used for the elaboration the creation of...process is shown in Figure 2. To 20 create a new event graph in Viskit, first, Viskit tool must be launched via Netbeans or from the executable

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

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.

Experiential learning implementation based on joint responsibility in women's cooperative development (Case study on Farmer Women Cooperative, Sumedang, West Java)

NASA Astrophysics Data System (ADS)

Suseno, Gijanto Purbo; Nataliningsih

2017-09-01

Cooperative extension is one form of non-formal education. The follow up of cooperative extension is a coaching that aims to cooperative boards and members apply the knowledge and skills acquired during extension. Learning from the experience (experience learning) of others combined with the concept of joint responsibility is expected to develop the participation of cooperative members as indicated by the repayment of loans on time. The research was conducted at Sumedang Farmer Women Cooperative of West Java with the stages of cooperative extension and coaching for 6 months so it can be evaluated its impact. The results showed that from 30 extension participants who stated willingness to be a member of joint responsibility group as many as 15 people (50%), which then divided into 3 groups of mutual responsibility with member of each group is 5 people. The result of impact evaluation showed the development of group dynamics of the joint liability shown by 9 people (60%) developing business, 3 people (20%) business stagnant and 3 (20%) less profitable business. Implementation of experiental learning based on the concept of mutual responsibility encourages the improvement of entrepreneurship and cooperative skills and the ability of members to pay loan installments on cooperatives in a timely manner.

Program Instrumentation and Trace Analysis

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Goldberg, Allen; Filman, Robert; Rosu, Grigore; Koga, Dennis (Technical Monitor)

2002-01-01

Several attempts have been made recently to apply techniques such as model checking and theorem proving to the analysis of programs. This shall be seen as a current trend to analyze real software systems instead of just their designs. This includes our own effort to develop a model checker for Java, the Java PathFinder 1, one of the very first of its kind in 1998. However, model checking cannot handle very large programs without some kind of abstraction of the program. This paper describes a complementary scalable technique to handle such large programs. Our interest is turned on the observation part of the equation: How much information can be extracted about a program from observing a single execution trace? It is our intention to develop a technology that can be applied automatically and to large full-size applications, with minimal modification to the code. We present a tool, Java PathExplorer (JPaX), for exploring execution traces of Java programs. The tool prioritizes scalability for completeness, and is directed towards detecting errors in programs, not to prove correctness. One core element in JPaX is an instrumentation package that allows to instrument Java byte code files to log various events when executed. The instrumentation is driven by a user provided script that specifies what information to log. Examples of instructions that such a script can contain are: 'report name and arguments of all called methods defined in class C, together with a timestamp'; 'report all updates to all variables'; and 'report all acquisitions and releases of locks'. In more complex instructions one can specify that certain expressions should be evaluated and even that certain code should be executed under various conditions. The instrumentation package can hence be seen as implementing Aspect Oriented Programming for Java in the sense that one can add functionality to a Java program without explicitly changing the code of the original program, but one rather writes an aspect and compiles it into the original program using the instrumentation. Another core element of JPaX is an observation package that supports the analysis of the generated event stream. Two kinds of analysis are currently supported. In temporal analysis the execution trace is evaluated against formulae written in temporal logic. We have implemented a temporal logic evaluator on finite traces using the Maude rewriting system from SRI International, USA. Temporal logic is defined in Maude by giving its syntax as a signature and its semantics as rewrite equations. The resulting semantics is extremely efficient and can handle event streams of hundreds of millions events in few minutes. Furthermore, the implementation is very succinct. The second form of even stream analysis supported is error pattern analysis where an execution trace is analyzed using various error detection algorithms that can identify error-prone programming practices that may potentially lead to errors in some different executions. Two such algorithms focusing on concurrency errors have been implemented in JPaX, one for deadlocks and the other for data races. It is important to note, that a deadlock or data race potential does not need to occur in order for its potential to be detected with these algorithms. This is what makes them very scalable in practice. The data race algorithm implemented is the Eraser algorithm from Compaq, however adopted to Java. The tool is currently being applied to a code base for controlling a spacecraft by the developers of that software in order to evaluate its applicability.

Java implementation of Class Association Rule algorithms

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

Tamura, Makio

2007-08-30

Java implementation of three Class Association Rule mining algorithms, NETCAR, CARapriori, and clustering based rule mining. NETCAR algorithm is a novel algorithm developed by Makio Tamura. The algorithm is discussed in a paper: UCRL-JRNL-232466-DRAFT, and would be published in a peer review scientific journal. The software is used to extract combinations of genes relevant with a phenotype from a phylogenetic profile and a phenotype profile. The phylogenetic profiles is represented by a binary matrix and a phenotype profile is represented by a binary vector. The present application of this software will be in genome analysis, however, it could be appliedmore » more generally.« less

Small area estimation (SAE) model: Case study of poverty in West Java Province

NASA Astrophysics Data System (ADS)

Suhartini, Titin; Sadik, Kusman; Indahwati

2016-02-01

This paper showed the comparative of direct estimation and indirect/Small Area Estimation (SAE) model. Model selection included resolve multicollinearity problem in auxiliary variable, such as choosing only variable non-multicollinearity and implemented principal component (PC). Concern parameters in this paper were the proportion of agricultural venture poor households and agricultural poor households area level in West Java Province. The approach for estimating these parameters could be performed based on direct estimation and SAE. The problem of direct estimation, three area even zero and could not be conducted by directly estimation, because small sample size. The proportion of agricultural venture poor households showed 19.22% and agricultural poor households showed 46.79%. The best model from agricultural venture poor households by choosing only variable non-multicollinearity and the best model from agricultural poor households by implemented PC. The best estimator showed SAE better then direct estimation both of the proportion of agricultural venture poor households and agricultural poor households area level in West Java Province. The solution overcame small sample size and obtained estimation for small area was implemented small area estimation method for evidence higher accuracy and better precision improved direct estimator.

GIS-based interactive tool to map the advent of world conquerors

NASA Astrophysics Data System (ADS)

Lakkaraju, Mahesh

The objective of this thesis is to show the scale and extent of some of the greatest empires the world has ever seen. This is a hybrid project between the GIS based interactive tool and the web-based JavaScript tool. This approach lets the students learn effectively about the emperors themselves while understanding how long and far their empires spread. In the GIS based tool, a map is displayed with various points on it, and when a user clicks on one point, the relevant information of what happened at that particular place is displayed. Apart from this information, users can also select the interactive animation button and can walk through a set of battles in chronological order. As mentioned, this uses Java as the main programming language, and MOJO (Map Objects Java Objects) provided by ESRI. MOJO is very effective as its GIS related features can be included in the application itself. This app. is a simple tool and has been developed for university or high school level students. D3.js is an interactive animation and visualization platform built on the Javascript framework. Though HTML5, CSS3, Javascript and SVG animations can be used to derive custom animations, this tool can help bring out results with less effort and more ease of use. Hence, it has become the most sought after visualization tool for multiple applications. D3.js has provided a map-based visualization feature so that we can easily display text-based data in a map-based interface. To draw the map and the points on it, D3.js uses data rendered in TOPO JSON format. The latitudes and longitudes can be provided, which are interpolated into the Map svg. One of the main advantages of doing it this way is that more information is retained when we use a visual medium.

Fuselet Authoring, Execution, and Management in Support of Global Strike Operations

DTIC Science & Technology

2008-07-01

can be implemented in a variety of languages such as Java , Extensible Stylesheet Language Transformations (XSLT), Groovy, and Jython. A primary...measurable and manageable. By creating transformations from reusable, parameterizable components rather than ad-hoc scripts , transformation logic is...deployable to any Java 2 Platform, Enterprise Edition (J2EE) server, but is tested regularly on the JBoss Application Server (AS) version 4.0.4.GA

Cloud Computing Trace Characterization and Synthetic Workload Generation

DTIC Science & Technology

2013-03-01

measurements [44]. Olio is primarily for learning Web 2.0 technologies, evaluating the three implementations (PHP, Java EE, and RubyOnRails (ROR...Add Event 17 Olio is well documented, but assumes prerequisite knowledge with setup and operation of apache web servers and MySQL databases. Olio...Faban supports numerous servers such as Apache httpd, Sun Java System Web, Portal and Mail Servers, Oracle RDBMS, memcached, and others [18]. Perhaps

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.

Modelling and Implementation of Catalogue Cards Using FreeMarker

ERIC Educational Resources Information Center

Radjenovic, Jelen; Milosavljevic, Branko; Surla, Dusan

2009-01-01

Purpose: The purpose of this paper is to report on a study involving the specification (using Unified Modelling Language (UML) 2.0) of information requirements and implementation of the software components for generating catalogue cards. The implementation in a Java environment is developed using the FreeMarker software.…

Impact of Implementation of Direct Cash Transfer Program 2008/2009 on Household Consumption in Central Java Province

NASA Astrophysics Data System (ADS)

Subanti, S.; Hakim, A. R.; Hakim, I. M.

2017-04-01

This study aims to see the impact of direct cash transfer program for 2008/2009 on household consumption of food, nonfood, education, and health in Central Java Province. The study is expected to provide important findings for the improvement of a similar program in the future. This study findings that (1) the increasing in food and non-food consumption for direct cash transfer recipients than non direct cash transfer recipients; (2) the impact of households expenditure on education for direct cash transfer recipients is higher than non direct cash transfer recipients; (3) the impact of households expenditure on health for direct cash transfer recipients is lower than non direct cash transfer recipients. This study recommended that (1) implementation of direct cash transfer program 2008/2009 must be managed to be better because this program can defend household welfare. It shows from several indicators of well-being such as consumption spending, education, and health; (2) data targets for poor households (very poor, poor, nearly poor) must be updated.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

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

NASA Astrophysics Data System (ADS)

Kongko, W.; Schlurmann, T.

2009-04-01

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

Brandenburg 3D - a comprehensive 3D Subsurface Model, Conception of an Infrastructure Node and a Web Application

NASA Astrophysics Data System (ADS)

Kerschke, Dorit; Schilling, Maik; Simon, Andreas; Wächter, Joachim

2014-05-01

The Energiewende and the increasing scarcity of raw materials will lead to an intensified utilization of the subsurface in Germany. Within this context, geological 3D modeling is a fundamental approach for integrated decision and planning processes. Initiated by the development of the European Geospatial Infrastructure INSPIRE, the German State Geological Offices started digitizing their predominantly analog archive inventory. Until now, a comprehensive 3D subsurface model of Brandenburg did not exist. Therefore the project B3D strived to develop a new 3D model as well as a subsequent infrastructure node to integrate all geological and spatial data within the Geodaten-Infrastruktur Brandenburg (Geospatial Infrastructure, GDI-BB) and provide it to the public through an interactive 2D/3D web application. The functionality of the web application is based on a client-server architecture. Server-sided, all available spatial data is published through GeoServer. GeoServer is designed for interoperability and acts as the reference implementation of the Open Geospatial Consortium (OGC) Web Feature Service (WFS) standard that provides the interface that allows requests for geographical features. In addition, GeoServer implements, among others, the high performance certified compliant Web Map Service (WMS) that serves geo-referenced map images. For publishing 3D data, the OGC Web 3D Service (W3DS), a portrayal service for three-dimensional geo-data, is used. The W3DS displays elements representing the geometry, appearance, and behavior of geographic objects. On the client side, the web application is solely based on Free and Open Source Software and leans on the JavaScript API WebGL that allows the interactive rendering of 2D and 3D graphics by means of GPU accelerated usage of physics and image processing as part of the web page canvas without the use of plug-ins. WebGL is supported by most web browsers (e.g., Google Chrome, Mozilla Firefox, Safari, and Opera). The web application enables an intuitive navigation through all available information and allows the visualization of geological maps (2D), seismic transects (2D/3D), wells (2D/3D), and the 3D-model. These achievements will alleviate spatial and geological data management within the German State Geological Offices and foster the interoperability of heterogeneous systems. It will provide guidance to a systematic subsurface management across system, domain and administrative boundaries on the basis of a federated spatial data infrastructure, and include the public in the decision processes (e-Governance). Yet, the interoperability of the systems has to be strongly propelled forward through agreements on standards that need to be decided upon in responsible committees. The project B3D is funded with resources from the European Fund for Regional Development (EFRE).

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 to ground water extraction needed to support the increasing population and industrial activities.

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.

Fast simulation of Proton Induced X-Ray Emission Tomography using CUDA

NASA Astrophysics Data System (ADS)

Beasley, D. G.; Marques, A. C.; Alves, L. C.; da Silva, R. C.

2013-07-01

A new 3D Proton Induced X-Ray Emission Tomography (PIXE-T) and Scanning Transmission Ion Microscopy Tomography (STIM-T) simulation software has been developed in Java and uses NVIDIA™ Common Unified Device Architecture (CUDA) to calculate the X-ray attenuation for large detector areas. A challenge with PIXE-T is to get sufficient counts while retaining a small beam spot size. Therefore a high geometric efficiency is required. However, as the detector solid angle increases the calculations required for accurate reconstruction of the data increase substantially. To overcome this limitation, the CUDA parallel computing platform was used which enables general purpose programming of NVIDIA graphics processing units (GPUs) to perform computations traditionally handled by the central processing unit (CPU). For simulation performance evaluation, the results of a CPU- and a CUDA-based simulation of a phantom are presented. Furthermore, a comparison with the simulation code in the PIXE-Tomography reconstruction software DISRA (A. Sakellariou, D.N. Jamieson, G.J.F. Legge, 2001) is also shown. Compared to a CPU implementation, the CUDA based simulation is approximately 30× faster.

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.

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.

Processes in KaffeOS: Isolation, Resource Management, and Sharing in Java

DTIC Science & Technology

2000-04-01

separation of garbage collection costs is not possible. Balfanz and Gong [2] describe a multi- processing JVM developed to explore the secu- rity...line in Java. In Proc. of the 7th HotOS, Rio Rico, AZ, Mar. 1999. IEEE Computer Society. [2] D. Balfanz and L. Gong. Experience with secure multi

Toward Managing & Automating CyberCIEGE Scenario Definition File Creation

DTIC Science & Technology

2004-03-01

Deitel , H & Deitel , P. (2002). Java: How to Program fourth Ed. New Jersey: Prentice Hall. [Fisher 2003] Fisher, C., Chiricosta, T. & Witherspoon, T...experience with the Java programming language. Precious time was required to learn how to implement some of the more complicated interface components...demonstrating the risks of the Internet and open networks [Irvine1 2003]. Policy is subtle, and there is no easy way to demonstrate how one small change

Large-scale Graph Computation on Just a PC

DTIC Science & Technology

2014-05-01

edges for several vertices simultaneously). We compared the performance of GraphChi-DB to Neo4j using their Java API (we discuss MySQL comparison in the...75 4.7.6 Comparison to RDBMS ( MySQL ) . . . . . . . . . . . . . . . . . . . . . 75 4.7.7 Summary of the...Windows method, GraphChi. The C++ implementation has circa 8,000 lines of code. We have also de- veloped a Java -version of GraphChi, but it does not

Mitochondrial D-loop sequence of domesticated waterfowl in Central Java: goose and muscovy duck

NASA Astrophysics Data System (ADS)

Susanti, R.; Iswari, R. S.

2018-03-01

This study aims to determine the genetic characterization of domesticated waterfowl (goose and Muscovy duck) in Central Java based on a D-loop mtDNA gene. The D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method. Multiple alignments of D-loop gene obtained were 710 nucleotides at position 74 to 783 at the 5’ end (for goose) and 712 nucleotides at position 48 to 759 at the 5’ end (for Muscovy duck). The results of the polymorphism analysis on D-loop sequences of muscovy duck produced 3 haplotypes. In the D-loop gene of goose does not show polymorphism, with substitution at G117A. Phylogenetic trees reconstructions of goose and Muscovy duck, which was collected during this research compared with another species from Anser, Chairina and Anas was generated 2 forms of clusters. The first group consists of all kind of Muscovy duck together with Chairina moschata and Anas, while the second group consists of all geese and Anser cygnoides the other. The determination of Muscovy duck and geese identity can be distinguished from the genetic marker information. Based on the phylogenetic analysis, it can be concluded that the Muscovy duck is closely related to Chairina moschata, while geese is closely related to Anser cygnoides.

Test Input Generation for Red-Black Trees using Abstraction

NASA Technical Reports Server (NTRS)

Visser, Willem; Pasareanu, Corina S.; Pelanek, Radek

2005-01-01

We consider the problem of test input generation for code that manipulates complex data structures. Test inputs are sequences of method calls from the data structure interface. We describe test input generation techniques that rely on state matching to avoid generation of redundant tests. Exhaustive techniques use explicit state model checking to explore all the possible test sequences up to predefined input sizes. Lossy techniques rely on abstraction mappings to compute and store abstract versions of the concrete states; they explore under-approximations of all the possible test sequences. We have implemented the techniques on top of the Java PathFinder model checker and we evaluate them using a Java implementation of red-black trees.

Rapid 3D bioprinting from medical images: an application to bone scaffolding

NASA Astrophysics Data System (ADS)

Lee, Daniel Z.; Peng, Matthew W.; Shinde, Rohit; Khalid, Arbab; Hong, Abigail; Pennacchi, Sara; Dawit, Abel; Sipzner, Daniel; Udupa, Jayaram K.; Rajapakse, Chamith S.

2018-03-01

Bioprinting of tissue has its applications throughout medicine. Recent advances in medical imaging allows the generation of 3-dimensional models that can then be 3D printed. However, the conventional method of converting medical images to 3D printable G-Code instructions has several limitations, namely significant processing time for large, high resolution images, and the loss of microstructural surface information from surface resolution and subsequent reslicing. We have overcome these issues by creating a JAVA program that skips the intermediate triangularization and reslicing steps and directly converts binary dicom images into G-Code. In this study, we tested the two methods of G-Code generation on the application of synthetic bone graft scaffold generation. We imaged human cadaveric proximal femurs at an isotropic resolution of 0.03mm using a high resolution peripheral quantitative computed tomography (HR-pQCT) scanner. These images, of the Digital Imaging and Communications in Medicine (DICOM) format, were then processed through two methods. In each method, slices and regions of print were selected, filtered to generate a smoothed image, and thresholded. In the conventional method, these processed images are converted to the STereoLithography (STL) format and then resliced to generate G-Code. In the new, direct method, these processed images are run through our JAVA program and directly converted to G-Code. File size, processing time, and print time were measured for each. We found that this new method produced a significant reduction in G-Code file size as well as processing time (92.23% reduction). This allows for more rapid 3D printing from medical images.

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.

PubMed

Jin, Xian; Awale, Mahendra; Zasso, Michaël; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis

2015-10-23

The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB. ᅟ

CoJACK: A High-Level Cognitive Architecture with Demonstrations of Moderators, Variability, and Implications for Situation Awareness

DTIC Science & Technology

2012-01-01

defined, to CoJACK (Ritter, Reifers, Klein, & Schoelles, 2007) based on task appraisal theory (e.g., Cannon, 1932; Lazarus & Folkman , 1984; Selye...Cambridge, MA: MIT Press. Lazarus , R. S., & Folkman , S. (1984). Stress, appraisal and coping. New York: Springer Publishing. Lovett, M. C., Daily, L...promising. 0 0.5 1 1.5 2 2.5 3 3.5 4 Java JACK Default CoJack CoJack Caffeine CoJack Challenged CoJack Threatened Agent Type Ta n k s D es tr o y e d

One dimensional P wave velocity structure of the crust beneath west Java and accurate hypocentre locations from local earthquake inversion

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

Supardiyono; Santosa, Bagus Jaya; Physics Department, Faculty of Mathematics and Natural Sciences, Sepuluh Nopember Institute of Technology, Surabaya

A one-dimensional (1-D) velocity model and station corrections for the West Java zone were computed by inverting P-wave arrival times recorded on a local seismic network of 14 stations. A total of 61 local events with a minimum of 6 P-phases, rms 0.56 s and a maximum gap of 299 Degree-Sign were selected. Comparison with previous earthquake locations shows an improvement for the relocated earthquakes. Tests were carried out to verify the robustness of inversion results in order to corroborate the conclusions drawn out from our reasearch. The obtained minimum 1-D velocity model can be used to improve routine earthquakemore » locations and represents a further step toward more detailed seismotectonic studies in this area of West Java.« less

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.

Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML).

PubMed

Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

2005-07-01

This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging.

Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML)*

PubMed Central

Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

2005-01-01

This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging. PMID:15973760

Delta agent (Hepatitis D)

MedlinePlus

... this page: //medlineplus.gov/ency/article/000216.htm Hepatitis D (Delta agent) To use the sharing features on this page, please enable JavaScript. Hepatitis D is a viral infection caused by the ...

Innovative Active Networking Services

DTIC Science & Technology

2004-03-01

implementation of the ML programming language and runtime system. OCaml offers a programming environment that can be formally analyzed; 3. University... language such as Java or OCaml . A typical PLANet (PLAN Active network) node would look as in Figure 1. The University of Kansas /ITTC 6 Innovative... language . Hence we will be discussing it alone. 2.1.2 OCaml OCaml provides several of the design goals required for a service level language . Some of

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

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

Shark: SQL and Analytics with Cost-Based Query Optimization on Coarse-Grained Distributed Memory

DTIC Science & Technology

2014-01-13

RDBMS and contains a database (often MySQL or Derby) with a namespace for tables, table metadata and partition information. Table data is stored in an...serialization/deserialization) Java interface implementations with corresponding object inspectors. The Hive driver controls the processing of queries, coordinat...native API, RDD operations are invoked through a functional interface similar to DryadLINQ [32] in Scala, Java or Python. For example, the Scala code for

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

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

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

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

PubMed

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

2012-01-01

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

FlaME: Flash Molecular Editor - a 2D structure input tool for the web.

PubMed

Dallakian, Pavel; Haider, Norbert

2011-02-01

So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions.

Utilizing Instructional Media for Teaching Infrastructure Administration

ERIC Educational Resources Information Center

Fajriah, Ulfah Nur; Churiyah, Madziatul

2016-01-01

This study aims to produce instructional media Corel VideoStudio Pro X7-based on teaching infrastructure administration at class XI of APK in SMKN 1 Ngawi, East Java, Indonesia. This study uses Research and Development research design (R & D) through 10 steps, namely: (1) the potential and problems, (2) data collection, (3) the design of the…

A new version of code Java for 3D simulation of the CCA model

NASA Astrophysics Data System (ADS)

Zhang, Kebo; Xiong, Hailing; Li, Chao

2016-07-01

In this paper we present a new version of the program of CCA model. In order to benefit from the advantages involved in the latest technologies, we migrated the running environment from JDK1.6 to JDK1.7. And the old program was optimized into a new framework, so promoted extendibility.

a Procedural Solution to Model Roman Masonry Structures

NASA Astrophysics Data System (ADS)

Cappellini, V.; Saleri, R.; Stefani, C.; Nony, N.; De Luca, L.

2013-07-01

The paper will describe a new approach based on the development of a procedural modelling methodology for archaeological data representation. This is a custom-designed solution based on the recognition of the rules belonging to the construction methods used in roman times. We have conceived a tool for 3D reconstruction of masonry structures starting from photogrammetric surveying. Our protocol considers different steps. Firstly we have focused on the classification of opus based on the basic interconnections that can lead to a descriptive system used for their unequivocal identification and design. Secondly, we have chosen an automatic, accurate, flexible and open-source photogrammetric pipeline named Pastis Apero Micmac - PAM, developed by IGN (Paris). We have employed it to generate ortho-images from non-oriented images, using a user-friendly interface implemented by CNRS Marseille (France). Thirdly, the masonry elements are created in parametric and interactive way, and finally they are adapted to the photogrammetric data. The presented application, currently under construction, is developed with an open source programming language called Processing, useful for visual, animated or static, 2D or 3D, interactive creations. Using this computer language, a Java environment has been developed. Therefore, even if the procedural modelling reveals an accuracy level inferior to the one obtained by manual modelling (brick by brick), this method can be useful when taking into account the static evaluation on buildings (requiring quantitative aspects) and metric measures for restoration purposes.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Online spectral fit tool (OSFT) for analyzing reflectance spectra

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

SMS Security System on Mobile Devices Using Tiny Encryption Algorithm

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

JMS Proxy and C/C++ Client SDK

NASA Technical Reports Server (NTRS)

Wolgast, Paul; Pechkam, Paul

2007-01-01

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

Proposal and Implementation of SSH Client System Using Ajax

NASA Astrophysics Data System (ADS)

Kosuda, Yusuke; Sasaki, Ryoichi

Technology called Ajax gives web applications the functionality and operability of desktop applications. In this study, we propose and implement a Secure Shell (SSH) client system using Ajax, independent of the OS or Java execution environment. In this system, SSH packets are generated on a web browser by using JavaScript and a web server works as a proxy in communication with an SSH server to realize end-to-end SSH communication. We implemented a prototype program and confirmed by experiment that it runs on several web browsers and mobile phones. This system has enabled secure SSH communication from a PC at an Internet cafe or any mobile phone. By measuring the processing performance, we verified satisfactory performance for emergency use, although the speed was unsatisfactory in some cases with mobile phone. The system proposed in this study will be effective in various fields of E-Business.

Distributed 3D Information Visualization - Towards Integration of the Dynamic 3D Graphics and Web Services

NASA Astrophysics Data System (ADS)

Vucinic, Dean; Deen, Danny; Oanta, Emil; Batarilo, Zvonimir; Lacor, Chris

This paper focuses on visualization and manipulation of graphical content in distributed network environments. The developed graphical middleware and 3D desktop prototypes were specialized for situational awareness. This research was done in the LArge Scale COllaborative decision support Technology (LASCOT) project, which explored and combined software technologies to support human-centred decision support system for crisis management (earthquake, tsunami, flooding, airplane or oil-tanker incidents, chemical, radio-active or other pollutants spreading, etc.). The performed state-of-the-art review did not identify any publicly available large scale distributed application of this kind. Existing proprietary solutions rely on the conventional technologies and 2D representations. Our challenge was to apply the "latest" available technologies, such Java3D, X3D and SOAP, compatible with average computer graphics hardware. The selected technologies are integrated and we demonstrate: the flow of data, which originates from heterogeneous data sources; interoperability across different operating systems and 3D visual representations to enhance the end-users interactions.

Helios: a Multi-Purpose LIDAR Simulation Framework for Research, Planning and Training of Laser Scanning Operations with Airborne, Ground-Based Mobile and Stationary Platforms

NASA Astrophysics Data System (ADS)

Bechtold, S.; Höfle, B.

2016-06-01

In many technical domains of modern society, there is a growing demand for fast, precise and automatic acquisition of digital 3D models of a wide variety of physical objects and environments. Laser scanning is a popular and widely used technology to cover this demand, but it is also expensive and complex to use to its full potential. However, there might exist scenarios where the operation of a real laser scanner could be replaced by a computer simulation, in order to save time and costs. This includes scenarios like teaching and training of laser scanning, development of new scanner hardware and scanning methods, or generation of artificial scan data sets to support the development of point cloud processing and analysis algorithms. To test the feasibility of this idea, we have developed a highly flexible laser scanning simulation framework named Heidelberg LiDAR Operations Simulator (HELIOS). HELIOS is implemented as a Java library and split up into a core component and multiple extension modules. Extensible Markup Language (XML) is used to define scanner, platform and scene models and to configure the behaviour of modules. Modules were developed and implemented for (1) loading of simulation assets and configuration (i.e. 3D scene models, scanner definitions, survey descriptions etc.), (2) playback of XML survey descriptions, (3) TLS survey planning (i.e. automatic computation of recommended scanning positions) and (4) interactive real-time 3D visualization of simulated surveys. As a proof of concept, we show the results of two experiments: First, a survey planning test in a scene that was specifically created to evaluate the quality of the survey planning algorithm. Second, a simulated TLS scan of a crop field in a precision farming scenario. The results show that HELIOS fulfills its design goals.

Initial experiences with building a health care infrastructure based on Java and object-oriented database technology.

PubMed

Dionisio, J D; Sinha, U; Dai, B; Johnson, D B; Taira, R K

1999-01-01

A multi-tiered telemedicine system based on Java and object-oriented database technology has yielded a number of practical insights and experiences on their effectiveness and suitability as implementation bases for a health care infrastructure. The advantages and drawbacks to their use, as seen within the context of the telemedicine system's development, are discussed. Overall, these technologies deliver on their early promise, with a few remaining issues that are due primarily to their relative newness.

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

Dr. George L. Mesina; Steven P. Miller

The XMGR5 graphing package [1] for drawing RELAP5 [2] plots is being re-written in Java [3]. Java is a robust programming language that is available at no cost for most computer platforms from Sun Microsystems, Inc. XMGR5 is an extension of an XY plotting tool called ACE/gr extended to plot data from several US Nuclear Regulatory Commission (NRC) applications. It is also the most popular graphing package worldwide for making RELAP5 plots. In Section 1, a short review of XMGR5 is given, followed by a brief overview of Java. In Section 2, shortcomings of both tkXMGR [4] and XMGR5 aremore » discussed and the value of converting to Java is given. Details of the conversion to Java are given in Section 3. The progress to date, some conclusions and future work are given in Section 4. Some screen shots of the Java version are shown.« less

Coalbed methane: A partial solution to Indonesia`s growing energy problems

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

Murray, D.K.; Gold, J.P.

1995-04-01

Indonesia contains the largest resources of coal in Southeast Asia. Indonesian scientists estimate that the in-place coalbed methane resource in 16 onshore basins is about 213 Tcf ({approximately}6 Tcm). This volume is approximately double Indonesia`s current reserves of natural gas. Indonesia is a rapidly industrializing nation of 186 million people, of which 111 million live in Java and 38 million in Sumatra. As industrialization progresses from the present low level, the growth in energy demand will be very rapid. Indonesia`s domestic gas demand is expected to increase form 1.6 Bcf/d (0.05 Bcm/d) in 1991 to 5.7 Bcf/d (0.2 Bcm/d) inmore » 2021. Because the major gas resources of East Kalimantan, North Sumatra, and Natuna are so remote from the main consuming area in northwest Java and are dedicated for export by virtue of the national energy policy, the need is becoming urgent to develop new resources of natural gas, including coalbed methane, for the domestic market. Due to the high geothermal gradient, the coal deposits in the back-arc basins of Sumatra and Java are expected to be of higher than normal rank at depths favorable for coalbed methane production. The oil- and gas-productive Jatibarang sub-basin in northwest Java, with estimated in-place resources of coalbed methane in excess of 20 Tcf (0.6 Tcm), is considered to be the most prospective area in Indonesia for the near-term development of coalbed methane. This area includes Jakarta and vicinity, the most populous and most heavily industrialized part of Indonesia.« less

Performance Management of High Performance Computing for Medical Image Processing in Amazon Web Services.

PubMed

Bao, Shunxing; Damon, Stephen M; Landman, Bennett A; Gokhale, Aniruddha

2016-02-27

Adopting high performance cloud computing for medical image processing is a popular trend given the pressing needs of large studies. Amazon Web Services (AWS) provide reliable, on-demand, and inexpensive cloud computing services. Our research objective is to implement an affordable, scalable and easy-to-use AWS framework for the Java Image Science Toolkit (JIST). JIST is a plugin for Medical-Image Processing, Analysis, and Visualization (MIPAV) that provides a graphical pipeline implementation allowing users to quickly test and develop pipelines. JIST is DRMAA-compliant allowing it to run on portable batch system grids. However, as new processing methods are implemented and developed, memory may often be a bottleneck for not only lab computers, but also possibly some local grids. Integrating JIST with the AWS cloud alleviates these possible restrictions and does not require users to have deep knowledge of programming in Java. Workflow definition/management and cloud configurations are two key challenges in this research. Using a simple unified control panel, users have the ability to set the numbers of nodes and select from a variety of pre-configured AWS EC2 nodes with different numbers of processors and memory storage. Intuitively, we configured Amazon S3 storage to be mounted by pay-for-use Amazon EC2 instances. Hence, S3 storage is recognized as a shared cloud resource. The Amazon EC2 instances provide pre-installs of all necessary packages to run JIST. This work presents an implementation that facilitates the integration of JIST with AWS. We describe the theoretical cost/benefit formulae to decide between local serial execution versus cloud computing and apply this analysis to an empirical diffusion tensor imaging pipeline.

Performance management of high performance computing for medical image processing in Amazon Web Services

NASA Astrophysics Data System (ADS)

Bao, Shunxing; Damon, Stephen M.; Landman, Bennett A.; Gokhale, Aniruddha

2016-03-01

Adopting high performance cloud computing for medical image processing is a popular trend given the pressing needs of large studies. Amazon Web Services (AWS) provide reliable, on-demand, and inexpensive cloud computing services. Our research objective is to implement an affordable, scalable and easy-to-use AWS framework for the Java Image Science Toolkit (JIST). JIST is a plugin for Medical- Image Processing, Analysis, and Visualization (MIPAV) that provides a graphical pipeline implementation allowing users to quickly test and develop pipelines. JIST is DRMAA-compliant allowing it to run on portable batch system grids. However, as new processing methods are implemented and developed, memory may often be a bottleneck for not only lab computers, but also possibly some local grids. Integrating JIST with the AWS cloud alleviates these possible restrictions and does not require users to have deep knowledge of programming in Java. Workflow definition/management and cloud configurations are two key challenges in this research. Using a simple unified control panel, users have the ability to set the numbers of nodes and select from a variety of pre-configured AWS EC2 nodes with different numbers of processors and memory storage. Intuitively, we configured Amazon S3 storage to be mounted by pay-for- use Amazon EC2 instances. Hence, S3 storage is recognized as a shared cloud resource. The Amazon EC2 instances provide pre-installs of all necessary packages to run JIST. This work presents an implementation that facilitates the integration of JIST with AWS. We describe the theoretical cost/benefit formulae to decide between local serial execution versus cloud computing and apply this analysis to an empirical diffusion tensor imaging pipeline.

Performance Management of High Performance Computing for Medical Image Processing in Amazon Web Services

PubMed Central

Bao, Shunxing; Damon, Stephen M.; Landman, Bennett A.; Gokhale, Aniruddha

2016-01-01

Adopting high performance cloud computing for medical image processing is a popular trend given the pressing needs of large studies. Amazon Web Services (AWS) provide reliable, on-demand, and inexpensive cloud computing services. Our research objective is to implement an affordable, scalable and easy-to-use AWS framework for the Java Image Science Toolkit (JIST). JIST is a plugin for Medical-Image Processing, Analysis, and Visualization (MIPAV) that provides a graphical pipeline implementation allowing users to quickly test and develop pipelines. JIST is DRMAA-compliant allowing it to run on portable batch system grids. However, as new processing methods are implemented and developed, memory may often be a bottleneck for not only lab computers, but also possibly some local grids. Integrating JIST with the AWS cloud alleviates these possible restrictions and does not require users to have deep knowledge of programming in Java. Workflow definition/management and cloud configurations are two key challenges in this research. Using a simple unified control panel, users have the ability to set the numbers of nodes and select from a variety of pre-configured AWS EC2 nodes with different numbers of processors and memory storage. Intuitively, we configured Amazon S3 storage to be mounted by pay-for-use Amazon EC2 instances. Hence, S3 storage is recognized as a shared cloud resource. The Amazon EC2 instances provide pre-installs of all necessary packages to run JIST. This work presents an implementation that facilitates the integration of JIST with AWS. We describe the theoretical cost/benefit formulae to decide between local serial execution versus cloud computing and apply this analysis to an empirical diffusion tensor imaging pipeline. PMID:27127335

Acoustic Metadata Management and Transparent Access to Networked Oceanographic Data Sets

DTIC Science & Technology

2013-09-30

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

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.

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

DTIC Science & Technology

2014-10-01

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

A GIS Based 3D Online Decision Assistance System for Underground Energy Storage in Northern Germany

NASA Astrophysics Data System (ADS)

Nolde, M.; Schwanebeck, M.; Biniyaz, E.; Duttmann, R.

2014-12-01

We would like to present a GIS-based 3D online decision assistance system for underground energy storage. Its aim is to support the local land use planning authorities through pre-selection of possible sites for thermal, electrical and substantial underground energy storages. Since the extension of renewable energies has become legal requirement in Germany, the underground storing of superfluously produced green energy (such as during a heavy wind event) in the form of compressed air, gas or heated water has become increasingly important. However, the selection of suitable sites is a complex task. The assistance system uses data of geological features such as rock layers, salt caverns and faults enriched with attribute data such as rock porosity and permeability. This information is combined with surface data of the existing energy infrastructure, such as locations of wind and biogas stations, power line arrangement and cable capacity, and energy distribution stations. Furthermore, legal obligations such as protected areas on the surface and current underground mining permissions are used for the decision finding process. Not only the current situation but also prospective scenarios, such as expected growth in produced amount of energy are incorporated in the system. The decision process is carried out via the 'Analytic Hierarchy Process' (AHP) methodology of the 'Multi Object Decision Making' (MODM) approach. While the process itself is completely automated, the user has full control of the weighting of the different factors via the web interface. The system is implemented as an online 3D server GIS environment, with no software needed to be installed on the user side. The results are visualized as interactive 3d graphics. The implementation of the assistance system is based exclusively on free and open source software, and utilizes the 'Python' programming language in combination with current web technologies, such as 'HTML5', 'CSS3' and 'JavaScript'. It is developed at Kiel University for the federal state of Schleswig-Holstein in northern Germany. This work is part of project 'ANGUS+', lead by Prof. Dr. Sebastian Bauer and funded by the German Ministry for Education and Research (BMBF).

A Case Study: The Potential of Energy Efficiency in Senior High School of Semarang Regency, Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Yustika, Ana; Purwanto; Hermawan, H.

2018-02-01

The increasing of energy supply trend in Indonesia seems to be a serious problem in the implementation of sustainable development. This study case research aimed to determine the potential of energy efficiency in school environment. The subject of this research was SMA N 1 Ambarawa, located on Semarang Regency of Central Java, Indonesia. The data collection was done by used documentation, observation and interview method. The results showed that the average of electrical energy consumption in this school reached 11022.008 kWh/month, which resulted in the emergence of secondary emissions of CO2 by 9644.257 kg CO2/month. Overall, the consumption of electrical energy in this school was very efficient, with an Intensity of Energy Consumption (IEC) average 1.7957 kWh/m2/month. In this case, the implementation of short-term no cost, long-term no cost, middle-cost, short-term high cost and long-term high-cost recommendation could save electricity energy sequent by 3.159%; 7.536%; 9.499%; 35.278% - 36.626%; and 42.084%. In conclusion, the school environment had a big potential of energy efficiency that could reduce the energy consumption and CO2 gas emissions.

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.

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.

Developing On-line Exams.

ERIC Educational Resources Information Center

Hartsell, Taralynn S.; Yuen, Steve Chi-Yin

2003-01-01

Discusses advantages and limitations of online exams, describes available software tools for creating computer-based tests (CGI, JavaScript, commercial programs, course authoring tools), and offers suggestions for implementation. (JOW)

Environmental Management Model for Road Maintenance Operation Involving Community Participation

NASA Astrophysics Data System (ADS)

Triyono, A. R. H.; Setyawan, A.; Sobriyah; Setiono, P.

2017-07-01

Public expectations of Central Java, which is very high on demand fulfillment, especially road infrastructure as outlined in the number of complaints and community expectations tweeter, Short Mail Massage (SMS), e-mail and public reports from various media, Highways Department of Central Java province requires development model of environmental management in the implementation of a routine way by involving the community in order to fulfill the conditions of a representative, may serve road users safely and comfortably. This study used survey method with SEM analysis and SWOT with Latent Independent Variable (X), namely; Public Participation in the regulation, development, construction and supervision of road (PSM); Public behavior in the utilization of the road (PMJ) Provincial Road Service (PJP); Safety in the Provincial Road (KJP); Integrated Management System (SMT) and latent dependent variable (Y) routine maintenance of the provincial road that is integrated with the environmental management system and involve the participation of the community (MML). The result showed the implementation of routine maintenance of road conditions in Central Java province has yet to implement an environmental management by involving the community; Therefore developed environmental management model with the results of H1: Community Participation (PSM) has positive influence on the Model of Environmental Management (MML); H2: Behavior Society in Jalan Utilization (PMJ) positive effect on Model Environmental Management (MML); H3: Provincial Road Service (PJP) positive effect on Model Environmental Management (MML); H4: Safety in the Provincial Road (KJP) positive effect on Model Environmental Management (MML); H5: Integrated Management System (SMT) has positive influence on the Model of Environmental Management (MML). From the analysis obtained formulation model describing the relationship / influence of the independent variables PSM, PMJ, PJP, KJP, and SMT on the dependent variable MML as follows: MML = 0.13 + 0.07 PSM PJP PMJ + 0.09 + 0.19 + 0.48 KJP SMT + e

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.

Pointer Animation Implementation at Development of Multimedia Learning of Java Programming

ERIC Educational Resources Information Center

Rusli, Muhammad; Atmojo, Yohanes Priyo

2015-01-01

This research represents the development research using the references of previous research results related to the development of interactive multimedia learning (learner controlled), specially about the effectiveness and efficiency of multimedia learning of a content that developed by pointer animation implementation showing the content in…

Polymorphous Computing Architectures

DTIC Science & Technology

2007-12-12

provide a multiprocessor implementation. In this work, we introduce the Atomos transactional programming language, which is the first to include...implicit transactions, strong atomicity, and a scalable multiprocessor implementation [47]. Atomos is derived from Java, but replaces its synchronization...and conditional waiting constructs with transactional alternatives. The Atomos conditional waiting proposal is tailored to allow efficient

The implement of Talmud property allocation algorithm based on graphic point-segment way

NASA Astrophysics Data System (ADS)

Cen, Haifeng

2017-04-01

Under the guidance of the Talmud allocation scheme's theory, the paper analyzes the algorithm implemented process via the perspective of graphic point-segment way, and designs the point-segment way's Talmud property allocation algorithm. Then it uses Java language to implement the core of allocation algorithm, by using Android programming to build a visual interface.

Simulation for Dynamic Situation Awareness and Prediction III

DTIC Science & Technology

2010-03-01

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

Hardware Assisted Stealthy Diversity (CHECKMATE)

DTIC Science & Technology

2013-09-01

applicable across multiple architectures. Figure 29 shows an example an attack against an interpreted environment with a Java executable. CHECKMATE can...Architectures ARM PPCx86 Java VM Java VMJava VM Java Executable Attack APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED 33 a user executes “/usr/bin/wget...Server 1 - Administration Server 2 – Database ( mySQL ) Server 3 – Web server (Mongoose) Server 4 – File server (SSH) Server 5 – Email server

Towards a 3d Based Platform for Cultural Heritage Site Survey and Virtual Exploration

NASA Astrophysics Data System (ADS)

Seinturier, J.; Riedinger, C.; Mahiddine, A.; Peloso, D.; Boï, J.-M.; Merad, D.; Drap, P.

2013-07-01

This paper present a 3D platform that enables to make both cultural heritage site survey and its virtual exploration. It provides a single and easy way to use framework for merging multi scaled 3D measurements based on photogrammetry, documentation produced by experts and the knowledge of involved domains leaving the experts able to extract and choose the relevant information to produce the final survey. Taking into account the interpretation of the real world during the process of archaeological surveys is in fact the main goal of a survey. New advances in photogrammetry and the capability to produce dense 3D point clouds do not solve the problem of surveys. New opportunities for 3D representation are now available and we must to use them and find new ways to link geometry and knowledge. The new platform is able to efficiently manage and process large 3D data (points set, meshes) thanks to the implementation of space partition methods coming from the state of the art such as octrees and kd-trees and thus can interact with dense point clouds (thousands to millions of points) in real time. The semantisation of raw 3D data relies on geometric algorithms such as geodetic path computation, surface extraction from dense points cloud and geometrical primitive optimization. The platform provide an interface that enables expert to describe geometric representations of interesting objects like ashlar blocs, stratigraphic units or generic items (contour, lines, … ) directly onto the 3D representation of the site and without explicit links to underlying algorithms. The platform provide two ways for describing geometric representation. If oriented photographs are available, the expert can draw geometry on a photograph and the system computes its 3D representation by projection on the underlying mesh or the points cloud. If photographs are not available or if the expert wants to only use the 3D representation then he can simply draw objects shape on it. When 3D representations of objects of a surveyed site are extracted from the mesh, the link with domain related documentation is done by means of a set of forms designed by experts. Information from these forms are linked with geometry such that documentation can be attached to the viewed objects. Additional semantisation methods related to specific domains have been added to the platform. Beyond realistic rendering of surveyed site, the platform embeds non photorealistic rendering (NPR) algorithms. These algorithms enable to dynamically illustrate objects of interest that are related to knowledge with specific styles. The whole platform is implemented with a Java framework and relies on an actual and effective 3D engine that make available latest rendering methods. We illustrate this work on various photogrammetric survey, in medieval archaeology with the Shawbak castle in Jordan and in underwater archaeology on different marine sites.

A Comparative Study on Java Technologies for Focus and Cursor Handling in Accessible Dynamic Interactions.

PubMed

Jitngernmadan, Prajaks; Miesenberger, Klaus

2015-01-01

For an interactive application, supporting and guiding the user in fulfilling tasks is most important. The behavior of the application that will guide users through the procedures until they finish the task has to be designed intuitively and well guiding, especially if the users has only restricted or no access to the visual and spatial arrangement on the screen. Therefore, the focus/cursor management plays an important role for orientation and navigating through the interaction. In the frame of ongoing research on a software tool supporting blind people in more efficiently doing mathematical calculations, we researched how Java technologies support implementing an accessible Graphical User Interface (GUI) with an additional focus on usable accessibility in terms of guiding blind users through the process of solving mathematical calculations. We used Java Swing [1] and Eclipse SWT [2] APIs for creating a series of prototypes. We tested a) accessibility and usability of the prototypes for blind people when using screen reader software and refreshable Braille display and b) the implementation support to developers provided by both technologies. It turned out that Eclipse SWT API delivered best results under Windows operating system.

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

PubMed

Pirooznia, Mehdi; Deng, Youping

2006-12-12

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

Interactive Vulnerability Analysis Enhancement Results

DTIC Science & Technology

2012-12-01

from JavaEE web based applications to other non-web based Java programs. Technology developed in this effort should be generally applicable to other...Generating a rule is a 2 click process that requires no input from the user. • Task 3: Added support for non- Java EE applications Aspect’s...investigated a variety of Java -based technologies and how IAST can support them. We were successful in adding support for Scala, a popular new language, and

Generalisation and extension of a web-based data collection system for clinical studies using Java and CORBA.

PubMed

Eich, H P; Ohmann, C

1999-01-01

Inadequate informatical support of multi-centre clinical trials lead to pure quality. In order to support a multi-centre clinical trial a data collection via WWW and Internet based on Java has been developed. In this study a generalization and extension of this prototype has been performed. The prototype has been applied to another clinical trial and a knowledge server based on C+t has been integrated via CORBA. The investigation and implementation of security aspects of web-based data collection is now under evaluation.

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.

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.

Hydrological information system based on on-line monitoring--from strategy to implementation in the Brantas River Basin, East Java, Indonesia.

PubMed

Marini, G W; Wellguni, H

2003-01-01

The worsening environmental situation of the Brantas River, East Java, is addressed by a comprehensive basin management strategy which relies on accurate water quantity and quality data retrieved from a newly installed online monitoring network. Integrated into a Hydrological Information System, the continuously measured indicative parameters allow early warning, control and polluter identification. Additionally, long-term analyses have been initiated for improving modelling applications like flood forecasting, water resource management and pollutant propagation. Preliminary results illustrate the efficiency of the installed system.

Reducing software security risk through an integrated approach

NASA Technical Reports Server (NTRS)

Gilliam, D.; Powell, J.; Kelly, J.; Bishop, M.

2001-01-01

The fourth quarter delivery, FY'01 for this RTOP is a Property-Based Testing (PBT), 'Tester's Assistant' (TA). The TA tool is to be used to check compiled and pre-compiled code for potential security weaknesses that could be exploited by hackers. The TA Instrumenter, implemented mostly in C++ (with a small part in Java), parsels two types of files: Java and TASPEC. Security properties to be checked are written in TASPEC. The Instrumenter is used in conjunction with the Tester's Assistant Specification (TASpec)execution monitor to verify the security properties of a given program.

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/

The Implementation of Schools' Policy in the Development of the Local Content Curriculum in Primary Schools in Pacitan, Indonesia

ERIC Educational Resources Information Center

Maryono

2016-01-01

This study aims to describe the culture and local potential in Pacitan, East Java, as well as the implementation of local content in primary schools in the area, and some factors that support and hinder their implementation. This research is a qualitative case study. There were five primary schools used as samples obtained through purposive…

[Establishment of the database of the 3D facial models for the plastic surgery based on network].

PubMed

Liu, Zhe; Zhang, Hai-Lin; Zhang, Zheng-Guo; Qiao, Qun

2008-07-01

To collect the three-dimensional (3D) facial data of 30 facial deformity patients by the 3D scanner and establish a professional database based on Internet. It can be helpful for the clinical intervention. The primitive point data of face topography were collected by the 3D scanner. Then the 3D point cloud was edited by reverse engineering software to reconstruct the 3D model of the face. The database system was divided into three parts, including basic information, disease information and surgery information. The programming language of the web system is Java. The linkages between every table of the database are credibility. The query operation and the data mining are convenient. The users can visit the database via the Internet and use the image analysis system to observe the 3D facial models interactively. In this paper we presented a database and a web system adapt to the plastic surgery of human face. It can be used both in clinic and in basic research.

An object-oriented watershed management tool (QnD-VFS) to engage stakeholders in targeted implementation of filter strips in an arid surface irrigation area

NASA Astrophysics Data System (ADS)

Campo, M. A.; Perez-Ovilla, O.; Munoz-Carpena, R.; Kiker, G.; Ullman, J. L.

2012-12-01

Agricultural nonpoint source pollution cause the majority of the 1,224 different waterbodies failing to meet designated water use criteria in Washington. Although various best management practices (BMPs) are effective in mitigating agricultural pollutants, BMP placement is often haphazard and fails to address specific high-risk locations. Limited financial resources necessitate optimization of conservation efforts to meet water quality goals. Thus, there is a critical need to develop decision-making tools that target BMP implementation in order to maximize water quality protection. In addition to field parameters, it is essential to incorporate economic and social determinants in the decision-making process to encourage producer involvement. Decision-making tools that identify strategic pollution sources and integrate socio-economic factors will lead to more cost-effective water quality improvement, as well as encourage producer participation by incorporating real-world limitations. Therefore, this study examines vegetative filter strip use under different scenarios as a BMP to mitigate sediment and nutrients in the highly irrigated Yakima River Basin of central Washington. We developed QnD-VFS to integrate and visualize alternative, spatially-explicit, water management strategies and its economic impact. The QnDTM system was created as a decision education tool that incorporates management, economic, and socio- political issues in a user-friendly scenario framework. QnDTM, which incorporates elements of Multi-Criteria Decision Analysis (MCDA) and risk assessment, is written in object-oriented Java and can be deployed as a stand-alone program or a web-accessed tool. The model performs Euler numerical integration of various rate transformation and mass-balance transfer equations. The novelty of this object-oriented approach is that these differential equations are detailed in modular XML format for instantiation within the Java code. This design allows many levels of complexity to be quickly designed and rendered in QnDTM without time-consuming additions of new Java code. Thus, temporal and spatial scales used in the equations become part of model development and iteration. A salient aspect is that QnDTM links spatial components within GIS (ArcInfo Shape) files to the abiotic (e.g., climate), biotic and chemical/contaminant interactions. QnD-VFS integrates environmental, management and socio-economic/cultural factors identified through stakeholder input. Several scenarios have been studied. Thus one of the main results show that changing water management, improved irrigation, is equivalent to changing length of vegetative filter strips, with a low economic impacts for farmers. Concurrently, these interactive tools allow resource managers to identify economic and social determinants that may impede conservation efforts.

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

Newman, T. S.; Wang, C.; Gallagher, D. L.

2005-12-01

A suite of tools that enable discovery of terrestrial plasmasphere characteristics from NASA IMAGE Extreme Ultra Violet (EUV) images is described. The tool suite is web-accessible, allowing easy remote access without the need for any software installation on the user's computer. The features supported by the tool include reconstruction of the plasmasphere plasma density distribution from a short sequence of EUV images, semi-automated selection of the plasmapause boundary in an EUV image, and mapping of the selected boundary to the geomagnetic equatorial plane. EUV image upload and result download is also supported. The tool suite's plasmapause mapping feature is achieved via the Roelof and Skinner (2000) Edge Algorithm. The plasma density reconstruction is achieved through a tomographic technique that exploits physical constraints to allow for a moderate resolution result. The tool suite's software architecture uses Java Server Pages (JSP) and Java Applets on the front side for user-software interaction and Java Servlets on the server side for task execution. The compute-intensive components of the tool suite are implemented in C++ and invoked by the server via Java Native Interface (JNI).

Collection of process data after cardiac surgery: initial implementation with a Java-based intranet applet.

PubMed

Ratcliffe, M B; Khan, J H; Magee, K M; McElhinney, D B; Hubner, C

2000-06-01

Using a Java-based intranet program (applet), we collected postoperative process data after coronary artery bypass grafting. A Java-based applet was developed and deployed on a hospital intranet. Briefly, the nurse entered patient process data using a point and click interface. The applet generated a nursing note, and process data were saved in a Microsoft Access database. In 10 patients, this method was validated by comparison with a retrospective chart review. In 45 consecutive patients, weekly control charts were generated from the data. When aberrations from the pathway occurred, feedback was initiated to restore the goals of the critical pathway. The intranet process data collection method was verified by a manual chart review with 98% sensitivity. The control charts for time to extubation, intensive care unit stay, and hospital stay showed a deviation from critical pathway goals after the first 20 patients. Feedback modulation was associated with a return to critical pathway goals. Java-based applets are inexpensive and can collect accurate postoperative process data, identify critical pathway deviations, and allow timely feedback of process data.

Network Application Server Using Extensible Mark-Up Language (XML) to Support Distributed Databases and 3D Environments

DTIC Science & Technology

2001-12-01

diides.ncr.disa.mil/xmlreg/user/index.cfm] [ Deitel ] Deitel , H., Deitel , P., Java How to Program 3rd Edition, Prentice Hall, 1999. [DL99...presentation, and data) of information and the programming functionality. The Web framework addressed ability to provide a framework for the distribution...BLANK v ABSTRACT Advances in computer communication technology and an increased awareness of how enhanced information access can lead to improved

Contamination Analysis Tools

NASA Technical Reports Server (NTRS)

Brieda, Lubos

2015-01-01

This talk presents 3 different tools developed recently for contamination analysis:HTML QCM analyzer: runs in a web browser, and allows for data analysis of QCM log filesJava RGA extractor: can load in multiple SRS.ana files and extract pressure vs. time dataC++ Contamination Simulation code: 3D particle tracing code for modeling transport of dust particulates and molecules. Uses residence time to determine if molecules stick. Particulates can be sampled from IEST-STD-1246 and be accelerated by aerodynamic forces.

E2GPR - Edit your geometry, Execute GprMax2D and Plot the Results!

NASA Astrophysics Data System (ADS)

Pirrone, Daniele; Pajewski, Lara

2015-04-01

In order to predict correctly the Ground Penetrating Radar (GPR) response from a particular scenario, Maxwell's equations have to be solved, subject to the physical and geometrical properties of the considered problem and to its initial conditions. Several techniques have been developed in computational electromagnetics, for the solution of Maxwell's equations. These methods can be classified into two main categories: differential and integral equation solvers, which can be implemented in the time or spectral domain. All of the different methods present compromises between computational efficiency, stability, and the ability to model complex geometries. The Finite-Difference Time-Domain (FDTD) technique has several advantages over alternative approaches: it has inherent simplicity, efficiency and conditional stability; it is suitable to treat impulsive behavior of the electromagnetic field and can provide either ultra-wideband temporal waveforms or the sinusoidal steady-state response at any frequency within the excitation spectrum; it is accurate and highly versatile; and it has become a mature and well-researched technique. Moreover, the FDTD technique is suitable to be executed on parallel-processing CPU-based computers and to exploit the modern computer visualisation capabilities. GprMax [1] is a very well-known and largely validated FDTD software tool, implemented by A. Giannopoulos and available for free public download on www.gprmax.com, together with examples and a detailled user guide. The tool includes two electromagnetic wave simulators, GprMax2D and GprMax3D, for the full-wave simulation of two-dimensional and three-dimensional GPR models. In GprMax, everything can be done with the aid of simple commands that are used to define the model parameters and results to be calculated. These commands need to be entered in a simple ASCII text file. GprMax output files can be stored in ASCII or binary format. The software is provided with MATLAB functions, which can be employed to import synthetic data created by GprMax using the binary-format option into MATLAB, in order to be processed and/or visualized. Further MATLAB procedures for the visualization of GprMax synthetic data have been developed within the COST Action TU1208 [2] and are available for free public download on www.GPRadar.eu. The current version of GprMax3D is compiled with OpenMP, supporting multi-platform shared memory multiprocessing which allows GprMax3D to take advantage of multiple cores/CPUs. GprMax2D, instead, exploits a single core when executed. E2GPR is a new software tool, available free of charge for both academic and commercial use, conceived to: 1) assist in the creation, modification and analysis of GprMax2D models, through a Computer-Aided Design (CAD) system; 2) allow parallel and/or distributed computing with GprMax2D, on a network of computers; 3) automatically plot A-scans and B-scans generated by GprMax2D. The CAD and plotter parts of the tool are implemented in Java and can run on any Java Virtual Machine (JVM) regardless of computer architecture. The part of the tool devoted to supporting parallel and/or distributed computing, instead, requires the set up of a Web-Service (on a server emulator or server); in fact, it is currently configured only for Windows Server and Internet Information Services (IIS). In this work, E2GPR is presented and examples are provided which demonstrate its use. The tool can be currently obtained by contacting the authors. It will soon be possible to download it from www.GPRadar.eu. Acknowledgement This work is a contribution to the COST Action TU1208 'Civil Engineering Applications of Ground Penetrating Radar.' The authors thank COST for funding the Action TU1208. References [1] A. Giannopoulos, 'Modelling ground penetrating radar by GprMax,' Construction and Building Materials, vol. 19, pp. 755-762, 2005. [2] L. Pajewski, A. Benedetto, X. Dérobert, A. Giannopoulos, A. Loizos, G. Manacorda, M. Marciniak, C. Plati, G. Schettini, I. Trinks, "Applications of Ground Penetrating Radar in Civil Engineering - COST Action TU1208," Proc. 7th International Workshop on Advanced Ground Penetrating Radar (IWAGPR), 2-5 July 2013, Nantes, France, pp. 1-6.

Automatic Web-based Calibration of Network-Capable Shipboard Sensors

DTIC Science & Technology

2007-09-01

Server, Java , Applet, and Servlet . 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT Unclassified 18. SECURITY CLASSIFICATION OF THIS PAGE...49 b. Sensor Applet...........................................................................49 3. Java Servlet ...Table 1. Required System Environment Variables for Java Servlet Development. ......25 Table 2. Payload Data Format of the POST Requests from

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.

Building generic anatomical models using virtual model cutting and iterative registration.

PubMed

Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W

2010-02-08

Using 3D generic models to statistically analyze trends in biological structure changes is an important tool in morphometrics research. Therefore, 3D generic models built for a range of populations are in high demand. However, due to the complexity of biological structures and the limited views of them that medical images can offer, it is still an exceptionally difficult task to quickly and accurately create 3D generic models (a model is a 3D graphical representation of a biological structure) based on medical image stacks (a stack is an ordered collection of 2D images). We show that the creation of a generic model that captures spatial information exploitable in statistical analyses is facilitated by coupling our generalized segmentation method to existing automatic image registration algorithms. The method of creating generic 3D models consists of the following processing steps: (i) scanning subjects to obtain image stacks; (ii) creating individual 3D models from the stacks; (iii) interactively extracting sub-volume by cutting each model to generate the sub-model of interest; (iv) creating image stacks that contain only the information pertaining to the sub-models; (v) iteratively registering the corresponding new 2D image stacks; (vi) averaging the newly created sub-models based on intensity to produce the generic model from all the individual sub-models. After several registration procedures are applied to the image stacks, we can create averaged image stacks with sharp boundaries. The averaged 3D model created from those image stacks is very close to the average representation of the population. The image registration time varies depending on the image size and the desired accuracy of the registration. Both volumetric data and surface model for the generic 3D model are created at the final step. Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease. Java-based implementation allows our method to be used on various visualization systems including personal computers, workstations, computers equipped with stereo displays, and even virtual reality rooms such as the CAVE Automated Virtual Environment. The technique allows biologists to build generic 3D models of their interest quickly and accurately.

Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities.

PubMed

Covington, Kelsie; McCreedy, Evan S; Chen, Min; Carass, Aaron; Aucoin, Nicole; Landman, Bennett A

2010-05-25

Clinical research with medical imaging typically involves large-scale data analysis with interdependent software toolsets tied together in a processing workflow. Numerous, complementary platforms are available, but these are not readily compatible in terms of workflows or data formats. Both image scientists and clinical investigators could benefit from using the framework which is a most natural fit to the specific problem at hand, but pragmatic choices often dictate that a compromise platform is used for collaboration. Manual merging of platforms through carefully tuned scripts has been effective, but exceptionally time consuming and is not feasible for large-scale integration efforts. Hence, the benefits of innovation are constrained by platform dependence. Removing this constraint via integration of algorithms from one framework into another is the focus of this work. We propose and demonstrate a light-weight interface system to expose parameters across platforms and provide seamless integration. In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer. We explore three case studies: (1) providing a system for MIPAV to expose internal algorithms and utilize these algorithms within JIST, (2) exposing JIST modules through self-documenting command line interface for inclusion in scripting environments, and (3) detecting and using JIST modules in 3D Slicer. We review the challenges and opportunities for light-weight software integration both within development language (e.g., Java in MIPAV and JIST) and across languages (e.g., C/C++ in 3D Slicer and shell in command line tools).

Assembling Components with Aspect-Oriented Modeling/Specification

DTIC Science & Technology

2003-10-01

2 COM: Component Object Mod 3 EJB: Enterprise Java Beans, h 4 CCM: CORBA® Component M 5 http...nt (GM of the co mbly of ct weav el, http: ttp:// java odel, htFigure 2: Connector as a Containertructure in the form of framework, which...assembles components in EJB3 , CCM4; or a package, using such way as manifest file to JavaBeans5. Also such connector in some cases plays the role as

IBS: an illustrator for the presentation and visualization of biological sequences

PubMed Central

Liu, Wenzhong; Xie, Yubin; Ma, Jiyong; Luo, Xiaotong; Nie, Peng; Zuo, Zhixiang; Lahrmann, Urs; Zhao, Qi; Zheng, Yueyuan; Zhao, Yong; Xue, Yu; Ren, Jian

2015-01-01

Summary: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26069263

77 FR 10358 - Investment Adviser Performance Compensation

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-22

...?SelectedTable=64&ViewSeries=NO&Java=no&Request3Place=N&3Place=N&FromView=YES&Freq=Year&FirstYear=1997&LastYear=2010&3Place=N&Update=Update&JavaBox=no#Mid . \\27\\ Rule 205-3(e) provides that the assets-under...

WEB-IS2: Next Generation Web Services Using Amira Visualization Package

NASA Astrophysics Data System (ADS)

Yang, X.; Wang, Y.; Bollig, E. F.; Kadlec, B. J.; Garbow, Z. A.; Yuen, D. A.; Erlebacher, G.

2003-12-01

Amira (www.amiravis.com) is a powerful 3-D visualization package and has been employed recently by the science and engineering communities to gain insight into their data. We present a new web-based interface to Amira, packaged in a Java applet. We have developed a module called WEB-IS/Amira (WEB-IS2), which provides web-based access to Amira. This tool allows earth scientists to manipulate Amira controls remotely and to analyze, render and view large datasets over the internet, without regard for time or location. This could have important ramifications for GRID computing. The design of our implementation will soon allow multiple users to visually collaborate by manipulating a single dataset through a variety of client devices. These clients will only require a browser capable of displaying Java applets. As the deluge of data continues, innovative solutions that maximize ease of use without sacrificing efficiency or flexibility will continue to gain in importance, particularly in the Earth sciences. Major initiatives, such as Earthscope (http://www.earthscope.org), which will generate at least a terabyte of data daily, stand to profit enormously by a system such as WEB-IS/Amira (WEB-IS2). We discuss our use of SOAP (Livingston, D., Advanced SOAP for Web development, Prentice Hall, 2002), a novel 2-way communication protocol, as a means of providing remote commands, and efficient point-to-point transfer of binary image data. We will present our initial experiences with the use of Naradabrokering (www.naradabrokering.org) as a means to decouple clients and servers. Information is submitted to the system as a published item, while it is retrieved through a subscription mechanisms, via what is known as "topics". These topic headers, their contents, and the list of subscribers are automatically tracked by Naradabrokering. This novel approach promises a high degree of fault tolerance, flexibility with respect to client diversity, and language independence for the services (Erlebacher, G., Yuen, D.A., and F. Dubuffet, Current trends and demands in visualization in the geosciences, Electron. Geosciences, 4, 2001).

Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications.

Structural Technology Evaluation and Analysis Program (STEAP). Delivery Order 0035: Dynamics and Control and Computational Design of Flapping Wing Micro Air Vehicles

DTIC Science & Technology

2012-10-01

library as a principal Requestor. The M3CT requestor is written in Java , leveraging the cross platform deployment capabilities needed for a broadly...each application to the Java programming language, the independently generated sources are wrapped with JNA or Groovy. The Java wrapping process...unlimited. Figure 13. Leveraging Languages Once the underlying product is available to the Java source as a library, the application leverages

76 FR 27959 - Investment Adviser Performance Compensation

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-13

...://www.bea.gov/national/nipaweb/TableView.asp?SelectedTable=64&ViewSeries=NO&Java=no&Request3Place=N&3Place=N&FromView=YES&Freq=Year&FirstYear=1997&LastYear=2010&3Place=N&Update=Update&JavaBox=no#Mid . \\21...

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

Gupta, N.; Gupta, V.; Okaya, D.; Kamb, L.; Maechling, P.

2003-12-01

Web services offer scientific communities a new paradigm for sharing research codes and communicating results. While there are formal technical definitions of what constitutes a web service, for a user community such as the Southern California Earthquake Center (SCEC), we may conceptually consider a web service to be functionality provided on-demand by an application which is run on a remote computer located elsewhere on the Internet. The value of a web service is that it can (1) run a scientific code without the user needing to install and learn the intricacies of running the code; (2) provide the technical framework which allows a user's computer to talk to the remote computer which performs the service; (3) provide the computational resources to run the code; and (4) bundle several analysis steps and provide the end results in digital or (post-processed) graphical form. Within an NSF-sponsored ITR project coordinated by SCEC, we are constructing web services using architectural protocols and programming languages (e.g., Java). However, because the SCEC community has a rich pool of scientific research software (written in traditional languages such as C and FORTRAN), we also emphasize making existing scientific codes available by constructing web service frameworks which wrap around and directly run these codes. In doing so we attempt to broaden community usage of these codes. Web service wrapping of a scientific code can be done using a "web servlet" construction or by using a SOAP/WSDL-based framework. This latter approach is widely adopted in IT circles although it is subject to rapid evolution. Our wrapping framework attempts to "honor" the original codes with as little modification as is possible. For versatility we identify three methods of user access: (A) a web-based GUI (written in HTML and/or Java applets); (B) a Linux/OSX/UNIX command line "initiator" utility (shell-scriptable); and (C) direct access from within any Java application (and with the correct API interface from within C++ and/or C/Fortran). This poster presentation will provide descriptions of the following selected web services and their origin as scientific application codes: 3D community velocity models for Southern California, geocoordinate conversions (latitude/longitude to UTM), execution of GMT graphical scripts, data format conversions (Gocad to Matlab format), and implementation of Seismic Hazard Analysis application programs that calculate hazard curve and hazard map data sets.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

An Evaluative Review of School Accreditation Implementation Program in Indonesian Contexts

ERIC Educational Resources Information Center

Haryati, Sri

2014-01-01

This paper critically reviews and evaluates the implementation of School Accreditation Program for the period of 2013 with a particular reference to Central Java Schools, consisting of Kindergarten (TK) Elementary School (SD), Junior High School (SMP) and Senior High School (SMA) (Note 1). The aim of the review is to see to what extent they can…

Framework for Managing Metadata Security Tags as the Basis for Making Security Decisions.

DTIC Science & Technology

2002-12-01

and Performance,” D.H. Associates, Inc., Sep 2001. [3] Deitel , H. M., and Deitel , P. J., Java How to Program , 3rd Edition, Prentice Hall Inc...1999. [4] Deitel , H. M., Deitel , P. J., and Nieto, T. R., Internet and The World Wide Web: How to Program , 2nd Edition, 2002. [5] Grohn, M. J., A...words) This thesis presents an analysis of a capability to employ CAPCO (Controlled Access Program Coordination Office) compliant Metadata security

User-friendly cognitive training for the elderly: a technical report.

PubMed

Boquete, Luciano; Rodríguez-Ascariz, José Manuel; Amo-Usanos, Carlos; Martínez-Arribas, Alejandro; Amo-Usanos, Javier; Otón, Salvador

2011-01-01

This article presents a system that implements a cognitive training program in users' homes. The system comprises various applications designed to create a daily brain-fitness regime. The proposed mental training system uses television and a remote control specially designed for the elderly. This system integrates Java applications to promote brain-fitness training in three areas: arithmetic, memory, and idea association. The system comprises the following: Standard television set, simplified wireless remote control, black box (system's core hardware and software), brain-fitness games (language Java), and Wi-Fi-enabled Internet-connected router. All data from the user training sessions are monitored through a control center. This control center analyzes the evolution of the user and the proper performance of the system during the test. The implemented system has been tested by six healthy volunteers. The results for this user group demonstrated the accessibility and usability of the system in a controlled real environment. The impressions of the users were very favorable, and they reported high adaptability to the system. The mean score for usability and accessibility assigned by the users was 3.56 out of 5 points. The operation stress test (over 200 h) was successful. The proposed system was used to implement a cognitive training program in users' homes, which was developed to be a low-cost tool with a high degree of user interactivity. The results of this preliminary study indicate that this user-friendly system could be adopted as a form of cognitive training for the elderly.

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.

Hard Real-Time: C++ Versus RTSJ

NASA Technical Reports Server (NTRS)

Dvorak, Daniel L.; Reinholtz, William K.

2004-01-01

In the domain of hard real-time systems, which language is better: C++ or the Real-Time Specification for Java (RTSJ)? Although ordinary Java provides a more productive programming environment than C++ due to its automatic memory management, that benefit does not apply to RTSJ when using NoHeapRealtimeThread and non-heap memory areas. As a result, RTSJ programmers must manage non-heap memory explicitly. While that's not a deterrent for veteran real-time programmers-where explicit memory management is common-the lack of certain language features in RTSJ (and Java) makes that manual memory management harder to accomplish safely than in C++. This paper illustrates the problem for practitioners in the context of moving data and managing memory in a real-time producer/consumer pattern. The relative ease of implementation and safety of the C++ programming model suggests that RTSJ has a struggle ahead in the domain of hard real-time applications, despite its other attractive features.

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.

A Test Generation Framework for Distributed Fault-Tolerant Algorithms

NASA Technical Reports Server (NTRS)

Goodloe, Alwyn; Bushnell, David; Miner, Paul; Pasareanu, Corina S.

2009-01-01

Heavyweight formal methods such as theorem proving have been successfully applied to the analysis of safety critical fault-tolerant systems. Typically, the models and proofs performed during such analysis do not inform the testing process of actual implementations. We propose a framework for generating test vectors from specifications written in the Prototype Verification System (PVS). The methodology uses a translator to produce a Java prototype from a PVS specification. Symbolic (Java) PathFinder is then employed to generate a collection of test cases. A small example is employed to illustrate how the framework can be used in practice.

Military Interoperable Digital Hospital Testbed (MIDHT) Phase III

DTIC Science & Technology

2014-10-01

silently changed, it is common knowledge  that some  Java  Development  Kit (JDK) implementations create slightly differently  formatted PEM and  DER...tracking software  JKS  Java  KeyStore  LDAP  Lightweight Directory Access Protocol  MHS  Military Health System  MIMC  Conemaugh Miners Medical... MySQL ~ Conemaugh Health System ’-J Common Access Layer (CAL) Interface I I t J J AIIScripts I I McKe-n J Sunque.st Horizon EHR Lab Patient

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.

Development, Deployment, and Cost Effectiveness of a Self-Administered Stereo Non Mydriatic Automated Retinal Camera (SNARC) Containing Automated Retinal Lesion (ARL) Detection Using Adaptive Optics

DTIC Science & Technology

2010-10-01

Requirements Application Server  BEA Weblogic Express 9.2 or higher  Java v5Apache Struts v2  Hibernate v2  C3PO  SQL*Net client / JDBC Database Server...designed for the desktop o An HTML and JavaScript browser-based front end designed for mobile Smartphones - A Java -based framework utilizing Apache...Technology Requirements The recommended technologies are as follows: Technology Use Requirements Java Application Provides the backend application

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.

Ajax Architecture Implementation Techniques

NASA Astrophysics Data System (ADS)

Hussaini, Syed Asadullah; Tabassum, S. Nasira; Baig, Tabassum, M. Khader

2012-03-01

Today's rich Web applications use a mix of Java Script and asynchronous communication with the application server. This mechanism is also known as Ajax: Asynchronous JavaScript and XML. The intent of Ajax is to exchange small pieces of data between the browser and the application server, and in doing so, use partial page refresh instead of reloading the entire Web page. AJAX (Asynchronous JavaScript and XML) is a powerful Web development model for browser-based Web applications. Technologies that form the AJAX model, such as XML, JavaScript, HTTP, and XHTML, are individually widely used and well known. However, AJAX combines these technologies to let Web pages retrieve small amounts of data from the server without having to reload the entire page. This capability makes Web pages more interactive and lets them behave like local applications. Web 2.0 enabled by the Ajax architecture has given rise to a new level of user interactivity through web browsers. Many new and extremely popular Web applications have been introduced such as Google Maps, Google Docs, Flickr, and so on. Ajax Toolkits such as Dojo allow web developers to build Web 2.0 applications quickly and with little effort.

Online Spectral Fit Tool for Analyzing Reflectance Spectra

NASA Astrophysics Data System (ADS)

Penttilä, A.; Kohout, T.

2015-11-01

The Online Spectral Fit Tool is developed for analyzing Vis-NIR spectral behavior of asteroids and meteorites. Implementation is done using JavaScript/HTML. Fitted spectra consist of spline continuum and gamma distributions for absorption bands.

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

New web technologies for astronomy

NASA Astrophysics Data System (ADS)

Sprimont, P.-G.; Ricci, D.; Nicastro, L.

2014-12-01

Thanks to the new HTML5 capabilities and the huge improvements of the JavaScript language, it is now possible to design very complex and interactive web user interfaces. On top of that, the once monolithic and file-server oriented web servers are evolving into easily programmable server applications capable to cope with the complex interactions made possible by the new generation of browsers. We believe that the whole community of amateur and professionals astronomers can benefit from the potential of these new technologies. New web interfaces can be designed to provide the user with a large deal of much more intuitive and interactive tools. Accessing astronomical data archives, schedule, control and monitor observatories, and in particular robotic telescopes, supervising data reduction pipelines, all are capabilities that can now be implemented in a JavaScript web application. In this paper we describe the Sadira package we are implementing exactly to this aim.

HYDRA Hyperspectral Data Research Application Tom Rink and Tom Whittaker

NASA Astrophysics Data System (ADS)

Rink, T.; Whittaker, T.

2005-12-01

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

Automated Environment Generation for Software Model Checking

NASA Technical Reports Server (NTRS)

Tkachuk, Oksana; Dwyer, Matthew B.; Pasareanu, Corina S.

2003-01-01

A key problem in model checking open systems is environment modeling (i.e., representing the behavior of the execution context of the system under analysis). Software systems are fundamentally open since their behavior is dependent on patterns of invocation of system components and values defined outside the system but referenced within the system. Whether reasoning about the behavior of whole programs or about program components, an abstract model of the environment can be essential in enabling sufficiently precise yet tractable verification. In this paper, we describe an approach to generating environments of Java program fragments. This approach integrates formally specified assumptions about environment behavior with sound abstractions of environment implementations to form a model of the environment. The approach is implemented in the Bandera Environment Generator (BEG) which we describe along with our experience using BEG to reason about properties of several non-trivial concurrent Java programs.

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.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

A Distance Instructional System with Learning Performance Evaluation Mechanism: Moodle-Based Educational System Design

ERIC Educational Resources Information Center

Lee, Ying-Chen; Terashima, Nobuyoshi

2012-01-01

In this paper, a Moodle-based educational system has been constructed by providing friendly interface to fit most students in e-learning. For the website implementation, the authors take the course "Multimedia Implementation Using JAVA" as a case study. From the modified Moodle-based educational system, the browsing time of each web page for…

Implementation and Assessment of a Virtual Laboratory of Parallel Robots Developed for Engineering Students

ERIC Educational Resources Information Center

Gil, Arturo; Peidró, Adrián; Reinoso, Óscar; Marín, José María

2017-01-01

This paper presents a tool, LABEL, oriented to the teaching of parallel robotics. The application, organized as a set of tools developed using Easy Java Simulations, enables the study of the kinematics of parallel robotics. A set of classical parallel structures was implemented such that LABEL can solve the inverse and direct kinematic problem of…

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

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Wilson, A.

2012-12-01

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

Inclusive blue swimming crab fishery management initiative in Betahwalang Demak, Indonesia

NASA Astrophysics Data System (ADS)

Ghofar, A.; Redjeki, S.; Madduppa, H.; Abbey, M.; Tasunar, N.

2018-02-01

There has been a growing interest in the sustainability of the blue swimming crab (Portunus pelagicus, BSC) fisheries in Indonesia. The fishery is operated on a small-scale basis and yet it significantly contributes to the Indonesia’s fisheries as the third biggest export commodities following tuna and shrimp. The project inclusively (i) brings together coastal and fishing communities, university, the private sector, government at various levels and international agencies, (ii) bottom up approach is integrated with top-down (government policy) approach and (iii) integration o f conservation into fisheries management. This approach resulted in better understanding and participation among the coastal fishing communities on sustainable fisheries and the necessity to perform fisheries management. This led to the establishment of BSC fishery management body (legally support by Village Regulation - No.06/2013 on BSC fishery management in 2013, followed by a District Regulation No.523/0166/2014 on BSC fishery management in 2014. More recently, the Governor of Central Java issued a Governor Regulation No. 33/2017 on Crab and Lobster fisheries management and a Governor Decree No. 523/93/2017 on the establishment of the BSC fisheries management committee in Central Java. Further impacts have been raised awareness in sustainable BSC fishery management in surrounding districts in other provinces, namely East Java and Southeast Sulawesi. There remains, further needs to strengthen fishery governance by means of integrating national and local government effort in sustaining the fisheries, including the Issuance and effective implementation of the provincial decree on BSC fishery management for Central Java, that will enable the use of province’s resource to implement fisheries management and strengthen law enforcement. To help improve the stock, a plan for stock enhancement should also be developed with proper monitoring program and community commitment to avoid “put and take” practices.

Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

Establishing an Integrated Catchment Management (ICM) program in East Java, Indonesia.

PubMed

Booth, C A; Warianti, A; Wrigley, T

2001-01-01

The Brantas is one of Indonesia's most important catchments. It is the "rice bowl" of Java and nationally important for its industrial activity. Surabaya, Indonesia's second largest city, is located at the mouth of the Brantas River which is pivotal to the city's water supply. The challenges associated with the institutional framework for natural resource management in East Java parallels that of many states and provinces around the globe. It is multi-layered and complex. Integrated Catchment Management (ICM) may be defined as "the co-ordinated and sustainable management of land, water, soil vegetation, fauna and other natural resources on a water catchment basis". Over a period of six months, an ICM Strategy was researched and facilitated for the Brantas River Catchment in East Java via a short term advisor attachment. The aim of the Strategy is to improve coordination, co-operation, communication and consistency of government and community efforts towards sustaining the catchment's environmental, economic and social values. The attachment was part of the Pollution Control Implementation (PCI) Project funded by AusAid and the Indonesian Government. The ICM Strategy developed was broad based and addressed the priority natural resource management issues facing the Brantas Catchment. It was co-ordinated by BAPEDALDA, the Provincial Environmental Protection Agency, and developed by all agencies involved in natural resource management in the catchment. Various Universities and Non Government Organisations (NGOs) were also involved in the ICM process which developed the Strategy. At the conclusion of the attachment, a draft ICM Strategy and a proposed institutional framework had been developed. A working group of key agencies was also established to further enhance local "ownership", finalise timescales and implementation responsibilities within the Strategy and bring the institutional arrangements into being through a Governor's Decree.

Informing rubella vaccination strategies in East Java, Indonesia through transmission modelling.

PubMed

Wu, Yue; Wood, James; Khandaker, Gulam; Waddington, Claire; Snelling, Thomas

2016-11-04

An estimated 110,000 babies are born with congenital rubella syndrome (CRS) worldwide annually; a significant proportion of cases occur in Southeast Asia. Rubella vaccine programs have led to successful control of rubella and CRS, and even the elimination of disease in many countries. However, if vaccination is poorly implemented it might increase the number of women reaching childbearing age who remain susceptible to rubella and thereby paradoxically increase CRS. We used an age-structured transmission model to compare seven alternative vaccine strategies for their impact on reducing CRS disease burden in East Java, a setting which is yet to implement a rubella vaccine program. We also investigated the robustness of model predictions to variation in vaccine coverage and other key epidemiological factors. Without rubella vaccination, approximately 700 babies are estimated to be born with CRS in East Java every year at an incidence of 0.77 per 1000live births. This incidence could be reduced to 0.0045 per 1000 live births associated with 99.9% annual reduction in rubella infections after 20 years if the existing two doses of measles vaccine are substituted with two doses of measles plus rubella combination vaccine with the same coverage (87.8% of 9-month-old infants and 80% of 6-year-old children). By comparison a single dose of rubella vaccine will take longer to reduce the burden of rubella and CRS and will be less robust to lower vaccine coverage. While the findings of this study should be informative for settings similar to East Java, the conclusions are dependent on vaccine coverage which would need consideration before applying to all of Indonesia and elsewhere in Asia. Copyright © 2016 Elsevier Ltd. All rights reserved.

Semi-automatic image personalization tool for variable text insertion and replacement

NASA Astrophysics Data System (ADS)

Ding, Hengzhou; Bala, Raja; Fan, Zhigang; Eschbach, Reiner; Bouman, Charles A.; Allebach, Jan P.

2010-02-01

Image personalization is a widely used technique in personalized marketing,1 in which a vendor attempts to promote new products or retain customers by sending marketing collateral that is tailored to the customers' demographics, needs, and interests. With current solutions of which we are aware such as XMPie,2 DirectSmile,3 and AlphaPicture,4 in order to produce this tailored marketing collateral, image templates need to be created manually by graphic designers, involving complex grid manipulation and detailed geometric adjustments. As a matter of fact, the image template design is highly manual, skill-demanding and costly, and essentially the bottleneck for image personalization. We present a semi-automatic image personalization tool for designing image templates. Two scenarios are considered: text insertion and text replacement, with the text replacement option not offered in current solutions. The graphical user interface (GUI) of the tool is described in detail. Unlike current solutions, the tool renders the text in 3-D, which allows easy adjustment of the text. In particular, the tool has been implemented in Java, which introduces flexible deployment and eliminates the need for any special software or know-how on the part of the end user.

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

Generic Bluetooth Data Module

DTIC Science & Technology

2002-09-01

to Ref (1). 34 RS232.java Serial Coomunication port class To Bluetooth module HCI.java Host Control Interface class L2CAP.java Logical Link Control...standard protocol for transporting IP datagrams over point-to-point link . It is designed to run over RFCOMM to accomplish point-to-point connections...Control and Adaption Host Controller Interface Link Manager Baseband / Link Controller Radio Figure 2. Bluetooth layers (From Ref. [3].) C

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

Werner, Mike

Why this utility? After years of upgrading the Java Runtime Environment (JRE) or the Java Software Development Kit (JDK/SDK), a Windows computer becomes littered with so many old versions that the machine may become a security risk due to exploits targeted at those older versions. This utility helps mitigate those vulnerabilities by searching for, and removing, versions 1.3.x thru 1.7.x of the Java JRE and/or JDK/SDK.

Model Checking Degrees of Belief in a System of Agents

NASA Technical Reports Server (NTRS)

Raimondi, Franco; Primero, Giuseppe; Rungta, Neha

2014-01-01

Reasoning about degrees of belief has been investigated in the past by a number of authors and has a number of practical applications in real life. In this paper we present a unified framework to model and verify degrees of belief in a system of agents. In particular, we describe an extension of the temporal-epistemic logic CTLK and we introduce a semantics based on interpreted systems for this extension. In this way, degrees of beliefs do not need to be provided externally, but can be derived automatically from the possible executions of the system, thereby providing a computationally grounded formalism. We leverage the semantics to (a) construct a model checking algorithm, (b) investigate its complexity, (c) provide a Java implementation of the model checking algorithm, and (d) evaluate our approach using the standard benchmark of the dining cryptographers. Finally, we provide a detailed case study: using our framework and our implementation, we assess and verify the situational awareness of the pilot of Air France 447 flying in off-nominal conditions.

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

PubMed

Bielejec, Filip; Baele, Guy; Vrancken, Bram; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2016-08-01

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

PubMed

Ren, Jian; Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

2010-01-01

During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0).

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore

PubMed Central

Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

2010-01-01

During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). PMID:19783819

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.

A Comprehensive Context for Mobile-Code Deployment

DTIC Science & Technology

2005-01-01

18 Gal, Probst, Franz, 2003 Freund, Mitchell, 1999 Sohr, 1999, 2001 Microsoft, 2000 LSDRG, 2002 Dean, Felten, Balfanz , Wallach, 2003 Govindavajhala...D. Balfanz . Java security: Web browsers and beyond. In D. E. Denning and P. J. Denning, editors, Internet Besieged: Countering Cyberspace Scofflaws

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.

Rule-Based Runtime Verification

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

SuperNatural: a searchable database of available natural compounds

PubMed Central

Dunkel, Mathias; Fullbeck, Melanie; Neumann, Stefanie; Preissner, Robert

2006-01-01

Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of ∼50 000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used. The SuperNatural Database is publicly available at . Viewing requires the free Chime-plugin from MDL (Chime) or Java2 Runtime Environment (MView), which is also necessary for using Marvin application for chemical drawing. PMID:16381957

Triggering and dynamic evolution of the LUSI mud volcano, Indonesia

NASA Astrophysics Data System (ADS)

Svensen, H.; Mazzini, A.; Akhmanov, G. G.; Aloisi, G.; Planke, S.; Sørenssen, A.; Istadi, B.

2007-12-01

Mud volcanoes are geologically important manifestations of vertical fluid flow and mud eruption in sedimentary basins worldwide. Their formation is predominantly ascribed to release of overpressure from clay- and organic- rich sediments, leading to impressive buildup of mud mountains in submarine and subaerial settings. Here we report data from two fieldworks on a newly born mud volcano named LUSI eruption in Eastern Java (Indonesia). The eruption site appears close to an active magmatic complex in a backarc sedimentary basin in Indonesia. Its specific location results in a high background temperature gradient that triggers mineralogical transformations and geochemical reactions at shallow depth. The eruption of 100 deg.C mud and gas that started the 29th of May 2006 flooded a large area within the Sidoarjo village in Northeast Java. Thousands of people have so far been evacuated and, since the initial eruption, the flow rate escalated from 5000 to 120,000 m3/d during the first eleven weeks. Then the erupted volume started to pulsate between almost zero and 120,000 m3/d in the period August-September, whereas it increased dramatically following swarms of earthquakes in September, before reaching almost 180,000 m3/d in December 2006. Fifteen months after the initial burst, LUSI is still vigorously erupting up to 111,000 m3/d, the average subsidence of the area reached 11 m. Seismic images show that a pre-existing structure was present before the eruption. Based on geochemical and field results, we propose a mechanism where the eruptions started following the 27th of May earthquake due to fracturing and accompanied depressurization of >100 deg.C pore fluids from > 1700 m depth released from a structure in already critical conditions. This resulted in the formation of a quasi-hydrothermal system with a geyser-like surface expression and with an activity influenced by the regional seismicity.

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.

StreamQRE: Modular Specification and Efficient Evaluation of Quantitative Queries over Streaming Data.

PubMed

Mamouras, Konstantinos; Raghothaman, Mukund; Alur, Rajeev; Ives, Zachary G; Khanna, Sanjeev

2017-06-01

Real-time decision making in emerging IoT applications typically relies on computing quantitative summaries of large data streams in an efficient and incremental manner. To simplify the task of programming the desired logic, we propose StreamQRE, which provides natural and high-level constructs for processing streaming data. Our language has a novel integration of linguistic constructs from two distinct programming paradigms: streaming extensions of relational query languages and quantitative extensions of regular expressions. The former allows the programmer to employ relational constructs to partition the input data by keys and to integrate data streams from different sources, while the latter can be used to exploit the logical hierarchy in the input stream for modular specifications. We first present the core language with a small set of combinators, formal semantics, and a decidable type system. We then show how to express a number of common patterns with illustrative examples. Our compilation algorithm translates the high-level query into a streaming algorithm with precise complexity bounds on per-item processing time and total memory footprint. We also show how to integrate approximation algorithms into our framework. We report on an implementation in Java, and evaluate it with respect to existing high-performance engines for processing streaming data. Our experimental evaluation shows that (1) StreamQRE allows more natural and succinct specification of queries compared to existing frameworks, (2) the throughput of our implementation is higher than comparable systems (for example, two-to-four times greater than RxJava), and (3) the approximation algorithms supported by our implementation can lead to substantial memory savings.

StreamQRE: Modular Specification and Efficient Evaluation of Quantitative Queries over Streaming Data*

PubMed Central

Mamouras, Konstantinos; Raghothaman, Mukund; Alur, Rajeev; Ives, Zachary G.; Khanna, Sanjeev

2017-01-01

Real-time decision making in emerging IoT applications typically relies on computing quantitative summaries of large data streams in an efficient and incremental manner. To simplify the task of programming the desired logic, we propose StreamQRE, which provides natural and high-level constructs for processing streaming data. Our language has a novel integration of linguistic constructs from two distinct programming paradigms: streaming extensions of relational query languages and quantitative extensions of regular expressions. The former allows the programmer to employ relational constructs to partition the input data by keys and to integrate data streams from different sources, while the latter can be used to exploit the logical hierarchy in the input stream for modular specifications. We first present the core language with a small set of combinators, formal semantics, and a decidable type system. We then show how to express a number of common patterns with illustrative examples. Our compilation algorithm translates the high-level query into a streaming algorithm with precise complexity bounds on per-item processing time and total memory footprint. We also show how to integrate approximation algorithms into our framework. We report on an implementation in Java, and evaluate it with respect to existing high-performance engines for processing streaming data. Our experimental evaluation shows that (1) StreamQRE allows more natural and succinct specification of queries compared to existing frameworks, (2) the throughput of our implementation is higher than comparable systems (for example, two-to-four times greater than RxJava), and (3) the approximation algorithms supported by our implementation can lead to substantial memory savings. PMID:29151821

Study of 3D bathymetry modelling using LAPAN Surveillance Unmanned Aerial Vehicle 02 (LSU-02) photo data with stereo photogrammetry technique, Wawaran Beach, Pacitan, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Sari, N. M.; Nugroho, J. T.; Chulafak, G. A.; Kushardono, D.

2018-05-01

Coastal is an ecosystem that has unique object and phenomenon. The potential of the aerial photo data with very high spatial resolution covering coastal area is extensive. One of the aerial photo data can be used is LAPAN Surveillance UAV 02 (LSU-02) photo data which is acquired in 2016 with a spatial resolution reaching 10cm. This research aims to create an initial bathymetry model with stereo photogrammetry technique using LSU-02 data. In this research the bathymetry model was made by constructing 3D model with stereo photogrammetry technique that utilizes the dense point cloud created from overlapping of those photos. The result shows that the 3D bathymetry model can be built with stereo photogrammetry technique. It can be seen from the surface and bathymetry transect profile.

Gesture Interaction Browser-Based 3D Molecular Viewer.

PubMed

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2016-01-01

The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

Jettison Engineering Trajectory Tool

NASA Technical Reports Server (NTRS)

Zaczek, Mariusz; Walter, Patrick; Pascucci, Joseph; Armstrong, Phyllis; Hallbick, Patricia; Morgan, Randal; Cooney, James

2013-01-01

The Jettison Engineering Trajectory Tool (JETT) performs the jettison analysis function for any orbiting asset. It provides a method to compute the relative trajectories between an orbiting asset and any jettisoned item (intentional or unintentional) or sublimating particles generated by fluid dumps to assess whether an object is safe to jettison, or if there is a risk with an item that was inadvertently lost overboard. The main concern is the interaction and possible recontact of the jettisoned object with an asset. This supports the analysis that jettisoned items will safely clear the vehicle, ensuring no collisions. The software will reduce the jettison analysis task from one that could take days to complete to one that can be completed in hours, with an analysis that is more comprehensive than the previous method. It provides the ability to define the jettison operation relative to International Space Station (ISS) structure, and provides 2D and 3D plotting capability to allow an analyst to perform a subjective clearance assessment with ISS structures. The developers followed the SMP to create the code and all supporting documentation. The code makes extensive use of the object-oriented format of Java and, in addition, the Model-View-Controller architecture was used in the organization of the code, allowing each piece to be independent of updates to the other pieces. The model category is for maintaining data entered by the user and generated by the analysis. The view category provides capabilities for data entry and displaying all or a portion of the analysis data in tabular, 2D, and 3D representation. The controller category allows for handling events that affect the model or view(s). The JETT utilizes orbital mechanics with complex algorithms. Since JETT is written in JAVA, it is essentially platform-independent.

A New System to Monitor Data Analyses and Results of Physics Data Validation Between Pulses at DIII-D

NASA Astrophysics Data System (ADS)

Flanagan, S.; Schachter, J. M.; Schissel, D. P.

2001-10-01

A Data Analysis Monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility. The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded thus increasing the efficiency of experimental time. An example of a consistency check is comparing the stored energy from integrating the measured kinetic profiles to that calculated from magnetic measurements by EFIT. This new system also tracks the progress of MDSplus dispatching of software for data analysis and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, Clips to implement expert system logic, and displays its results to multiple web clients via HTML. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse. A demonstration of this system including a simulated DIII-D pulse cycle will be presented.

The Cascading Impacts of Technology Selection: Incorporating Ruby on Rails into ECHO

NASA Astrophysics Data System (ADS)

Pilone, D.; Cechini, M.

2010-12-01

NASA’s Earth Observing System (EOS) ClearingHOuse (ECHO) is a SOA based Earth Science Data search and order system implemented in Java with one significant exception: the web client used by 98% of our users is written in Perl. After several decades of maintenance the Perl based application had reached the end of its serviceable life and ECHO was tasked with implementing a replacement. Despite a broad investment in Java, the ECHO team conducted a survey of modern development technologies including Flex, Python/Django, JSF2/Spring and Ruby on Rails. The team ultimately chose Ruby on Rails (RoR) with Cucumber for testing due to its perceived applicability to web application development and corresponding development efficiency gains. Both positive and negative impacts on the entire ECHO team, including our stakeholders, were immediate and sometimes subtle. The technology selection caused shifts in our architecture and design, development and deployment procedures, requirement definition approach, testing approach, and, somewhat surprisingly, our project team structure and software process. This presentation discusses our experiences, including technical, process, and psychological, using RoR on a production system. During this session we will discuss: - Real impacts of introducing a dynamic language to a Java team - Real and perceived efficiency advantages - Impediments to adoption and effectiveness - Impacts of transition from Test Driven Development to Behavior Driven Development - Leveraging Cucumber to provide fully executable requirement documents - Impacts on team structure and roles

Socializing the policy on public transportation to the community

NASA Astrophysics Data System (ADS)

Asmawi, A.; Mariana, D.; Sjoraida, D. F.

2018-03-01

This article discusses how public policies on transportation can be communicated to the society in Sukabumi City, West Java, Indonesia. It is important for the community because the development of transportation services has a very close relationship with social welfare and economic growth of the region. This can be demonstrated with an indication that the region whose better transportation system tends to have better levels of social welfare and economic growth. The study here used a multiple case method. The cases consist of activities which were the implementation of the government’s program of socialization to the people of Sukabumi City on transportation. This regency is a door to an expansion of West Java development to the Southwest area that there are things new in government services, including in the field of transportation. Interviews, observation and document analyses were used to collect the data. Face to face interviews using a list of questions were also developed for this study. The findings of the study indicate that in addition to its own designing and implementing transportation development plan in Sukabumi City itself, there is also a transportation development involving West Java provincial government, even the national government of Indonesia in the region. All of the transportation plans could be properly communicated to the public because it used a variety of media, including the traditional, the modern, and the social.

Review of disaster management implementation for the community safety in the vicinity of oil and gas field

NASA Astrophysics Data System (ADS)

Musa, R. Abdullah; Harjanto, Meddy; Heni, Siti

2015-04-01

Sukowati site which is operated by Production Sharing Contract (PSC) Joint Operating Body Pertamina Petrochina East Java (JOB P-PEJ) located at Bojonegoro regency East Java Province. This site is close to densely populated settlements with approximately 6,010 people within a radius less than 600 m. The fluid produced have a dangerous potential to the above mention community, due to accompanying of hydrogen sulphide gas (H2S) with a concentration about 0.6% - 2% from the total gas produced. In 2006, there was incident of gas leak from drilling development well of Sukowati # 5. The incident made the surrounding community panic due to lack of preparedness and awareness. Learning from the incident, the company together with the government and local communities initiated to make improvements through the disaster management system approach. The efforts are carried out in accordance with the 4 (four) periods in a continuous cycle consist of (1) mitigation; (2) preparation; (3) response and (4) recovery. Emergency response drills conducted regularly at least once a year, its main purpose is to find out the results of the implementation of the existing disaster management. The results of the drills showed an increase in public awareness and responsiveness to emergency situations caused by the operational failures of oil and gas exploration and production activities near their settlement.

A Web-based, secure, light weight clinical multimedia data capture and display system.

PubMed

Wang, S S; Starren, J

2000-01-01

Computer-based patient records are traditionally composed of textual data. Integration of multimedia data has been historically slow. Multimedia data such as image, audio, and video have been traditionally more difficult to handle. An implementation of a clinical system for multimedia data is discussed. The system implementation uses Java, Secure Socket Layer (SSL), and Oracle 8i. The system is on top of the Internet so it is architectural independent, cross-platform, cross-vendor, and secure. Design and implementations issues are discussed.

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

PubMed

Ezra Tsur, Elishai

2017-01-01

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

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

PubMed Central

Frankewitsch, T.; Prokosch, U.

1999-01-01

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

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

PubMed

Frankewitsch, T; Prokosch, U

1999-01-01

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

EntrezAJAX: direct web browser access to the Entrez Programming Utilities.

PubMed

Loman, Nicholas J; Pallen, Mark J

2010-06-21

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

Web tools for effective retrieval, visualization, and evaluation of cardiology medical images and records

NASA Astrophysics Data System (ADS)

Masseroli, Marco; Pinciroli, Francesco

2000-12-01

To provide easy retrieval, integration and evaluation of multimodal cardiology images and data in a web browser environment, distributed application technologies and java programming were used to implement a client-server architecture based on software agents. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. The client side is a Java applet running in a web browser and providing a friendly medical user interface to perform queries on patient and medical test dat and integrate and visualize properly the various query results. A set of tools based on Java Advanced Imaging API enables to process and analyze the retrieved cardiology images, and quantify their features in different regions of interest. The platform-independence Java technology makes the developed prototype easy to be managed in a centralized form and provided in each site where an intranet or internet connection can be located. Giving the healthcare providers effective tools for querying, visualizing and evaluating comprehensively cardiology medical images and records in all locations where they can need them- i.e. emergency, operating theaters, ward, or even outpatient clinics- the developed prototype represents an important aid in providing more efficient diagnoses and medical treatments.

Un nouveau crâne humain fossile dans le dôme de Sangiran (Java, Indonésie)A recently discovered fossil human skull from the Sangiran dome (Java, Indonesia).

NASA Astrophysics Data System (ADS)

Widianto, Harry; Grimaud-Hervé, Dominique

2000-06-01

The study of new human remains discovered at the Grogol Wetan hamlet, in the Kabuh layers of the Sangiran stratigraphy dated between 0.8 and 0.25 million years, allows us to show morphological characters very similar to those observed on the other hominids of the same stratigraphical layers of this site. So, we can attribute this human fossil to this very homogeneous population of asiatic Homo erectus.

MyChemise: A 2D drawing program that uses morphing for visualisation purposes

PubMed Central

2011-01-01

MyChemise (My Chemical Structure Editor) is a new 2D structure editor. It is designed as a Java applet that enables the direct creation of structures in the Internet using a web browser. MyChemise saves files in a digital format (.cse) and the import and export of .mol files using the appropriate connection tables is also possible. MyChemise is available as a free online version in English and German. The MyChemise GUI is designed to be user friendly and can be used intuitively. There is also an English and German program description available as a PDF file. In addition to the known ways of drawing chemical structure formulas, there are also parts implemented in the program that allow the creation of different types of presentation. The morphing module uses this technology as a component for dynamic visualisation. For example, it enables a clear and simple illustration of molecule vibrations and reaction sequences. PMID:22152022

Secure Proactive Recovery a Hardware Based Mission Assurance Scheme

DTIC Science & Technology

2011-08-01

Room, January. Kalbarczyk, Z., Iyer, R.K., Bagchi, S. and Whisnant, K. (1999) " Chameleon : a software infrastructure for adaptive fault tolerance...components of this evaluation include a JAVA implementation based on Chameleon ARMORs (Kalbarczyk et al. 1999), ARENA simulation (http

A Novel and Freely Available Interactive 3d Model of the Internal Carotid Artery.

PubMed

Valera-Melé, Marc; Puigdellívol-Sánchez, Anna; Mavar-Haramija, Marija; Juanes-Méndez, Juan A; San-Román, Luis; de Notaris, Matteo; Prats-Galino, Alberto

2018-03-05

We describe a new and freely available 3D interactive model of the intracranial internal carotid artery (ICA) and the skull base that also allows to display and compare its main segment classifications. High-resolution 3D human angiography (isometric voxel's size 0.36 mm) and Computed Tomography angiography images were exported to Virtual Reality Modeling Language (VRML) format for processing in a 3D software platform and embedding in a 3D Portable Document Format (PDF) document that can be freely downloaded at http://diposit.ub.edu/dspace/handle/2445/112442 and runs under Acrobat Reader on Mac and Windows computers and Windows 10 tablets. The 3D-PDF allows for visualisation and interaction through JavaScript-based functions (including zoom, rotation, selective visualization and transparentation of structures or a predefined sequence view of the main segment classifications if desired). The ICA and its main branches and loops, the Gasserian ganglion, the petrolingual ligament and the proximal and distal dural rings within the skull base environment (anterior and posterior clinoid processes, silla turcica, ethmoid and sphenoid bones, orbital fossae) may be visualized from different perspectives. This interactive 3D-PDF provides virtual views of the ICA and becomes an innovative tool to improve the understanding of the neuroanatomy of the ICA and surrounding structures.

The Implementation of Collaborative Learning Model "Find Someone Who and Flashcard Game" to Enhance Social Studies Learning Motivation for the Fifth Grade Students

ERIC Educational Resources Information Center

Nurhaniyah, Binti; Soetjipto, Budi Eko; Hanurawan, Fattah

2015-01-01

The aims of this classroom action research are to describe: (1) the implementation of cooperative learning model "find someone who and flashcard game" to boost students' motivation to learn social studies for the fifth grade students; (2) the response of the fifth grade students at SDN Klanderan, Kediri, East Java on the implementation…

An Interactive Decision Support System for Scheduling Fighter Pilot Training

DTIC Science & Technology

2002-03-26

Deitel , H.M. and Deitel , P.J. C: How to Program , 2nd ed., Prentice Hall, 1994. 8. Deitel , H.M. and Deitel , P.J. How to Program Java...Visual Basic Programming language, the Excel tool is modified in several ways. Scheduling Dispatch rules are implemented to automatically generate... programming language, the Excel tool was modified in several ways. Scheduling dispatch rules are implemented to automatically generate

Improvement of Human Resources Quality through Vocational Training in Tourism in Karimunjawa Islands (Central Java, Indonesia): A Pro-Economical Tourism Approach

ERIC Educational Resources Information Center

Putro, S. Eko; Sukirno; Budi, S.; Didik, W.

2016-01-01

The effort to improve human resource quality is not easy to be implemented. This effort becomes more complicated to do when implemented to the group of poor community, especially in this case marginal community of small island. This research analyzes the characteristic of poor household in small island as well as the strategy of poverty…

Implementing ARFORGEN: Installation Capability and Feasibility Study of Meeting ARFORGEN Guidelines

DTIC Science & Technology

2007-07-26

aligning troop requirements with the Army’s new strategic mission, the force stabilization element of ARFORGEN was developed to raise the morale of...a discrete event simulation model developed for the project to mirror the reset process. The Unit Reset model is implemented in Java as a discrete...and transportation. Further, the typical installation support staff is manned by a Table of Distribution and Allowance ( TDA ) designed to

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

The Coordinated Canyon Experiment (CCE) in Monterey Submarine Canyon has produced a wealth of oceanographic measurements whose analysis will improve understanding of turbidity current processes. Exploration of this data set, consisting of over 60 parameters from 15 platforms, is facilitated by using the open source Spatial Temporal Oceanographic Query System (STOQS) software (https://github.com/stoqs/stoqs). The Monterey Bay Aquarium Research Institute (MBARI) originally developed STOQS to help manage and visualize upper water column oceanographic measurements, but the generality of its data model permits effective use for any kind of spatial/temporal measurement data. STOQS consists of a PostgreSQL database and server-side Python/Django software; the client-side is jQuery JavaScript supporting AJAX requests to update a single page web application. The User Interface (UI) is optimized to provide a quick overview of data in spatial and temporal dimensions, as well as in parameter, platform, and data value space. A user may zoom into any feature of interest and select it, initiating a filter operation that updates the UI with an overview of all the data in the new filtered selection. When details are desired, radio buttons and checkboxes are selected to generate a number of different types of visualizations. These include color-filled temporal section and line plots, parameter-parameter plots, 2D map plots, and interactive 3D spatial visualizations. The Extensible 3D (X3D) standard and X3DOM JavaScript library provide the technology for presenting animated 3D data directly within the web browser. Most of the oceanographic measurements from the CCE (e.g. mooring mounted ADCP and CTD data) are easily visualized using established methods. However, unified integration and multiparameter display of several concurrently deployed sensors across a network of platforms is a challenge we hope to solve. Moreover, STOQS also allows display of data from a new instrument - the Benthic Event Detector (BED). The BED records 50Hz samples of orientation and acceleration when it moves. These data are converted to the CF-NetCDF format and then loaded into a STOQS database. Using the Spatial-3D view a user may interact with a virtual playback of BED motions, giving new insight into submarine canyon sediment density flows.

Design and implementation of handheld and desktop software for the structured reporting of hepatic masses using the LI-RADS schema.

PubMed

Clark, Toshimasa J; McNeeley, Michael F; Maki, Jeffrey H

2014-04-01

The Liver Imaging Reporting and Data System (LI-RADS) can enhance communication between radiologists and clinicians if applied consistently. We identified an institutional need to improve liver imaging report standardization and developed handheld and desktop software to serve this purpose. We developed two complementary applications that implement the LI-RADS schema. A mobile application for iOS devices written in the Objective-C language allows for rapid characterization of hepatic observations under a variety of circumstances. A desktop application written in the Java language allows for comprehensive observation characterization and standardized report text generation. We chose the applications' languages and feature sets based on the computing resources of target platforms, anticipated usage scenarios, and ease of application installation, deployment, and updating. Our primary results are the publication of the core source code implementing the LI-RADS algorithm and the availability of the applications for use worldwide via our website, http://www.liradsapp.com/. The Java application is free open-source software that can be integrated into nearly any vendor's reporting system. The iOS application is distributed through Apple's iTunes App Store. Observation categorizations of both programs have been manually validated to be correct. The iOS application has been used to characterize liver tumors during multidisciplinary conferences of our institution, and several faculty members, fellows, and residents have adopted the generated text of Java application into their diagnostic reports. Although these two applications were developed for the specific reporting requirements of our liver tumor service, we intend to apply this development model to other diseases as well. Through semiautomated structured report generation and observation characterization, we aim to improve patient care while increasing radiologist efficiency. Published by Elsevier Inc.

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

Presentation and response timing accuracy in Adobe Flash and HTML5/JavaScript Web experiments.

PubMed

Reimers, Stian; Stewart, Neil

2015-06-01

Web-based research is becoming ubiquitous in the behavioral sciences, facilitated by convenient, readily available participant pools and relatively straightforward ways of running experiments: most recently, through the development of the HTML5 standard. Although in most studies participants give untimed responses, there is a growing interest in being able to record response times online. Existing data on the accuracy and cross-machine variability of online timing measures are limited, and generally they have compared behavioral data gathered on the Web with similar data gathered in the lab. For this article, we took a more direct approach, examining two ways of running experiments online-Adobe Flash and HTML5 with CSS3 and JavaScript-across 19 different computer systems. We used specialist hardware to measure stimulus display durations and to generate precise response times to visual stimuli in order to assess measurement accuracy, examining effects of duration, browser, and system-to-system variability (such as across different Windows versions), as well as effects of processing power and graphics capability. We found that (a) Flash and JavaScript's presentation and response time measurement accuracy are similar; (b) within-system variability is generally small, even in low-powered machines under high load; (c) the variability of measured response times across systems is somewhat larger; and (d) browser type and system hardware appear to have relatively small effects on measured response times. Modeling of the effects of this technical variability suggests that for most within- and between-subjects experiments, Flash and JavaScript can both be used to accurately detect differences in response times across conditions. Concerns are, however, noted about using some correlational or longitudinal designs online.

BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.

PubMed

Shi, Xu; Barnes, Robert O; Chen, Li; Shajahan-Haq, Ayesha N; Hilakivi-Clarke, Leena; Clarke, Robert; Wang, Yue; Xuan, Jianhua

2015-07-15

Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence. The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.

PubMed

Deelen, Patrick; Bonder, Marc Jan; van der Velde, K Joeri; Westra, Harm-Jan; Winder, Erwin; Hendriksen, Dennis; Franke, Lude; Swertz, Morris A

2014-12-11

To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about which genomic strand is used as reference. Genotype Harmonizer (GH) is a command-line tool to harmonize genetic datasets by automatically solving issues concerning genomic strand and file format. GH solves the unknown strand issue by aligning ambiguous A/T and G/C SNPs to a specified reference, using linkage disequilibrium patterns without prior knowledge of the used strands. GH supports many common GWAS/NGS genotype formats including PLINK, binary PLINK, VCF, SHAPEIT2 & Oxford GEN. GH is implemented in Java and a large part of the functionality can also be used as Java 'Genotype-IO' API. All software is open source under license LGPLv3 and available from http://www.molgenis.org/systemsgenetics. GH can be used to harmonize genetic datasets across different file formats and can be easily integrated as a step in routine meta-analysis and imputation pipelines.

SoyFN: a knowledge database of soybean functional networks.

PubMed

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

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

NASA Astrophysics Data System (ADS)

Cha, Moon Hoe

2007-02-01

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

SOCR Motion Charts: An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data

PubMed Central

Al-Aziz, Jameel; Christou, Nicolas; Dinov, Ivo D.

2011-01-01

The amount, complexity and provenance of data have dramatically increased in the past five years. Visualization of observed and simulated data is a critical component of any social, environmental, biomedical or scientific quest. Dynamic, exploratory and interactive visualization of multivariate data, without preprocessing by dimensionality reduction, remains a nearly insurmountable challenge. The Statistics Online Computational Resource (www.SOCR.ucla.edu) provides portable online aids for probability and statistics education, technology-based instruction and statistical computing. We have developed a new Java-based infrastructure, SOCR Motion Charts, for discovery-based exploratory analysis of multivariate data. This interactive data visualization tool enables the visualization of high-dimensional longitudinal data. SOCR Motion Charts allows mapping of ordinal, nominal and quantitative variables onto time, 2D axes, size, colors, glyphs and appearance characteristics, which facilitates the interactive display of multidimensional data. We validated this new visualization paradigm using several publicly available multivariate datasets including Ice-Thickness, Housing Prices, Consumer Price Index, and California Ozone Data. SOCR Motion Charts is designed using object-oriented programming, implemented as a Java Web-applet and is available to the entire community on the web at www.socr.ucla.edu/SOCR_MotionCharts. It can be used as an instructional tool for rendering and interrogating high-dimensional data in the classroom, as well as a research tool for exploratory data analysis. PMID:21479108

Military Interoperable Digital Hospital Testbed (MIDHT)

DTIC Science & Technology

2013-10-01

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

Development and Utility of Automatic Language Processing Technologies. Volume 2

DTIC Science & Technology

2014-04-01

speech for each word using the existing Treetagger program. 3. Stem the word using the revised RevP stemmer, “RussianStemmer2013. java ” (see Section...KBaselineParaphrases2013. java ,” with the paraphrase table and a LM built from the TED training data. Information from the LM was called using the new utility query_interp...GATE/ Java Annotation Patterns Engine (JAPE) interface and on transliteration of Chinese named entities. Available Linguistic Data Consortium (LDC

A Recommender System in the Cyber Defense Domain

DTIC Science & Technology

2014-03-27

monitoring software is a java based program sending updates to the database on the sensor machine. The host monitoring program gathers information about...3.2.2 Database. A MySQL database located on the sensor machine acts as the storage for the sensors on the network. Snort, Nmap, vulnerability scores, and...machine with the IDS and the recommender is labeled “sensor”. The recommender system code is written in java and compiled using java version 1.6.024

Development of apprenticeship model for vocational school based on entrepreneurship

NASA Astrophysics Data System (ADS)

Sunyoto, Widodo, Joko; Samsudi

2018-03-01

The purpose of this study is to develop an apprenticeship model that focuses on the preparation of graduates of Vocational School to become entrepreneurs (entrepreneurs). The study was conducted by using Research and Development (R & D) method. The subjects were five Vocational Schools (State and Private) in Central Java. Data were collected through interview method and questionnaire. There were 26 teachers of Vocational School involved as respondent. In this research has produced an entrepreneurship-based model that is ready to be implemented at Vocational School. All respondents (100%) support the implementation of the offered model. There is only a small difference in the determination apprentice place whether at the business or industry sector. Most respondents (92.7%) agreed that apprenticeship place is in the small industry where the students can learn entrepreneurship from the entrepreneur. The rest of 7.7% of respondents prefer conduct the apprenticeship in the middle to upper industry where they would experience a modern and complete facility. It can be concluded that this model can be implemented with partners in small, medium, and large industries with a record of students can learn directly aspects of management with business owners instead of learning the technical aspects to employees only.

Cancer and lymph nodes

MedlinePlus

... page, please enable JavaScript. Lymph nodes are part of the lymph system , a network of organs, nodes, ducts, and vessels that support the ... urac.org). URAC's accreditation program is an independent audit to verify that A.D.A.M. follows rigorous standards of quality and accountability. A.D.A.M. is ...

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

NASA Technical Reports Server (NTRS)

Globus, Al; Menon, Madhu; Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

IBS: an illustrator for the presentation and visualization of biological sequences.

PubMed

Liu, Wenzhong; Xie, Yubin; Ma, Jiyong; Luo, Xiaotong; Nie, Peng; Zuo, Zhixiang; Lahrmann, Urs; Zhao, Qi; Zheng, Yueyuan; Zhao, Yong; Xue, Yu; Ren, Jian

2015-10-15

Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Implementation of integrated heterogeneous electronic electrocardiography data into Maharaj Nakorn Chiang Mai Hospital Information System.

PubMed

Khumrin, Piyapong; Chumpoo, Pitupoom

2016-03-01

Electrocardiography is one of the most important non-invasive diagnostic tools for diagnosing coronary heart disease. The electrocardiography information system in Maharaj Nakorn Chiang Mai Hospital required a massive manual labor effort. In this article, we propose an approach toward the integration of heterogeneous electrocardiography data and the implementation of an integrated electrocardiography information system into the existing Hospital Information System. The system integrates different electrocardiography formats into a consistent electrocardiography rendering by using Java software. The interface acts as middleware to seamlessly integrate different electrocardiography formats. Instead of using a common electrocardiography protocol, we applied a central format based on Java classes for mapping different electrocardiography formats which contains a specific parser for each electrocardiography format to acquire the same information. Our observations showed that the new system improved the effectiveness of data management, work flow, and data quality; increased the availability of information; and finally improved quality of care. © The Author(s) 2014.

Audio-based queries for video retrieval over Java enabled mobile devices

NASA Astrophysics Data System (ADS)

Ahmad, Iftikhar; Cheikh, Faouzi Alaya; Kiranyaz, Serkan; Gabbouj, Moncef

2006-02-01

In this paper we propose a generic framework for efficient retrieval of audiovisual media based on its audio content. This framework is implemented in a client-server architecture where the client application is developed in Java to be platform independent whereas the server application is implemented for the PC platform. The client application adapts to the characteristics of the mobile device where it runs such as screen size and commands. The entire framework is designed to take advantage of the high-level segmentation and classification of audio content to improve speed and accuracy of audio-based media retrieval. Therefore, the primary objective of this framework is to provide an adaptive basis for performing efficient video retrieval operations based on the audio content and types (i.e. speech, music, fuzzy and silence). Experimental results approve that such an audio based video retrieval scheme can be used from mobile devices to search and retrieve video clips efficiently over wireless networks.

Study on the generation technology of Li brocade pattern mutant genes based on the AI and Java technology

NASA Astrophysics Data System (ADS)

Zhou, Yuping; Zhang, Qi

2018-04-01

In the information environment, digital and information processing to Li brocade patterns reveals an important means of Li ethnic style and inheriting the national culture. Adobe Illustrator CS3 and Java language were used in the paper to make "variation" processing to Li brocade patterns, and generate "Li brocade pattern mutant genes". The generation of pattern mutant genes includes color mutation, shape mutation, adding and missing transform, and twisted transform, etc. Research shows that Li brocade pattern mutant genes can be generated by using the Adobe Illustrator CS3 and the image processing tools of Java language edit, etc.

The water quality and Cultivant enrichment potency of pond based on saprobic index at north coastal waters of Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Hidayat, Jafron W.

2018-05-01

Central Java is one of many areas which has long coastline, especially in the Northern Coast of Java Island. Intertidal activities occurred at this area may affect the transport of material and energy from surroundings. Cultivation activity supplies many inputs, i.e. feeds, chemicals (vitamin and mineral), including pollutants from feces and unconsumed feeds that affects the environment. One of water management is done through bioremediation by using vegetative agents (soft rehabilitation), such as seaweed and mangrove stands. The implementation of soft rehabilitation is highly depend on the existing environmental conditions of the ponds and surrounding waters. Therefore, it is very important to identify the condition of those waters first. The purpose of this study is to identify the quality of waters in the north coast of Central Java. Besides, it is also to analyze the potency of enriching cultivated commodity (cultivant), as well as a soft remediation mechanism using seaweed. The study was conducted in the coastal areas of Central Java, mainly to the locations commonly practicing cultivation in the pond waters; namely Brebes, Pemalang, Semarang, Demak, Pati and Jepara. Data were taken by sampling at least at 3 different sites as repetition, included ponds, public irrigations and coastline waters. The water sample was taken as much as 30 lt and filtered using plankton net no 25. Biodiversity of Shannon-Wiener Index (H'), evenness index (e) and Saprobic Index were used to analyze the plankton data. Result showed that plankton diversity in Central Java coasts were varied generally between 10 – 28 species. The most widely found species were Oscillatoria sp, Rhizosolenia styliformes, Surirella sp and Lyngbia conferoides. The diversity index varied from 1.83 to 2.9 with the stability status were between small to medium. The saprobic index showed a value between 0.33 up to 2.27; which indicated very small up to lightly contaminated status. The biggest stability disturbance was found in Batangan (Pati) water, especially because the existence of salt production practice in the pond during dry season. The optimum polyculture practice was found in Brebes, since this water was still suitable to support aquaculture in multitrophic basis, so called IMTA (Integrated Multitrophic Aquaculture). In general, the other pantura waters were still liable to be enriched with other cultivants, including seaweed which is also economically valuable (as a commodity) and also ecologically functional in controlling turbidity and contamination.

Computational Software to Fit Seismic Data Using Epidemic-Type Aftershock Sequence Models and Modeling Performance Comparisons

NASA Astrophysics Data System (ADS)

Chu, A.

2016-12-01

Modern earthquake catalogs are often analyzed using spatial-temporal point process models such as the epidemic-type aftershock sequence (ETAS) models of Ogata (1998). My work implements three of the homogeneous ETAS models described in Ogata (1998). With a model's log-likelihood function, my software finds the Maximum-Likelihood Estimates (MLEs) of the model's parameters to estimate the homogeneous background rate and the temporal and spatial parameters that govern triggering effects. EM-algorithm is employed for its advantages of stability and robustness (Veen and Schoenberg, 2008). My work also presents comparisons among the three models in robustness, convergence speed, and implementations from theory to computing practice. Up-to-date regional seismic data of seismic active areas such as Southern California and Japan are used to demonstrate the comparisons. Data analysis has been done using computer languages Java and R. Java has the advantages of being strong-typed and easiness of controlling memory resources, while R has the advantages of having numerous available functions in statistical computing. Comparisons are also made between the two programming languages in convergence and stability, computational speed, and easiness of implementation. Issues that may affect convergence such as spatial shapes are discussed.

A comparison of common programming languages used in bioinformatics.

PubMed

Fourment, Mathieu; Gillings, Michael R

2008-02-05

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

A comparison of common programming languages used in bioinformatics

PubMed Central

Fourment, Mathieu; Gillings, Michael R

2008-01-01

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

Parallel Implementation of Triangular Cellular Automata for Computing Two-Dimensional Elastodynamic Response on Arbitrary Domains

NASA Astrophysics Data System (ADS)

Leamy, Michael J.; Springer, Adam C.

In this research we report parallel implementation of a Cellular Automata-based simulation tool for computing elastodynamic response on complex, two-dimensional domains. Elastodynamic simulation using Cellular Automata (CA) has recently been presented as an alternative, inherently object-oriented technique for accurately and efficiently computing linear and nonlinear wave propagation in arbitrarily-shaped geometries. The local, autonomous nature of the method should lead to straight-forward and efficient parallelization. We address this notion on symmetric multiprocessor (SMP) hardware using a Java-based object-oriented CA code implementing triangular state machines (i.e., automata) and the MPI bindings written in Java (MPJ Express). We use MPJ Express to reconfigure our existing CA code to distribute a domain's automata to cores present on a dual quad-core shared-memory system (eight total processors). We note that this message passing parallelization strategy is directly applicable to computer clustered computing, which will be the focus of follow-on research. Results on the shared memory platform indicate nearly-ideal, linear speed-up. We conclude that the CA-based elastodynamic simulator is easily configured to run in parallel, and yields excellent speed-up on SMP hardware.

A mobile tool about causes and distribution of dramatic natural phenomena

NASA Astrophysics Data System (ADS)

Boppidi, Ravikanth Reddy

Most Research suggests that tablet computers could aid the study of many scientific concepts that are difficult to grasp, such as places, time and statistics. These occur especially in the study of geology, chemistry, biology and so on. Tapping the technology will soon become critical career training for future generations. Teaching through mobile is more interactive and helps students to grasp quickly. In this thesis an interactive mobile tool is developed which explains about the causes and distribution of natural disasters like Earthquakes, Tsunami, Tropical Cyclones, Volcanic Eruptions and Tornadoes. The application shows the places of disasters on an interactive map and it also contains YouTube embedded videos, which explain the disasters visually. The advantage of this tool is, it can be deployed onto major mobile operating systems like Android and IOS. The application's user interface (UI) is made very responsive using D3 JavaScript, JQuery, Java Script, HTML, CSS so that it can adapt to mobiles, tablets, and desktop screens.

Earthquake disaster mitigation of Lembang Fault West Java with electromagnetic method

NASA Astrophysics Data System (ADS)

Widodo

2015-04-01

The Lembang fault is located around eight kilometers from Bandung City, West Java, Indonesia. The existence of this fault runs through densely populated settlement and tourism area. It is an active fault structure with increasing seismic activity where the 28 August 2011 earthquake occurred. The seismic response at the site is strongly influenced by local geological conditions. The ambient noise measurements from the western part of this fault give strong implication for a complex 3-D tectonic setting. Hence, near surface Electromagnetic (EM) measurements are carried out to understand the location of the local active fault of the research area. Hence, near surface EM measurements are carried out to understand the location of the local active fault and the top of the basement structure of the research area. The Transientelectromagnetic (TEM) measurements are carried out along three profiles, which include 35 TEM soundings. The results indicate that TEM data give detailed conductivity distribution of fault structure in the study area.

Earthquake disaster mitigation of Lembang Fault West Java with electromagnetic method

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

Widodo, E-mail: widodo@gf.itb.ac.id

The Lembang fault is located around eight kilometers from Bandung City, West Java, Indonesia. The existence of this fault runs through densely populated settlement and tourism area. It is an active fault structure with increasing seismic activity where the 28 August 2011 earthquake occurred. The seismic response at the site is strongly influenced by local geological conditions. The ambient noise measurements from the western part of this fault give strong implication for a complex 3-D tectonic setting. Hence, near surface Electromagnetic (EM) measurements are carried out to understand the location of the local active fault of the research area. Hence,more » near surface EM measurements are carried out to understand the location of the local active fault and the top of the basement structure of the research area. The Transientelectromagnetic (TEM) measurements are carried out along three profiles, which include 35 TEM soundings. The results indicate that TEM data give detailed conductivity distribution of fault structure in the study area.« less

Combined aerial and terrestrial images for complete 3D documentation of Singosari Temple based on Structure from Motion algorithm

NASA Astrophysics Data System (ADS)

Hidayat, Husnul; Cahyono, A. B.

2016-11-01

Singosaritemple is one of cultural heritage building in East Java, Indonesia which was built in 1300s and restorated in 1934-1937. Because of its history and importance, complete documentation of this temple is required. Nowadays with the advent of low cost UAVs combining aerial photography with terrestrial photogrammetry gives more complete data for 3D documentation. This research aims to make complete 3D model of this landmark from aerial and terrestrial photographs with Structure from Motion algorithm. To establish correct scale, position, and orientation, the final 3D model was georeferenced with Ground Control Points in UTM 49S coordinate system. The result shows that all facades, floor, and upper structures can be modeled completely in 3D. In terms of 3D coordinate accuracy, the Root Mean Square Errors (RMSEs) are RMSEx=0,041 m; RMSEy=0,031 m; RMSEz=0,049 m which represent 0.071 m displacement in 3D space. In addition the mean difference of lenght measurements of the object is 0,057 m. With this accuracy, this method can be used to map the site up to 1:237 scale. Although the accuracy level is still in centimeters, the combined aerial and terrestrial photographs with Structure from Motion algorithm can provide complete and visually interesting 3D model.

An inconspicuous, conspicuous new species of Asian pipesnake, genus Cylindrophis (Reptilia: Squamata: Cylindrophiidae), from the south coast of Jawa Tengah, Java, Indonesia, and an overview of the tangled taxonomic history of C. ruffus (Laurenti, 1768).

PubMed

Kieckbusch, Max; Mecke, Sven; Hartmann, Lukas; Ehrmantraut, Lisa; O'shea, Mark; Kaiser, Hinrich

2016-03-20

We describe a new species of Cylindrophis currently known only from Grabag, Purworejo Regency, Jawa Tengah Pro-vince (Central Java), Java, Indonesia. Cylindrophis subocularis sp. nov. can be distinguished from all congeners by the presence of a single, eponymous subocular scale between the 3^rd and 4^th or 4^th and 5^th supralabial, preventing contact between the 4^th or 5^th supralabial and the orbit, and by having the prefrontal in narrow contact with or separated from the orbit. We preface our description with a detailed account of the tangled taxonomic history of the similar and putatively wide-ranging species C. ruffus, which leads us to (1) remove the name Scytale scheuchzeri from the synonymy of C. ruffus, (2) list the taxon C. rufa var. javanica as species inquirenda, and (3) synonymize C. mirzae with C. ruffus. We provide additional evidence to confirm that the type locality of C. ruffus is Java. Cylindrophis subocularis sp. nov. is the second species of Asian pipesnake from Java.

An Analysis Platform for Mobile Ad Hoc Network (MANET) Scenario Execution Log Data

DTIC Science & Technology

2016-01-01

these technologies. 4.1 Backend Technologies • Java 1.8 • my-sql-connector- java -5.0.8.jar • Tomcat • VirtualBox • Kali MANET Virtual Machine 4.2...Frontend Technologies • LAMPP 4.3 Database • MySQL Server 5. Database The SEDAP database settings and structure are described in this section...contains all the backend java functionality including the web services, should be placed in the webapps directory inside the Tomcat installation

A Telemetry Browser Built with Java Components

NASA Astrophysics Data System (ADS)

Poupart, E.

In the context of CNES balloon scientific campaigns and telemetry survey field, a generic telemetry processing product, called TelemetryBrowser in the following, was developed reusing COTS, Java Components for most of them. Connection between those components relies on a software architecture based on parameter producers and parameter consumers. The first one transmit parameter values to the second one which has registered to it. All of those producers and consumers can be spread over the network thanks to Corba, and over every kind of workstation thanks to Java. This gives a very powerful mean to adapt to constraints like network bandwidth, or workstations processing or memory. It's also very useful to display and correlate at the same time information coming from multiple and various sources. An important point of this architecture is that the coupling between parameter producers and parameter consumers is reduced to the minimum and that transmission of information on the network is made asynchronously. So, if a parameter consumer goes down or runs slowly, there is no consequence on the other consumers, because producers don't wait for their consumers to finish their data processing before sending it to other consumers. An other interesting point is that parameter producers, also called TelemetryServers in the following are generated nearly automatically starting from a telemetry description using Flavori component. Keywords Java components, Corba, distributed application, OpenORBii, software reuse, COTS, Internet, Flavor. i Flavor (Formal Language for Audio-Visual Object Representation) is an object-oriented media representation language being developed at Columbia University. It is designed as an extension of Java and C++ and simplifies the development of applications that involve a significant media processing component (encoding, decoding, editing, manipulation, etc.) by providing bitstream representation semantics. (flavor.sourceforge.net) ii OpenORB provides a Java implementation of the OMG Corba 2.4.2 specification (openorb.sourceforge.net) 1/16

Timely Diagnostic Feedback for Database Concept Learning

ERIC Educational Resources Information Center

Lin, Jian-Wei; Lai, Yuan-Cheng; Chuang, Yuh-Shy

2013-01-01

To efficiently learn database concepts, this work adopts association rules to provide diagnostic feedback for drawing an Entity-Relationship Diagram (ERD). Using association rules and Asynchronous JavaScript and XML (AJAX) techniques, this work implements a novel Web-based Timely Diagnosis System (WTDS), which provides timely diagnostic feedback…

Parallel Computing Using Web Servers and "Servlets".

ERIC Educational Resources Information Center

Lo, Alfred; Bloor, Chris; Choi, Y. K.

2000-01-01

Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

Indonesia's great frontier and migration policy.

PubMed

Maloney, C

1987-01-01

The population of Indonesia is 175 million, of which 65% live in Java. Java has only 7% of the land area, causing a population density of 2,000/square mile. This has lead the government to introduce a policy of transmigration which encourages people to move from Java to the larger outer islands. In the last 35 years 4.3 million people have moved from Java to Sumatra, Borneo, Celebes, and Irian Jaya. The total area of Indonesia stretches over 3,200 miles and has 16,000 islands of which 1,000 are inhabited. It has vast resources of oil, lumber, rubber, tin, palm oil, copra, coffee, tea, pepper, cloves, nutmeg, and quinine. Indonesia is also rich in minerals, including coal, bauxite, iron ore, and gold. Even with a national family planning program, population growth has reached 2.1% a year. 3 other islands that people are induced to move from are Madura, Bali, and Lombok, although their population densities are less then Java. The small islands near Singapore are being developed and Batam will be a free port to compete with Hong Kong. The most intense migration has been to Kalimantan (Borneo) which has 4 provinces. The migration policy began in 1905 and by 1930 100,000 people, had moved to other islands; 600,000 people were relocated to plantations in Java for labor needs. In 1979-84, a more ambitious program costing 2.3 billion moved 1.5 million people. In the most recent 1984-89 plan, a goal of 3.1 million were to be relocated but due to budgetary restrictions only 150,000 families have moved. The main social issue addresses the domination of other people by Javanese, not only in numbers but cultural differences. Some observers say the real reason for migration is political in ensuring the boundaries and geographic integrity of Indonesia.

Spatial Collaboration Model among Local Governments in Ratubangnegoro Region in the Boundary Area of Central Java and East Java Provinces, Indonesia

NASA Astrophysics Data System (ADS)

Wahyono, H.; Wahdah, L.

2018-02-01

In Indonesia, according to Law No. 23/2014 on Local Government, a local government can conduct cooperation with other local governments that are based on considerations of efficiency and effectiveness of public services and mutual benefit, in order to improve people's welfare. Such cooperation can be categorized into mandatory and voluntary cooperation. Cooperation shall be developed jointly between the adjacent areas for the implementation of government affairs which have cross-local government externalities; and the provision of public services more efficient if managed together. One of the parts of the area that is directly related to the implementation of the policy liabilities of inter-local government cooperation which is mandated is the he province boundary areas. The public management of the provincial boundary areas is different from the central province area. While the central province area considers only their own interests, the management of boundary development must consider the neighboring regions. On one hand, the area is influenced only by its own province policy, while on the other influenced by neighboring regions. Meanwhile, a local government tends to resist the influence and intervention of neighboring regions. Likewise, neighboring local governments also tend to resist the influence and intervention of other local governments. Therefore, when interacting on the boundary, inter-local government interaction is not only the potential for cooperation, but also conflict-prone regions. One of the boundary area provinces attempt to implement the collaborative planning approach is the boundary area of Central Java Province and East Java Province, which is known as Ratubangnegoro Region. Ratubangnegoro region is one of the strategic areas of both provinces. In order to the interaction between the region could take place, there are regencies in the region have formed and joined the Inter-Local Government Cooperation Agency (BKAD-Badan Kerjasama Antar Daerah) Ratubangnegoro. Based on the explanation, this article explains the institutional model of collaborative planning contained in BKAD Ratubangnegoro. The model is much more complex, because it involves two different levels of government, provincial and regency government hierarchies. Institutional model of cooperation in the regency boundary area should be different from that of between provinces. The results of this are expected to be input from related parties of the inter-regional cooperation institution, particularly cooperation in the area of the provincial boundary with the province, which is implemented by the regencies contained therein.

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.

PDBsum: Structural summaries of PDB entries.

PubMed

Laskowski, Roman A; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M

2018-01-01

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum. © 2017 The Protein Society.

McIDAS-V: Advanced Visualization for 3D Remote Sensing Data

NASA Astrophysics Data System (ADS)

Rink, T.; Achtor, T. H.

2010-12-01

McIDAS-V is a Java-based, open-source, freely available software package for analysis and visualization of geophysical data. Its advanced capabilities provide very interactive 4-D displays, including 3D volumetric rendering and fast sub-manifold slicing, linked to an abstract mathematical data model with built-in metadata for units, coordinate system transforms and sampling topology. A Jython interface provides user defined analysis and computation in terms of the internal data model. These powerful capabilities to integrate data, analysis and visualization are being applied to hyper-spectral sounding retrievals, eg. AIRS and IASI, of moisture and cloud density to interrogate and analyze their 3D structure, as well as, validate with instruments such as CALIPSO, CloudSat and MODIS. The object oriented framework design allows for specialized extensions for novel displays and new sources of data. Community defined CF-conventions for gridded data are understood by the software, and can be immediately imported into the application. This presentation will show examples how McIDAS-V is used in 3-dimensional data analysis, display and evaluation.

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 accommodated by the Java megathrust, and a much smaller parallel motion accommodated along the Baribis (∼ 5 ± 0.2 mm /yr) and Kendeng (∼ 2.3 ± 0.7 mm /yr) Thrusts. Our study highlights a correlation between the geodetically inferred active faults and historical seismic catalogs, emphasizing the importance of considering crustal fault activity within Java in future seismic assessments.

The enhancement model of ICT competence for the teachers of SMP Terbuka in Central Java to support long distance learning program

NASA Astrophysics Data System (ADS)

Widowati, Trisnani; Purwanti, Dwi

2017-03-01

ICT-based learning for SMP Terbuka is a manifestation of the first pillar of DEPDIKNAS Strategic Plan 2005-2009, about the use of ICT as the facility of long distance learning. By implementing ICT-based learning, the communication between the teacher and the students is possible to happen although both parties are in differnet places. The problem in implementing ICT-based learning for SMP Terbuka is the low competence of the teachers in ICT mastery, because this research is aimed to formulate the enhancement model of ICT competence for the teachers of SMP Terbuka in Central Java to support long distance learning program. This research shows that Supervised-Teachers and Tutor Teachers Competence in ICT is still low with the average of Supervised-Teachers competence in operating Ms.Word application of 59.6%, Ms.Excel 55.40%, Power Point 43.40% and internet mastery of 41.8%; while the competence of Tutor Teachers is lower with the average of 40.40% in operating Ms. Word, 35.20% in Ms.Excel, 28.00% in Power Point, and 29% in internet mastery. It means that Supervised-Teachers understand ICT, but they do not master it; while Tutor Teachers have just understood ICT and have a low mastery in Ms.Word. The output of this research is: The new findings of the enhancement model of ICT competence for the teachers of SMP Terbuka in Central Java to support long distance learning program.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

LibKiSAO: a Java library for Querying KiSAO.

PubMed

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

2012-09-24

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

A case Study of Applying Object-Relational Persistence in Astronomy Data Archiving

NASA Astrophysics Data System (ADS)

Yao, S. S.; Hiriart, R.; Barg, I.; Warner, P.; Gasson, D.

2005-12-01

The NOAO Science Archive (NSA) team is developing a comprehensive domain model to capture the science data in the archive. Java and an object model derived from the domain model weil address the application layer of the archive system. However, since RDBMS is the best proven technology for data management, the challenge is the paradigm mismatch between the object and the relational models. Transparent object-relational mapping (ORM) persistence is a successful solution to this challenge. In the data modeling and persistence implementation of NSA, we are using Hibernate, a well-accepted ORM tool, to bridge the object model in the business tier and the relational model in the database tier. Thus, the database is isolated from the Java application. The application queries directly on objects using a DBMS-independent object-oriented query API, which frees the application developers from the low level JDBC and SQL so that they can focus on the domain logic. We present the detailed design of the NSA R3 (Release 3) data model and object-relational persistence, including mapping, retrieving and caching. Persistence layer optimization and performance tuning will be analyzed. The system is being built on J2EE, so the integration of Hibernate into the EJB container and the transaction management are also explored.

CO2 flux from Javanese mud volcanism

NASA Astrophysics Data System (ADS)

Queißer, M.; Burton, M. R.; Arzilli, F.; Chiarugi, A.; Marliyani, G. I.; Anggara, F.; Harijoko, A.

2017-06-01

Studying the quantity and origin of CO2 emitted by back-arc mud volcanoes is critical to correctly model fluid-dynamical, thermodynamical, and geochemical processes that drive their activity and to constrain their role in the global geochemical carbon cycle. We measured CO2 fluxes of the Bledug Kuwu mud volcano on the Kendeng Fold and thrust belt in the back arc of Central Java, Indonesia, using scanning remote sensing absorption spectroscopy. The data show that the expelled gas is rich in CO2 with a volume fraction of at least 16 vol %. A lower limit CO2 flux of 1.4 kg s-1 (117 t d-1) was determined, in line with the CO2 flux from the Javanese mud volcano LUSI. Extrapolating these results to mud volcanism from the whole of Java suggests an order of magnitude total CO2 flux of 3 kt d-1, comparable with the expected back-arc efflux of magmatic CO2. After discussing geochemical, geological, and geophysical evidence we conclude that the source of CO2 observed at Bledug Kuwu is likely a mixture of thermogenic, biogenic, and magmatic CO2, with faulting controlling potential pathways for magmatic fluids. This study further demonstrates the merit of man-portable active remote sensing instruments for probing natural gas releases, enabling bottom-up quantification of CO2 fluxes.

DAKOTA JAGUAR 3.0 user's manual.

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

Adams, Brian M.; Bauman, Lara E; Chan, Ethan

2013-05-01

JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the features necessary to use JAGUAR.

Numerical simulations of block-and-ash flows using the Titan2D flow model: examples from the 2006 eruption of Merapi Volcano, Java, Indonesia

NASA Astrophysics Data System (ADS)

Charbonnier, S. J.; Gertisser, R.

2009-10-01

We present Titan2D simulations of two well-characterized block-and-ash flow (BAF) events of the 2006 eruption of Merapi (Java, Indonesia) that affected the Gendol valley on the volcano’s southern flank and adjacent, densely populated interfluve (non-valley) areas: (1) a single dome-collapse event to the south that generated one of the smaller, post-June 14 flows and (2) a sustained, multiple dome-collapse event, also directed to the south, that produced the largest flows of the 2006 eruption emplaced in the afternoon of June 14. Using spatially varying bed friction angles, Titan2D is capable of reproducing the paths, velocities, runout distance, areas covered and deposited volumes of these flows over highly complex topography. The model results provide the basis for estimating the areas and levels of hazards associated with BAFs generated during relatively short as well as prolonged dome-collapse periods and guidance during future eruptive crises at Merapi.

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

PubMed

Burger, Melanie C

2015-01-01

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

Bootstrapping Methods Applied for Simulating Laboratory Works

ERIC Educational Resources Information Center

Prodan, Augustin; Campean, Remus

2005-01-01

Purpose: The aim of this work is to implement bootstrapping methods into software tools, based on Java. Design/methodology/approach: This paper presents a category of software e-tools aimed at simulating laboratory works and experiments. Findings: Both students and teaching staff use traditional statistical methods to infer the truth from sample…

"Carbopolis": A Java Technology-Based Free Software for Environmental Education

ERIC Educational Resources Information Center

Eichler, Marcelo Leandro; Xavier, Paulo Rafael; Araujo, Roberto Costa; Forte, Rafael Castro; Del Pino, Jose Claudio

2005-01-01

The goals of this paper are to describe some characteristics of the pedagogical project of the "Carbopolis" software and some programming solutions that were found during the computational implementation of this software. Relative to the first goal, some pedagogical features that are considered necessary to developing computerized learning…

Virtually Exploring A Pillar Of Experimental Physics: The Hertz Experiment

NASA Astrophysics Data System (ADS)

Bonanno, A.; Sapia, P.; Camarca, M.; Oliva, A.

2008-05-01

In the present work we report on the implementation and early assessment of a multimedia learning object, developed using the Java programming language, which also integrates in a creative way some internet freely available educational resources, intended to support the teaching/learning process of the historical Hertz experiment.

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

PubMed Central

2010-01-01

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/ PMID:20565938

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.

Implementation of Kriging Methods in Mobile GIS to Estimate Damage to Buildings in Crisis Scenarios

NASA Astrophysics Data System (ADS)

Laun, S.; Rösch, N.; Breunig, M.; Doori, M. Al

2016-06-01

In the paper an example for the application of kriging methods to estimate damage to buildings in crisis scenarios is introduced. Furthermore, the Java implementations for Ordinary and Universal Kriging on mobile GIS are presented. As variogram models an exponential, a Gaussian and a spherical variogram are tested in detail. Different test constellations are introduced with various information densities. As test data set, public data from the analysis of the 2010 Haiti earthquake by satellite images are pre-processed and visualized in a Geographic Information System. As buildings, topography and other external influences cannot be seen as being constant for the whole area under investigation, semi variograms are calculated by consulting neighboured classified buildings using the so called moving window method. The evaluation of the methods shows that the underlying variogram model is the determining factor for the quality of the interpolation rather than the choice of the kriging method or increasing the information density of a random sample. The implementation is completely realized with the programming language Java. Thereafter, the implemented software component is integrated into GeoTech Mobile, a mobile GIS Android application based on the processing of standardized spatial data representations defined by the Open Geospatial Consortium (OGC). As a result the implemented methods can be used on mobile devices, i.e. they may be transferred to other application fields. That is why we finally point out further research with new applications in the Dubai region.

The VTIE telescope resource management system

NASA Astrophysics Data System (ADS)

Busschots, B.; Keating, J. G.

2005-06-01

The VTIE Telescope Resource Management System (TRMS) provides a frame work for managing a distributed group of internet telescopes as a single "Virtual Observatory". The TRMS provides hooks which allow for it to be connected to any Java Based web portal and for a Java based scheduler to be added to it. The TRMS represents each telescope and observatory in the system with a software agent and then allows the scheduler and web portal to communicate with these distributed resources in a simple transparent way, hence allowing the scheduler and portal designers to concentrate only on what they wish to do with these resources rather than how to communicate with them. This paper outlines the structure and implementation of this frame work.

Implementation Of Conservation Policy Through The Protection Of Life Support System In The Karimunjawa National Park

NASA Astrophysics Data System (ADS)

Ariyani, Nur Anisa Eka; Kismartini

2018-02-01

The Karimunjawa National Park as the only one marine protected area in Central Java, managed by zonation system has decreased natural resources in the form of decreasing mangrove forest area, coral cover, sea biota population such as clams and sea cucumbers. Conservation has been done by Karimunjawa National Park Authority through protection of life support system activities in order to protect the area from degradation. The objective of the research is to know the implementation of protection and security activities of Karimunjawa National Park Authority for the period of 2012 - 2016. The research was conducted by qualitative method, processing secondary data from Karimunjawa National Park Authority and interview with key informants. The results showed that protection and security activities in The Karimunjawa National Park were held with three activities: pre-emptive activities, preventive activities and repressive activities. Implementation of conservation policy through protection of life support system is influenced by factors of policy characteristic, resource factor and environmental policy factor. Implementation of conservation policy need support from various parties, not only Karimunjawa National Park Authority as the manager of the area, but also need participation of Jepara Regency, Central Java Provinces, communities, NGOs, researchers, developers and tourism actors to maintain and preserve existing biodiversity. Improving the quality of implementors through education and training activities, the availability of the state budget annually and the support of stakeholders is essential for conservation.

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.

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

Using Multimedia Metadata to Improve Network Efficiency

DTIC Science & Technology

2012-09-01

the north-aligned bounding box. When compared using all angular variations for the direction-of-travel-aligned 3:4 aspect ratio bounding box, the...programs that run the experiment are written in Java . The experiment consists of two distinct programs that communicate via Java sockets (TCP). 1

A NEW SYSTEM TO MONITOR DATA ANALYSES AND RESULTS OF PHYSICS DATA VALIDATION BETWEEN PULSES AT DIII-D

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

FLANAGAN,A; SCHACHTER,J.M; SCHISSEL,D.P

2003-02-01

A Data Analysis Monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility (http://nssrv1.gat.com:8000/dam). The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded thus increasing the efficiency of experimental time. An example of a consistency check is comparing the experimentally measured neutron rate and the expected neutron emission, RDD0D. A significant difference between these two values could indicate a problem with one ormore » more diagnostics, or the presence of unanticipated phenomena in the plasma. This new system also tracks the progress of MDSplus dispatched data analysis software and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, CLIPS to implement expert system logic, and displays its results to multiple web clients via HTML. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse.« less

System to monitor data analyses and results of physics data validation between pulses at DIII-D

NASA Astrophysics Data System (ADS)

Flanagan, S.; Schachter, J. M.; Schissel, D. P.

2004-06-01

A data analysis monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility (http://nssrv1.gat.com:8000/dam). The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded, thus increasing the efficiency of experimental time. An example of a consistency check is comparing the experimentally measured neutron rate and the expected neutron emission, RDD0D. A significant difference between these two values could indicate a problem with one or more diagnostics, or the presence of unanticipated phenomena in the plasma. This system also tracks the progress of MDSplus dispatched data analysis software and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, C Language Integrated Production System to implement expert system logic, and displays its results to multiple web clients via Hypertext Markup Language. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse.

Web mapping system for complex processing and visualization of environmental geospatial datasets

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny; Okladnikov, Igor

2016-04-01

Environmental geospatial datasets (meteorological observations, modeling and reanalysis results, etc.) are used in numerous research applications. Due to a number of objective reasons such as inherent heterogeneity of environmental datasets, big dataset volume, complexity of data models used, syntactic and semantic differences that complicate creation and use of unified terminology, the development of environmental geodata access, processing and visualization services as well as client applications turns out to be quite a sophisticated task. According to general INSPIRE requirements to data visualization geoportal web applications have to provide such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. It should be noted that modern web mapping systems as integrated geoportal applications are developed based on the SOA and might be considered as complexes of interconnected software tools for working with geospatial data. In the report a complex web mapping system including GIS web client and corresponding OGC services for working with geospatial (NetCDF, PostGIS) dataset archive is presented. There are three basic tiers of the GIS web client in it: 1. Tier of geospatial metadata retrieved from central MySQL repository and represented in JSON format 2. Tier of JavaScript objects implementing methods handling: --- NetCDF metadata --- Task XML object for configuring user calculations, input and output formats --- OGC WMS/WFS cartographical services 3. Graphical user interface (GUI) tier representing JavaScript objects realizing web application business logic Metadata tier consists of a number of JSON objects containing technical information describing geospatial datasets (such as spatio-temporal resolution, meteorological parameters, valid processing methods, etc). The middleware tier of JavaScript objects implementing methods for handling geospatial metadata, task XML object, and WMS/WFS cartographical services interconnects metadata and GUI tiers. The methods include such procedures as JSON metadata downloading and update, launching and tracking of the calculation task running on the remote servers as well as working with WMS/WFS cartographical services including: obtaining the list of available layers, visualizing layers on the map, exporting layers in graphical (PNG, JPG, GeoTIFF), vector (KML, GML, Shape) and digital (NetCDF) formats. Graphical user interface tier is based on the bundle of JavaScript libraries (OpenLayers, GeoExt and ExtJS) and represents a set of software components implementing web mapping application business logic (complex menus, toolbars, wizards, event handlers, etc.). GUI provides two basic capabilities for the end user: configuring the task XML object functionality and cartographical information visualizing. The web interface developed is similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Web mapping system developed has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical form. The work is supported by SB RAS Basic Program Projects VIII.80.2.1 and IV.38.1.7.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

Beginning a few thousand years ago, global climate and environmental change have become more and more affected by human activities. Hence, quantifying the 'human component' becomes increasingly important in order to predict future developments. Indonesia and the surrounding oceans are key in this respect, because it is in the region (i) that receives the highest inputs of water, sediment and associated dissolved and particulate substances and (ii) that suffers from anthropogenically modified landscapes and coastal zones. As opposing the global trend, land-based human activities have increased the sediment input into the ocean from Indonesia since pre-human times. Nevertheless, there are strong gradients in land use/cover and resulting river fluxes within Indonesia as, for example, between Java and Kalimantan. Major goal of this study is to identify the contribution of human activities in river catchments (i.e. land use/cover change, hydrological alterations) to gradients in carbon and nitrogen deposition in sediments of the Java Sea between densely populated Java and sparsely populated Kalimantan during the Late Holocene. We hypothesized that the riverine input of C and N increased during the late Holocene and increased more off Java than off Kalimantan. Sediment cores (80 to 130 cm long) off major river mouths from Java (2 cores off Bengawan Solo) and Kalimantan (1 core off Pembuang, 1 core off Jelai) were dated and analysed for Corg, Ntot, carbonate and stable isotope composition (δ13Corg, δ15N) in 3 cm intervals. Sedimentation rates off the Kalimantan rivers with 0.05-0.11 cm yr-1 were higher than off the Bengawan Solo, the largest river catchment on Java (<0.04 cm yr-1). Ntot contents in all sediment cores were low with ~0.07% and varied little over time. A higher Corg content, molar C/N ratio and variability over the past 5000 years in all parameters in the core closer to the river mouth off the Bengawan Solo than the one further offshore indicates that terrestrial input into the Java Sea was limited to approx. 15 km off the river mouth. Both cores off Kalimantan and the core off Java close to the Bengawan Solo had similar Corg contents (~0.8%) and molar C/N-ratios (11-19). δ13Corg of -24‰ and low carbonate contents (~7%) indicate an even higher contribution of terrigenous organic matter off the Kalimantan rivers than off the Bengawan Solo, where δ13Corg of -22‰ and CaCO3 contents of ~17% rather point to marine phytoplankton as major organic matter source. Our preliminary results indicate a higher input of terrigenous organic matter from Kalimantan than from Java and show little evidence for anthropogenic impact on organic matter inputs into the Java Sea during the late Holocene.

SuperNatural: a searchable database of available natural compounds.

PubMed

Dunkel, Mathias; Fullbeck, Melanie; Neumann, Stefanie; Preissner, Robert

2006-01-01

Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of approximately 50,000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used. The SuperNatural Database is publicly available at http://bioinformatics.charite.de/supernatural. Viewing requires the free Chime-plugin from MDL (Chime) or Java2 Runtime Environment (MView), which is also necessary for using Marvin application for chemical drawing.

Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.

PubMed

Piccolo, Brian D; Wankhade, Umesh D; Chintapalli, Sree V; Bhattacharyya, Sudeepa; Chunqiao, Luo; Shankar, Kartik

2018-03-15

Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive. DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed. bdpiccolo@uams.edu.

A Network Design Architecture for Distribution of Generic Scene Graphs

DTIC Science & Technology

1999-09-01

with UML. Addison Wesley. Deitel, H. and Deitel, P. 1994. C++ How to Program . Prentice Hall. Deitel, H. and Deitel, P. 1998. JAVA How ... to . Program . Prentice.Hall. Eckel, B. 1998. Thinking in JAVA. Prentice Hall. 141 Edwards, J. 1997. 3-Tier Client/Server At Work. John

TV Crime Reporter Missed Clues | NIH MedlinePlus the Magazine

MedlinePlus

... JavaScript on. Feature: Women and Heart Disease TV Crime Reporter Missed Clues Past Issues / Spring 2016 Table ... heart attack at the age of 36. A crime reporter for WJLA-TV in Washington, D.C., ...

Assessment of Differential Uplift Along South Java, Indonesia from Terrace Elevations Mapped with Structure from Motion Photogrammetry

NASA Astrophysics Data System (ADS)

Andreini, J.; Bunds, M. P.; Harris, R. A.; Yulianto, E.; Horns, D. M.; Prasetyadi, C.; Putra, P. S.

2016-12-01

Assessment of Differential Uplift Along South Java, Indonesia from Terrace Elevations Mapped with Structure from Motion Photogrammetry Jeremy Andreini, Michael Bunds, Ronald Harris, Eko Yulianto, Carolus Prasetyadi, Daniel Horns, Purna Putra Is differential uplift occurring on the south coast of Java? Java is on the southern edge of the Sunda plate, above the subducting Indo-Australian plate. Its south coast is 300 km north of the Java Trench and south of the volcanic arc that runs the length of Java. We are investigating relations between marine terraces and convergence, normal faulting associated with tectonically induced basin subsidence, eustatic sea level change, and variations in sediment supply from volcanic activity. Exposed bedrock along the coast includes upper Miocene basinal limestone, and localized exposure of underlying Miocene reef deposits and Oligo-miocene volcanic basement. Differential uplift in the past is implied by north-south trending horst-like ridges of Miocene reef sediment and volcanic basement that have been exhumed from greater depth than adjacent upper Miocene strata. We utilized Quaternary terrace elevations at four locations (Pangamalang, Pangandaran, Karanghawu, and Pacitan). Elevations were measured using traverses with handheld GPS units, profiles made with RTK GPS, and digital surface models (DSMs).The DSMs have 5 cm pixels and were constructed using structure-from-motion (SfM) software to process photos collected with quadcopters equipped with a 24 Mpixel Sony A5100 camera; their vertical RMS error relative to checkpoints measured on bare ground is 6 cm. SfM processing was done in the field with a specially built portable workstation. Four sets of terraces (T) with the following elevations were identified: T1 0-.5 m, T2 2 m, T3 17 m, T4 22 m. We interpret T1 to be the modern wave-cut platform, T2 to represent Holocene uplift of a Holocene terrace or possibly modern deposition, T3 to result from Marine Isotope Stage 5e. T4 occurs at every location except Pangamalang at the western tip of south Java. These results suggest late Quaternary uplift, and the 17 m elevation of T3 indicates an uplift rate of 0.17 mm/yr.

MK3TOOLS & NetCDF - storing VLBI data in a machine independent array oriented data format

NASA Astrophysics Data System (ADS)

Hobiger, T.; Koyama, Y.; Kondo, T.

2007-07-01

In the beginning of 2002 the International VLBI Service (IVS) has agreed to introduce a Platform-independent VLBI exchange format (PIVEX) which permits the exchange of observational data and stimulates the research across different analysis groups. Unfortunately PIVEX has never been implemented and many analysis software packages are still depending on prior processing (e.g. ambiguity resolution and computation of ionosphere corrections) done by CALC/SOLVE. Thus MK3TOOLS which handles MK3 databases without CALC/SOLVE being installed has been developed. It uses the NetCDF format to store the data and since interfaces exist for a variety of programming languages (FORTRAN, C/C++, JAVA, Perl, Python) it can be easily incorporated in existing and upcoming analysis software packages.

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

PubMed Central

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

2017-01-01

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

Integrating an Educational Game in Moodle LMS

ERIC Educational Resources Information Center

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

2012-01-01

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

Intention and Usage of Computer Based Information Systems in Primary Health Centers

ERIC Educational Resources Information Center

Hosizah; Kuntoro; Basuki N., Hari

2016-01-01

The computer-based information system (CBIS) is adopted by almost all of in health care setting, including the primary health center in East Java Province Indonesia. Some of softwares available were SIMPUS, SIMPUSTRONIK, SIKDA Generik, e-puskesmas. Unfortunately they were most of the primary health center did not successfully implemented. This…

A Novel Trust Service Provider for Internet Based Commerce Applications.

ERIC Educational Resources Information Center

Siyal, M. Y.; Barkat, B.

2002-01-01

Presents a framework for enhancing trust in Internet commerce. Shows how trust can be provided through a network of Trust Service Providers (TSp). Identifies a set of services that should be offered by a TSp. Presents a distributed object-oriented implementation of trust services using CORBA, JAVA and XML. (Author/AEF)

Evaluating real-time Java for mission-critical large-scale embedded systems

NASA Technical Reports Server (NTRS)

Sharp, D. C.; Pla, E.; Luecke, K. R.; Hassan, R. J.

2003-01-01

This paper describes benchmarking results on an RT JVM. This paper extends previously published results by including additional tests, by being run on a recently available pre-release version of the first commercially supported RTSJ implementation, and by assessing results based on our experience with avionics systems in other languages.

Teaching Design Patterns through Computer Game Development

ERIC Educational Resources Information Center

Gestwicki, Paul; Sun, Fu-Shing

2008-01-01

We present an approach for teaching design patterns that emphasizes object-orientation and patterns integration. The context of computer game development is used to engage and motivate students, and it is additionally rich with design patterns. A case study is presented based on "EEClone," an arcade-style computer game implemented in Java. Our…

Development of Distributed System for Electronic Business Based on Java-Technologies

ERIC Educational Resources Information Center

Kintonova, Aliya Zh.; Andassova, Bakkaisha Z.; Ermaganbetova, Madina A.; Maikibaeva, Elmira K.

2016-01-01

This paper describes the results of studies on the peculiarities of distributed information systems, and the research of distributed systems technology development. The paper also provides the results of the analysis of E-business market research in the Republic of Kazakhstan. The article briefly describes the implementation of a possible solution…

[Implementation of ontology-based clinical decision support system for management of interactions between antihypertensive drugs and diet].

PubMed

Park, Jeong Eun; Kim, Hwa Sun; Chang, Min Jung; Hong, Hae Sook

2014-06-01

The influence of dietary composition on blood pressure is an important subject in healthcare. Interactions between antihypertensive drugs and diet (IBADD) is the most important factor in the management of hypertension. It is therefore essential to support healthcare providers' decision making role in active and continuous interaction control in hypertension management. The aim of this study was to implement an ontology-based clinical decision support system (CDSS) for IBADD management (IBADDM). We considered the concepts of antihypertensive drugs and foods, and focused on the interchangeability between the database and the CDSS when providing tailored information. An ontology-based CDSS for IBADDM was implemented in eight phases: (1) determining the domain and scope of ontology, (2) reviewing existing ontology, (3) extracting and defining the concepts, (4) assigning relationships between concepts, (5) creating a conceptual map with CmapTools, (6) selecting upper ontology, (7) formally representing the ontology with Protégé (ver.4.3), (8) implementing an ontology-based CDSS as a JAVA prototype application. We extracted 5,926 concepts, 15 properties, and formally represented them using Protégé. An ontology-based CDSS for IBADDM was implemented and the evaluation score was 4.60 out of 5. We endeavored to map functions of a CDSS and implement an ontology-based CDSS for IBADDM.

Jefferson Lab Mass Storage and File Replication Services

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

Ian Bird; Ying Chen; Bryan Hess

Jefferson Lab has implemented a scalable, distributed, high performance mass storage system - JASMine. The system is entirely implemented in Java, provides access to robotic tape storage and includes disk cache and stage manager components. The disk manager subsystem may be used independently to manage stand-alone disk pools. The system includes a scheduler to provide policy-based access to the storage systems. Security is provided by pluggable authentication modules and is implemented at the network socket level. The tape and disk cache systems have well defined interfaces in order to provide integration with grid-based services. The system is in production andmore » being used to archive 1 TB per day from the experiments, and currently moves over 2 TB per day total. This paper will describe the architecture of JASMine; discuss the rationale for building the system, and present a transparent 3rd party file replication service to move data to collaborating institutes using JASMine, XM L, and servlet technology interfacing to grid-based file transfer mechanisms.« less

Modeling intelligent agent beliefs in a card game scenario

NASA Astrophysics Data System (ADS)

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

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

Design and Implementation of Telemedicine based on Java Media Framework

NASA Astrophysics Data System (ADS)

Xiong, Fengguang; Jia, Zhiyan

According to analyze the importance and problem of telemedicine in this paper, a telemedicine system based on JMF is proposed to design and implement capturing, compression, storage, transmission, reception and play of a medical audio and video. The telemedicine system can solve existing problems that medical information is not shared, platform-dependent is high, software is incompatibilities and so on. Experimental data prove that the system has low hardware cost, and is easy to transmission and storage, and is portable and powerful.

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.

Computer-based analysis of microvascular alterations in a mouse model for Alzheimer's disease

NASA Astrophysics Data System (ADS)

Heinzer, Stefan; Müller, Ralph; Stampanoni, Marco; Abela, Rafael; Meyer, Eric P.; Ulmann-Schuler, Alexandra; Krucker, Thomas

2007-03-01

Vascular factors associated with Alzheimer's disease (AD) have recently gained increased attention. To investigate changes in vascular, particularly microvascular architecture, we developed a hierarchical imaging framework to obtain large-volume, high-resolution 3D images from brains of transgenic mice modeling AD. In this paper, we present imaging and data analysis methods which allow compiling unique characteristics from several hundred gigabytes of image data. Image acquisition is based on desktop micro-computed tomography (µCT) and local synchrotron-radiation µCT (SRµCT) scanning with a nominal voxel size of 16 µm and 1.4 µm, respectively. Two visualization approaches were implemented: stacks of Z-buffer projections for fast data browsing, and progressive-mesh based surface rendering for detailed 3D visualization of the large datasets. In a first step, image data was assessed visually via a Java client connected to a central database. Identified characteristics of interest were subsequently quantified using global morphometry software. To obtain even deeper insight into microvascular alterations, tree analysis software was developed providing local morphometric parameters such as number of vessel segments or vessel tortuosity. In the context of ever increasing image resolution and large datasets, computer-aided analysis has proven both powerful and indispensable. The hierarchical approach maintains the context of local phenomena, while proper visualization and morphometry provide the basis for detailed analysis of the pathology related to structure. Beyond analysis of microvascular changes in AD this framework will have significant impact considering that vascular changes are involved in other neurodegenerative diseases as well as in cancer, cardiovascular disease, asthma, and arthritis.

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.

FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

PubMed

Erhard, Florian; Friedel, Caroline C; Zimmer, Ralf

2008-08-29

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary. In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment. FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modelled easily with FERN.

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). A production-level application of this technology is for one of the three candidate detectors of SPIRE (Spectral and Photometric Imaging REceiver), a focal plane instrument proposed for the European Space Agency's Far Infrared Space Telescope. The detectors are being developed by the Infrared Astrophysics Branch of NASA/GSFC.

Develop a Prototype Personal Health Record Application (PHR-A) that Captures Information About Daily Living Important for Diabetes and Provides Decision Support with Actionable Advice for Diabetes Self Care

DTIC Science & Technology

2012-10-01

higher  Java v5Apache Struts v2  Hibernate v2  C3PO  SQL*Net client / JDBC Database Server  Oracle 10.0.2 Desktop Client  Internet Explorer...for mobile Smartphones - A Java -based framework utilizing Apache Struts on the server - Relational database to handle data storage requirements B...technologies are as follows: Technology Use Requirements Java Application Provides the backend application software to drive the PHR-A 7 BEA Web

NIH Research: Advances in Parkinson's Disease Research

MedlinePlus

... of this page please turn JavaScript on. NIH Research: Advances in Parkinson's Disease Research Past Issues / Winter 2014 Table of Contents Story ... Photo courtesy of NIH Advances in Parkinson's Disease Research Story Landis, Ph.D., has been Director of ...

Type-Separated Bytecode - Its Construction and Evaluation

NASA Astrophysics Data System (ADS)

Adler, Philipp; Amme, Wolfram

A lot of constrained systems still use interpreters to run mobile applications written in Java. These interpreters demand for only a few resources. On the other hand, it is difficult to apply optimizations during the runtime of the application. Annotations could be used to achieve a simpler and faster code analysis, which would allow optimizations even for interpreters on constrained devices. Unfortunately, there is no viable way of transporting annotations to and verifying them at the code consumer. In this paper we present type-separated bytecode as an intermediate representation which allows to safely transport annotations as type-extensions. We have implemented several versions of this system and show that it is possible to obtain a performance comparable to Java Bytecode, even though we use a type-separated system with annotations.

Generic, Type-Safe and Object Oriented Computer Algebra Software

NASA Astrophysics Data System (ADS)

Kredel, Heinz; Jolly, Raphael

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

OHD/HL - National Weather Hydrology Laboratory

Science.gov Websites

resources and services. Design and Programming Standards and Guidelines General Programming C C++ FORTRAN Java v 2.0 updated 3/28/2008 Java v 1.9 Korn and Bash Shell Software Design Phase Guidelines OHD Design Specification Template OHD Design Specification Example Software Peer Review Guidelines and Checklists Software

Higher Education and the Labour Market in the Java Region, Indonesia.

ERIC Educational Resources Information Center

Notodihardjo, Hardjono; Sanyal, Bikas C.

Based on a survey of college students, graduates, and employers throughout Java, this report examines (1) reasons for pursuing higher education, channels of career information, frequency of and reasons for students changing majors, and the performance of the higher education system; (2) occupational expectations and their determinants; (3) methods…

The Live Access Server - A Web-Services Framework for Earth Science Data

NASA Astrophysics Data System (ADS)

Schweitzer, R.; Hankin, S. C.; Callahan, J. S.; O'Brien, K.; Manke, A.; Wang, X. Y.

2005-12-01

The Live Access Server (LAS) is a general purpose Web-server for delivering services related to geo-science data sets. Data providers can use the LAS architecture to build custom Web interfaces to their scientific data. Users and client programs can then access the LAS site to search the provider's on-line data holdings, make plots of data, create sub-sets in a variety of formats, compare data sets and perform analysis on the data. The Live Access server software has continued to evolve by expanding the types of data (in-situ observations and curvilinear grids) it can serve and by taking advantages of advances in software infrastructure both in the earth sciences community (THREDDS, the GrADS Data Server, the Anagram framework and Java netCDF 2.2) and in the Web community (Java Servlet and the Apache Jakarta frameworks). This presentation will explore the continued evolution of the LAS architecture towards a complete Web-services-based framework. Additionally, we will discuss the redesign and modernization of some of the support tools available to LAS installers. Soon after the initial implementation, the LAS architecture was redesigned to separate the components that are responsible for the user interaction (the User Interface Server) from the components that are responsible for interacting with the data and producing the output requested by the user (the Product Server). During this redesign, we changed the implementation of the User Interface Server from CGI and JavaScript to the Java Servlet specification using Apache Jakarta Velocity backed by a database store for holding the user interface widget components. The User Interface server is now quite flexible and highly configurable because we modernized the components used for the implementation. Meanwhile, the implementation of the Product Server has remained a Perl CGI-based system. Clearly, the time has come to modernize this part of the LAS architecture. Before undertaking such a modernization it is important to understand what we hope to gain. Specifically we would like to make it even easier to add new output products into our core system based on the Ferret analysis and visualization package. By carefully factoring the tasks needed to create a product we will be able to create new products simply by adding a description of the product into the configuration and by writing the Ferret script needed to create the product. No code will need to be added to the Product Server to bring the new product on-line. The new architecture should be faster at extracting and processing configuration information needed to address each request. Finally, the new Product Server architecture should make it even easier to pass specialized configuration information to the Product Server to deal with unanticipated special data structures or processing requirements.

Identification the geothermal system using 1-D audio-magnetotelluric inversion in Lamongan volcano field, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Ilham, N.; Niasari, S. W.

2018-04-01

Tiris village, Probolinggo, East Java, is one of geothermal potential areas in Indonesia. This area is located in a valley flank of Mount Lamongan and Argopuro volcanic complex. This research aimed to identify a geothermal system at Tiris area, particularly the fluid pathways. The geothermal potential can be seen from the presence of warm springs with temperature ranging 35-45°C. The warm spring locations are aligned in the same orientation with major fault structure in the area. The fault structure shows dominant northwest-southeast orientation. We used audio-magnetotelluric data in the frequency range of 10 Hz until 92 kHz. The total magnetotelluric sites are 6. From the data analysis, most of the data orientation were 2-D with geo-electrical direction north-south. We used 1-D inversion using Newton algorithm. The 1-D inversion resulted in low resistive anomaly that corresponds to Lamongan lavas. Additionally, the depth of the resistor are different between the area to the west (i.e. 75 m) and to the east (i.e. 25 m). This indicates that there is a fault around the aligned maar (e.g. Ranu Air).

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.

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements

PubMed Central

2013-01-01

Background The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms. Results We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set. Conclusions D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight. PMID:23617301

CO2 flux from Javanese mud volcanism.

PubMed

Queißer, M; Burton, M R; Arzilli, F; Chiarugi, A; Marliyani, G I; Anggara, F; Harijoko, A

2017-06-01

Studying the quantity and origin of CO 2 emitted by back-arc mud volcanoes is critical to correctly model fluid-dynamical, thermodynamical, and geochemical processes that drive their activity and to constrain their role in the global geochemical carbon cycle. We measured CO 2 fluxes of the Bledug Kuwu mud volcano on the Kendeng Fold and thrust belt in the back arc of Central Java, Indonesia, using scanning remote sensing absorption spectroscopy. The data show that the expelled gas is rich in CO 2 with a volume fraction of at least 16 vol %. A lower limit CO 2 flux of 1.4 kg s -1 (117 t d -1 ) was determined, in line with the CO 2 flux from the Javanese mud volcano LUSI. Extrapolating these results to mud volcanism from the whole of Java suggests an order of magnitude total CO 2 flux of 3 kt d -1 , comparable with the expected back-arc efflux of magmatic CO 2 . After discussing geochemical, geological, and geophysical evidence we conclude that the source of CO 2 observed at Bledug Kuwu is likely a mixture of thermogenic, biogenic, and magmatic CO 2 , with faulting controlling potential pathways for magmatic fluids. This study further demonstrates the merit of man-portable active remote sensing instruments for probing natural gas releases, enabling bottom-up quantification of CO 2 fluxes.

10,000 Years of explosive eruptions of Merapi Volcano, Central Java: archaeological and modern implications

USGS Publications Warehouse

Newhall, C.G.; Bronto, S.; Alloway, B.; Banks, N.G.; Bahar, I.; Del Marmol, M.A.; Hadisantono, R.D.; Holcomb, R.T.; McGeehin, J.; Miksic, J.N.; Rubin, M.; Sayudi, S.D.; Sukhyar, R.; Andreastuti, Supriyati; Tilling, R.I.; Torley, R.; Trimble, D.; Wirakusumah, A.D.

2000-01-01

Stratigraphy and radiocarbon dating of pyroclastic deposits at Merapi Volcano, Central Java, reveals ~10,000 years of explosive eruptions. Highlights include: (1) Construction of an Old Merapi stratovolcano to the height of the present cone or slightly higher. Our oldest age for an explosive eruption is 9630±60 14C y B.P.; construction of Old Merapi certainly began earlier. (2) Collapse(s) of Old Merapi that left a somma rim high on its eastern slope and sent one or more debris avalanche(s) down its southern and western flanks. Impoundment of Kali Progo to form an early Lake Borobudur at ~3400 14C y B.P. hints at a possible early collapse of Merapi. The latest somma-forming collapse occurred ~1900 14C y B.P. The current cone, New Merapi, began to grow soon thereafter. (3) Several large and many small Buddhist and Hindu temples were constructed in Central Java between 732 and ~900 A.D. (roughly, 1400-1000 14C y B.P.). Explosive Merapi eruptions occurred before, during and after temple construction. Some temples were destroyed and (or) buried soon after their construction, and we suspect that this destruction contributed to an abrupt shift of power and organized society to East Java in 928 A.D. Other temples sites, though, were occupied by "caretakers" for several centuries longer. (4) A partial collapse of New Merapi occurred 14C y B.P. Eruptions ~700-800 14C y B.P. (12-14th century A.D.) deposited ash on the floors of (still-occupied?) Candi Sambisari and Candi Kedulan. We speculate but cannot prove that these eruptions were triggered by (the same?) partial collapse of New Merapi, and that the eruptions, in turn, ended "caretaker" occupation at Candi Sambisari and Candi Kedulan. A new or raised Lake Borobudur also existed during part or all of the 12-14th centuries, probably impounded by deposits from Merapi. (5) Relatively benign lava-dome extrusion and dome-collapse pyroclastic flows have dominated activity of the 20th century, but explosive eruptions much larger than any of this century have occurred many times during Merapi's history, most recently during the 19th century. Are the relatively small eruptions of the 20th century a new style of open-vent, less hazardous activity that will persist for the foreseeable future? Or, alternatively, are they merely low-level "background" activity that could be interrupted upon relatively short notice by much larger explosive eruptions? The geologic record suggests the latter, which would place several hundred thousand people at risk. We know of no reliable method to forecast when an explosive eruption will interrupt the present interval of low-level activity. This conclusion has important implications for hazard evaluation.