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

NASA Astrophysics Data System (ADS)

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

2007-06-01

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

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.

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.

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

PubMed

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

2008-04-01

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

Electrostatic potential calculation for biomolecules--creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures.

PubMed

Rocchia, W; Neshich, G

2007-10-05

STING and Java Protein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and Java Protein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. BlueStar STING is available at http://www.cbi.cnptia.embrapa.br.

Assessing Students' Structured Programming Skills with Java: The "Blue, Berry, and Blueberry" Assignment

ERIC Educational Resources Information Center

Zhang, Xihui

2010-01-01

Java is an object-oriented programming language. From a software engineering perspective, object-oriented design and programming is used at the architectural design, and structured design and programming is used at the detailed design within methods. As such, structured programming skills are fundamental to more advanced object-oriented…

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

Crystals in Urine Test: MedlinePlus Lab Test Information

MedlinePlus

... medlineplus.gov/labtests/crystalsinurinetest.html Crystals in Urine Test To use the sharing features on this page, ... enable JavaScript. What is a Crystals in Urine Test? Your urine contains many chemicals. Sometimes these chemicals ...

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

PubMed

Patiny, Luc; Borel, Alain

2013-05-24

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

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

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

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

Hampton, J.; Simons, R.

1999-04-21

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

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure

PubMed Central

Neshich, Goran; Rocchia, Walter; Mancini, Adauto L.; Yamagishi, Michel E. B.; Kuser, Paula R.; Fileto, Renato; Baudet, Christian; Pinto, Ivan P.; Montagner, Arnaldo J.; Palandrani, Juliana F.; Krauchenco, Joao N.; Torres, Renato C.; Souza, Savio; Togawa, Roberto C.; Higa, Roberto H.

2004-01-01

JavaProtein Dossier (JPD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data grouping allows us to generate different parameters with the potential to provide new insights into the sequence–structure–function relationship. In JPD, residue selection can be performed according to multiple criteria. JPD can simultaneously display and analyze all the physicochemical parameters of any pair of structures, using precalculated structural alignments, allowing direct parameter comparison at corresponding amino acid positions among homologous structures. In order to focus on the physicochemical (and consequently pharmacological) profile of proteins, visualization tools (showing the structure and structural parameters) also had to be optimized. Our response to this challenge was the use of Java technology with its exceptional level of interactivity. JPD is freely accessible (within the Gold Sting Suite) at http://sms.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS, http://trantor.bioc.columbia.edu/SMS and http://www.es.embnet.org/SMS/ (Option: JavaProtein Dossier). PMID:15215458

TmoleX--a graphical user interface for TURBOMOLE.

PubMed

Steffen, Claudia; Thomas, Klaus; Huniar, Uwe; Hellweg, Arnim; Rubner, Oliver; Schroer, Alexander

2010-12-01

We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.

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.

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.

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.

Web-based three-dimensional geo-referenced visualization

NASA Astrophysics Data System (ADS)

Lin, Hui; Gong, Jianhua; Wang, Freeman

1999-12-01

This paper addresses several approaches to implementing web-based, three-dimensional (3-D), geo-referenced visualization. The discussion focuses on the relationship between multi-dimensional data sets and applications, as well as the thick/thin client and heavy/light server structure. Two models of data sets are addressed in this paper. One is the use of traditional 3-D data format such as 3-D Studio Max, Open Inventor 2.0, Vis5D and OBJ. The other is modelled by a web-based language such as VRML. Also, traditional languages such as C and C++, as well as web-based programming tools such as Java, Java3D and ActiveX, can be used for developing applications. The strengths and weaknesses of each approach are elaborated. Four practical solutions for using VRML and Java, Java and Java3D, VRML and ActiveX and Java wrapper classes (Java and C/C++), to develop applications are presented for web-based, real-time interactive and explorative visualization.

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.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

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

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

GREENER CHEMICAL PROCESS DESIGN ALTERNATIVES ARE REVEALED USING THE WASTE REDUCTION DECISION SUPPORT SYSTEM (WAR DSS)

EPA Science Inventory

The Waste Reduction Decision Support System (WAR DSS) is a Java-based software product providing comprehensive modeling of potential adverse environmental impacts (PEI) predicted to result from newly designed or redesigned chemical manufacturing processes. The purpose of this so...

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.

Upper crustal structure beneath East Java from ambient noise tomography: A preliminary result

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

Martha, Agustya Adi; Graduate Research on Earthquakes and Active Tectonics, Institut Teknologi Bandung, Bandung; Widiyantoro, Sri

East Java has a fairly complex geological structure. Physiographically East Java can be divided into three zones, i.e. the Southern Mountains zone in the southern part, the Kendeng zone in the middle part, and the Rembang zone in the northern part. Most of the seismic hazards in this region are due to processes in the upper crust. In this study, the Ambient Noise Tomography (ANT) method is used to image the upper crustal structure beneath East Java. We have used seismic waveform data recorded by 8Meteorological, Climatological and Geophysical Agency (BMKG) stationary seismographic stations and 16 portable seismographs installed formore » 2 to 8 weeks. The data were processed to obtain waveforms fromnoise cross-correlation between pairs of seismographic stations. Our preliminary results indicate that the Kendeng zone, an area of low gravity anomaly, is associated with a low velocity zone. On the other hand, the southern mountain range, which has a high gravity anomaly, is related to a high velocity anomaly as shown by our tomographic images.« less

Indonesian propolis: chemical composition, biological activity and botanical origin.

PubMed

Trusheva, Boryana; Popova, Milena; Koendhori, Eko Budi; Tsvetkova, Iva; Naydenski, Christo; Bankova, Vassya

2011-03-01

From a biologically active extract of Indonesian propolis from East Java, 11 compounds were isolated and identified: four alk(en)ylresorcinols (obtained as an inseparable mixture) (1-4) were isolated for the first time from propolis, along with four prenylflavanones (6-9) and three cycloartane-type triterpenes (5, 10 and 11). The structures of the components were elucidated based on their spectral properties. All prenylflavanones demonstrated significant radical scavenging activity against diphenylpicrylhydrazyl radicals, and compound 6 showed significant antibacterial activity against Staphylococcus aureus. For the first time Macaranga tanarius L. and Mangifera indica L. are shown as plant sources of Indonesian propolis.

Paradichlorobenzene poisoning

MedlinePlus

... poisoning URL of this page: //medlineplus.gov/ency/article/002902.htm Paradichlorobenzene poisoning To use the sharing features on this page, please enable JavaScript. Paradichlorobenzene is a white, solid chemical with a ...

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.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Monitoring Java Programs with Java PathExplorer

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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

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.

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.

Distriblets: Java-Based Distributed Computing on the Web.

ERIC Educational Resources Information Center

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

1999-01-01

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

Assessing Knowledge Change in Computer Science

ERIC Educational Resources Information Center

Nash, Jane Gradwohl; Bravaco, Ralph J.; Simonson, Shai

2006-01-01

The purpose of this study was to assess structural knowledge change across a two-week workshop designed to provide high-school teachers with training in Java and Object Oriented Programming. Both before and after the workshop, teachers assigned relatedness ratings to pairs of key concepts regarding Java and Object Oriented Programming. Their…

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.

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.

PDDL4J: a planning domain description library for java

NASA Astrophysics Data System (ADS)

Pellier, D.; Fiorino, H.

2018-01-01

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

Shear wave velocity model beneath CBJI station West Java, Indonesia from joint inversion of teleseismic receiver functions and surface wave dispersion

NASA Astrophysics Data System (ADS)

Simanungkalit, R. H.; Anggono, T.; Syuhada; Amran, A.; Supriyanto

2018-03-01

Earthquake signal observations around the world allow seismologists to obtain the information of internal structure of the Earth especially the Earth’s crust. In this study, we used joint inversion of receiver functions and surface wave group velocities to investigate crustal structure beneath CBJI station in West Java, Indonesia. Receiver function were calculated from earthquakes with magnitude more than 5 and at distance 30°-90°. Surface wave group velocities were calculated using frequency time analysis from earthquakes at distance of 30°- 40°. We inverted shear wave velocity model beneath the station by conducting joint inversion from receiver functions and surface wave dispersions. We suggest that the crustal thickness beneath CBJI station, West Java, Indonesia is about 35 km.

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.

FPV: fast protein visualization using Java 3D.

PubMed

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

2003-05-22

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

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

PubMed

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

2005-03-09

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

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.

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.

Chemical datuments as scientific enablers.

PubMed

Rzepa, Henry S

2013-01-23

This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution of scientific journals are discussed.

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

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.

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.

Sequence stratigraphy, structural style, and age of deformation of the Malaita accretionary prism (Solomon arc-Ontong Java Plateau convergent zone)

NASA Astrophysics Data System (ADS)

Phinney, Eric J.; Mann, Paul; Coffin, Millard F.; Shipley, Thomas H.

2004-10-01

Possibilities for the fate of oceanic plateaus at subduction zones range from complete subduction of the plateau beneath the arc to complete plateau-arc accretion and resulting collisional orogenesis. Deep penetration, multi-channel seismic reflection (MCS) data from the northern flank of the Solomon Islands reveal the sequence stratigraphy, structural style, and age of deformation of an accretionary prism formed during late Neogene (5-0 Ma) convergence between the ˜33-km-thick crust of the Ontong Java oceanic plateau and the ˜15-km-thick Solomon island arc. Correlation of MCS data with the satellite-derived, free-air gravity field defines the tectonic boundaries and internal structure of the 800-km-long, 140-km-wide accretionary prism. We name this prism the "Malaita accretionary prism" or "MAP" after Malaita, the largest and best-studied island exposure of the accretionary prism in the Solomon Islands. MCS data, gravity data, and stratigraphic correlations to islands and ODP sites on the Ontong Java Plateau (OJP) reveal that the offshore MAP is composed of folded and thrust faulted sedimentary rocks and upper crystalline crust offscraped from the Solomon the subducting Ontong Java Plateau (Pacific plate) and transferred to the Solomon arc. With the exception of an upper, sequence of Quaternary? island-derived terrigenous sediments, the deformed stratigraphy of the MAP is identical to that of the incoming Ontong Java Plateau in the North Solomon trench. We divide the MAP into four distinct, folded and thrust fault-bounded structural domains interpreted to have formed by diachronous, southeast-to-northwest, and highly oblique entry of the Ontong Java Plateau into a former trench now marked by the Kia-Kaipito-Korigole (KKK) left-lateral strike-slip fault zone along the suture between the Solomon arc and the MAP. The structural style within each of the four structural domains consists of a parallel series of three to four fault propagation folds formed by the seaward propagation of thrust faults roughly parallel to sub-horizontal layering in the upper crystalline part of the OJP. Thrust fault offsets, spacing between thrusts, and the amplitude of related fault propagation folds progressively decrease to the west in the youngest zone of active MAP accretion (Choiseul structural domain). Surficial faulting and folding in the most recently deformed, northwestern domain show active accretion of greater than 1 km of sedimentary rock and 6 km, or about 20%, of the upper crystalline part of the OJP. The eastern MAP (Malaita and Ulawa domains) underwent an earlier, similar style of partial plateau accretion. A pre-late Pliocene age of accretion (˜3.4 Ma) is constrained by an onshore and offshore major angular unconformity separating Pliocene reefal limestone and conglomerate from folded and faulted pelagic limestone of Cretaceous to Miocene age. The lower 80% of the Ontong Java Plateau crust beneath the MAP thrust decollement appears unfaulted and unfolded and is continuous with a southwestward-dipping subducted slab of presumably denser plateau material beneath most of the MAP, and is traceable to depths >200 km in the mantle beneath the Solomon Islands.

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

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

The diverse crustal structure and magmatic evolution of the Manihiki Plateau, central Pacific

NASA Astrophysics Data System (ADS)

Hochmuth, K.; Gohl, K.; Uenzelmann-Neben, G.; Werner, R.

2014-07-01

The Manihiki Plateau is a Large Igneous Province (LIP) in the central Pacific. It was emplaced as part of the "Super-LIP" Ontong Java Nui and experienced fragmentation into three sub-plateaus, possibly during the break-up of Ontong Java Nui. The Manihiki Plateau is presumably the centerpiece of this "Super-LIP" and its investigation can therefore decipher the break-up mechanisms as well as the evolution of the plateau after its initial emplacement. By analyzing two seismic refraction/wide-angle reflection profiles crossing the two largest sub-plateaus of the Manihiki Plateau, the High Plateau and the Western Plateaus, we give new insights into their crustal structure and magmatic evolution. The High Plateau shows a crustal structure of 20 km thickness and a seismic P wave velocity distribution, which is comparable to other LIPs. The High Plateau experienced a strong secondary volcanism, which can be seen in relicts of seamount chain volcanism. The Western Plateaus on the other hand show no extensive secondary volcanism and are mainly structured by fault systems and sedimentary basins. A constant decrease in Moho depth (9-17 km) is a further indicator of crustal stretching on the Western Plateaus. Those findings lead to the conclusion, that the two sub-plateaus of the Manihiki Plateau experienced a different magmatic and tectonic history. Whereas the High Plateau experienced a secondary volcanism, the Western Plateaus underwent crustal stretching during and after the break-up of Ontong Java Nui. This indicates, that the sub-plateaus of the Manihiki Plateau play an individual part in the break-up history of Ontong Java Nui.

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers.

PubMed

Monge, Aurélien; Arrault, Alban; Marot, Christophe; Morin-Allory, Luc

2006-08-01

The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, 'drug-like' and 'lead-like' properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million 'drug-like' molecules among which, more than one million are 'lead-like'. This study has been carried out using 'ScreeningAssistant', a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with 'in-house' scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. 'ScreeningAssistant' is freely available under the GPL license.

Effect of an Educational Intervention Related to Health and Nutrition on Pregnant Women in the Villages of Central Java Province, Indonesia

ERIC Educational Resources Information Center

Wijaya-Erhardt, Maria; Muslimatun, Siti; Erhardt, Juergen G.

2014-01-01

Objective: To assess the effects of a health and nutrition educational intervention on maternal knowledge, attitudes and practices. Design: Pre- and post-test design using structured interviews of pregnant women. Setting: Thirty-nine villages in Central Java Province, Indonesia. Method: Pregnant women (N = 252) at 12-20 weeks of gestation were…

Upper crustal structure of central Java, Indonesia, from transdimensional seismic ambient noise tomography

NASA Astrophysics Data System (ADS)

Zulfakriza, Z.; Saygin, E.; Cummins, P. R.; Widiyantoro, S.; Nugraha, A. D.; Lühr, B.-G.; Bodin, T.

2014-04-01

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. To overcome these difficulties, we apply the technique of ambient noise tomography (ANT) to data collected during the Merapi Amphibious Experiment (MERAMEX), which covered central Java with a temporary deployment of over 120 seismometers during 2004 May-October. More than 5000 Rayleigh wave Green's functions were extracted by cross-correlating the noise simultaneously recorded at available station pairs. We applied a fully non-linear 2-D Bayesian probabilistic inversion technique to the retrieved traveltimes. 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 ANT. 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.

Cleaner production options for reducing industrial waste: the case of batik industry in Malang, East Java-Indonesia

NASA Astrophysics Data System (ADS)

Sirait, M.

2018-01-01

The aim of this research is to conduct cleaner production options for improving the environmental performance during the production of batik industry, the case of UKM batik, Malang, East Java. Batik industry is one of small and medium textile industry which has contribution to economic growth in Malang. However, during production the batik, it generates wastewater that has potential to decrease the environmental performance. Wastewater from Celaket batik industry has BOD, COD, TSS, and pH level is far larger than the threshold of water quality standard as a result of use chemical substance during the dyes processing. In order to prevent generating wastewater, this study utilized cleaner production options, such as substitution of input material.Substitution of input material for dyes process was implemented by replacement chemical dyes (e.g.indigosol, nafthol, rapid) with natural dyes (e.g. Indigofero Tintoria). Modifying of technology/equipment was conducted by developing wastewater treatment equipment to reduce waste of batik production. The implementation of this strategy was carried out by changing input material from chemical dyes with natural dyes. The CP uptake could reduce significantly the environmental impact in term of reduction of COD, BOD, and TSS.

Verification of Java Programs using Symbolic Execution and Invariant Generation

NASA Technical Reports Server (NTRS)

Pasareanu, Corina; Visser, Willem

2004-01-01

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

An interactive tool for outdoor computer controlled cultivation of microalgae in a tubular photobioreactor system.

PubMed

Dormido, Raquel; Sánchez, José; Duro, Natividad; Dormido-Canto, Sebastián; Guinaldo, María; Dormido, Sebastián

2014-03-06

This paper describes an interactive virtual laboratory for experimenting with an outdoor tubular photobioreactor (henceforth PBR for short). This virtual laboratory it makes possible to: (a) accurately reproduce the structure of a real plant (the PBR designed and built by the Department of Chemical Engineering of the University of Almería, Spain); (b) simulate a generic tubular PBR by changing the PBR geometry; (c) simulate the effects of changing different operating parameters such as the conditions of the culture (pH, biomass concentration, dissolved O2, inyected CO2, etc.); (d) simulate the PBR in its environmental context; it is possible to change the geographic location of the system or the solar irradiation profile; (e) apply different control strategies to adjust different variables such as the CO2 injection, culture circulation rate or culture temperature in order to maximize the biomass production; (f) simulate the harvesting. In this way, users can learn in an intuitive way how productivity is affected by any change in the design. It facilitates the learning of how to manipulate essential variables for microalgae growth to design an optimal PBR. The simulator has been developed with Easy Java Simulations, a freeware open-source tool developed in Java, specifically designed for the creation of interactive dynamic simulations.

An Interactive Tool for Outdoor Computer Controlled Cultivation of Microalgae in a Tubular Photobioreactor System

PubMed Central

Dormido, Raquel; Sánchez, José; Duro, Natividad; Dormido-Canto, Sebastián; Guinaldo, María; Dormido, Sebastián

2014-01-01

This paper describes an interactive virtual laboratory for experimenting with an outdoor tubular photobioreactor (henceforth PBR for short). This virtual laboratory it makes possible to: (a) accurately reproduce the structure of a real plant (the PBR designed and built by the Department of Chemical Engineering of the University of Almería, Spain); (b) simulate a generic tubular PBR by changing the PBR geometry; (c) simulate the effects of changing different operating parameters such as the conditions of the culture (pH, biomass concentration, dissolved O2, inyected CO2, etc.); (d) simulate the PBR in its environmental context; it is possible to change the geographic location of the system or the solar irradiation profile; (e) apply different control strategies to adjust different variables such as the CO2 injection, culture circulation rate or culture temperature in order to maximize the biomass production; (f) simulate the harvesting. In this way, users can learn in an intuitive way how productivity is affected by any change in the design. It facilitates the learning of how to manipulate essential variables for microalgae growth to design an optimal PBR. The simulator has been developed with Easy Java Simulations, a freeware open-source tool developed in Java, specifically designed for the creation of interactive dynamic simulations. PMID:24662450

Chemical datuments as scientific enablers

PubMed Central

2013-01-01

This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution of scientific journals are discussed. PMID:23343381

The Software Maintenance Spectrum: Using More than Just New Toys

DTIC Science & Technology

2000-04-01

Deitel & Deitel, How to Program Java, Prentice Hall, Upper Saddle River, NJ, 1998. Bjarne Stroustrup, The C++ Programming Language, ATT Bell Labs, New... to Program Java, Prentice Hall, Upper Saddle River, NJ, 1998. Dershem, Herbert L and Michael J. Jipping, Programming Languages: Structures and Models...Chikofsky, Elliot and James Cross. Reverse Engineering and Design Recovery: A Taxonomy. IEEE Software, 7(1):13-17 (Jan 1990). Deitel & Deitel, How

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

PubMed

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

2004-03-01

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

Geological structure analysis in Central Java using travel time tomography technique of S waves

NASA Astrophysics Data System (ADS)

Palupi, I. R.; Raharjo, W.; Nurdian, S. W.; Giamboro, W. S.; Santoso, A.

2016-11-01

Java is one of the islands in Indonesia that is prone to the earthquakes, in south of Java, there is the Australian Plate move to the Java island and press with perpendicular direction. This plate movement formed subduction zone and cause earthquakes. The earthquake is the release of energy due to the sudden movement of the plates. When an earthquake occurs, the energy is released and record by seismometers in the waveform. The first wave recorded is called the P waves (primary) and the next wave is called S waves (secondary). Both of these waves have different characteristics in terms of propagation and direction of movement. S wave is composed of waves of Rayleigh and Love waves, with each direction of movement of the vertical and horizontal, subsurface imaging by using S wave tomography technique can describe the type of the S wave through the medium. The variation of wave velocity under Central Java (esearch area) is ranging from -10% to 10% at the depth of 20, 30 and 40 km, the velocity decrease with the depth increase. Moho discontinuity is lies in the depth of 32 km under the crust, it is indicates there is strong heterogenity in Moho.

Local Knowledge About The Structure, Function And Conversion Of Landscape In The Karangwangi Village, Cianjur, West Java, Indonesia

NASA Astrophysics Data System (ADS)

Ulfa Dwi Amelia, Fatiya; Iskandar, Johan

2017-10-01

Karangwangi people is one of indigenous people in West Java who has local knowledge about their nature thoroughly. They have local tradition about landscape ecosystem arrangement that based on sakral (sacred) norm. With this rule, local people will always try to preserve the sustainability of their natural environment. However, modernization, increasing population, decreasing forest, and increasing market economic penetration, causing this rule and structure of landscape in Karangwangi village has changed. Land conversion in Karangwangi was occur because of settlement and land investment by people outside the village. These behavior changes in tradition and landscape (structure, function and conversion) in Karangwangi may impact on their daily activities, and so do the changes in daily activities can change their behavior in tradition and landscape. This research was undertaken in the Village of Karangwangi, Sub-district of Cidaun, District of Cianjur, Province of West Java, Indonesia. This paper aims to identify how indigenous people in Karangwangi understand kinds of landscape and another conversion that was happen as a result of management. The method used in this paper is qualitative with ethno ecological approach. The resulted of the study show that local people in Karangwangi Village understand how chronological of landscape structure, function and conversion.

Linking Supply Chain Governance and Biosecurity in the Context of HPAI Control in Western Java: A Value Chain Perspective

PubMed Central

Indrawan, Dikky; Rich, Karl M.; van Horne, Peter; Daryanto, Arief; Hogeveen, Henk

2018-01-01

Despite extensive efforts to control the highly pathogenic avian influenza (HPAI), it remains endemic in Western Java, Indonesia. To understand the limited effectiveness of HPAI control measures, it is important to map the complex structure of the poultry sector. The governance of the poultry value chain in particular, could play a pivotal role, yet there is limited information on the different chain governance structures and their impacts on HPAI control. This article uses value chain analysis (VCA), focusing on an in-depth assessment of governance structures as well as transaction cost economics and quantitative estimates of the market power of different chain actors, to establish a theoretical framework to examine biosecurity and HPAI control in the Western Java poultry chain. During the research, semi-structured interviews were conducted with key value-chain stakeholders, and the economic performance of identified actors was estimated. Results indicated the co-existence of four different poultry value chains in West Java: the integrator chain, the semi-automated slaughterhouse chain, the controlled slaughter-point chain, and the private slaughter-point chain. The integrator chain was characterized by the highest levels of coordination and a tight, hierarchical governance. In contrast, the other three types of value chains were less coordinated. The market power of the different actors within the four value chains also differed. In more integrated chains, slaughterhouses held considerable market power, while in more informal value chains, market power was in the hands of traders. The economic effects of HPAI and biosecurity measures also varied for the identified actors in the different value chains. Implementation of biosecurity and HPAI control measures was strongly related to the governance structure of the chain, with interactions between different chains and governance structures accentuating the risk of HPAI. Our findings highlight that a proper understanding of the chain governance structure is vital to improve the effectiveness of HPAI control measures, by making the interventions more specific and fit-for-purpose given the incentive structures present in different chains. PMID:29770325

Linking Supply Chain Governance and Biosecurity in the Context of HPAI Control in Western Java: A Value Chain Perspective.

PubMed

Indrawan, Dikky; Rich, Karl M; van Horne, Peter; Daryanto, Arief; Hogeveen, Henk

2018-01-01

Despite extensive efforts to control the highly pathogenic avian influenza (HPAI), it remains endemic in Western Java, Indonesia. To understand the limited effectiveness of HPAI control measures, it is important to map the complex structure of the poultry sector. The governance of the poultry value chain in particular, could play a pivotal role, yet there is limited information on the different chain governance structures and their impacts on HPAI control. This article uses value chain analysis (VCA), focusing on an in-depth assessment of governance structures as well as transaction cost economics and quantitative estimates of the market power of different chain actors, to establish a theoretical framework to examine biosecurity and HPAI control in the Western Java poultry chain. During the research, semi-structured interviews were conducted with key value-chain stakeholders, and the economic performance of identified actors was estimated. Results indicated the co-existence of four different poultry value chains in West Java: the integrator chain, the semi-automated slaughterhouse chain, the controlled slaughter-point chain, and the private slaughter-point chain. The integrator chain was characterized by the highest levels of coordination and a tight, hierarchical governance. In contrast, the other three types of value chains were less coordinated. The market power of the different actors within the four value chains also differed. In more integrated chains, slaughterhouses held considerable market power, while in more informal value chains, market power was in the hands of traders. The economic effects of HPAI and biosecurity measures also varied for the identified actors in the different value chains. Implementation of biosecurity and HPAI control measures was strongly related to the governance structure of the chain, with interactions between different chains and governance structures accentuating the risk of HPAI. Our findings highlight that a proper understanding of the chain governance structure is vital to improve the effectiveness of HPAI control measures, by making the interventions more specific and fit-for-purpose given the incentive structures present in different chains.

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

An oceanic plateau subduction offshore Eastern Java

NASA Astrophysics Data System (ADS)

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

2010-12-01

The area offshore Java represents one of a few places globally where the early stage of subduction of an oceanic plateau is observed. We study the little investigated Roo Rise oceanic plateau on the Indian plate, subducting beneath Eurasia.Our study area is located south of eastern Java and covers the edge of the Roo Rise plateau, the Java trench and the entire forearc section. For the first time the detailed deep structure of the Roo Rise is studied, subduction of which has a significant effect on the forearc dynamics and evolution and the increase of the geohazards risks. The tsunamogenic earthquakes of 1994 and 2006 are associated with the oceanic plateau edge been subducted. We present integrated results of a refraction/wide-angle reflection tomography, gravity modeling, and multichannel reflection seismic imaging using data acquired in 2006 along a corridor centered around 113°E and composed of a 340 km long N-S profile and a 130 km long E-W oriented profile. The composite structural models reveal the previously unresolved deep geometry of the collision zone and the structure of the oceanic plateau. The crustal thickness of the Roo Rise plateau is ranging from 18 to 12 km. The structure of the upper crust of the incoming oceanic plate shows the extreme degree of fracturing in its top section, and is associated with a plate bending. The forearc Moho has a depth range from 16 to 20 km. The gravity modeling requires a sharp crustal thickness increase below Java. Within our profiles we do not recover any direct evidence for the presence of the bathymetric features on the oceanic plate currently present below the accretionary prism, responsible for the tsunamogenic earthquake triggering. However vertical variations of the forearc basement edge are observed on the trench-parallel profile, which opens a discussion on the origin of such basement undulations, together with a localized patchy uplift character of the forearc high.The complex geometry of the backstop suggests two models for the structural formation within this segment of the margin. The subducting plateau is affecting the stress field within the accretionary complex and the backstop edge, which favors the initiation of large, potentially tsunamogenic earthquakes such as the 1994 Mw=7.8 tsunamogenic event.

Earthquake effect on volcano and the geological structure in central java using tomography travel time method and relocation hypocenter by grid search method

NASA Astrophysics Data System (ADS)

Suharsono; Nurdian, S. W.; Palupi, I. R.

2016-11-01

Relocating hypocenter is a way to improve the velocity model of the subsurface. One of the method is Grid Search. To perform the distribution of the velocity in subsurface by tomography method, it is used the result of relocating hypocenter to be a reference for subsurface analysis in volcanic and major structural patterns, such as in Central Java. The main data of this study is the earthquake data recorded from 1952 to 2012 with the P wave number is 9162, the number of events is 2426 were recorded by 30 stations located in the vicinity of Central Java. Grid search method has some advantages they are: it can relocate the hypocenter more accurate because this method is dividing space lattice model into blocks, and each grid block can only be occupied by one point hypocenter. Tomography technique is done by travel time data that has had relocated with inversion pseudo bending method. Grid search relocated method show that the hypocenter's depth is shallower than before and the direction is to the south, the hypocenter distribution is modeled into the subduction zone between the continent of Eurasia with the Indo-Australian with an average angle of 14 °. The tomography results show the low velocity value is contained under volcanoes with value of -8% to -10%, then the pattern of the main fault structure in Central Java can be description by the results of tomography at high velocity that is from 8% to 10% with the direction is northwest and northeast-southwest.

Structural architecture of oceanic plateau subduction offshore Eastern Java and the potential implications for geohazards

NASA Astrophysics Data System (ADS)

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

2011-01-01

The region offshore Eastern Java represents one of the few places where the early stage of oceanic plateau subduction is occurring. We study the little investigated Roo Rise oceanic plateau on the Indian plate, subducting beneath Eurasia. The presence of the abnormal bathymetric features entering the trench has a strong effect on the evolution of the subduction system, and causes additional challenges on the assessment of geohazard risks. We present integrated results of a refraction/wide-angle reflection tomography, gravity modelling, and multichannel reflection seismic imaging using data acquired in 2006 south of Java near 113°E. The composite structural model reveals the previously unresolved deep geometry of the oceanic plateau and the subduction zone. The oceanic plateau crust is on average 15 km thick and covers an area of about 100 000 km2. Within our profile the Roo Rise crustal thickness ranges between 18 and 12 km. The upper oceanic crust shows high degree of fracturing, suggesting heavy faulting. The forearc crust has an average thickness of 14 km, with a sharp increase to 33 km towards Java, as revealed by gravity modelling. The complex geometry of the backstop suggests two possible models for the structural formation within this segment of the margin: either accumulation of the Roo Rise crustal fragments above the backstop or alternatively uplift of the backstop caused by basal accumulation of crustal fragments. The subducting plateau is affecting the stress field within the accretionary complex and the backstop edge, which favours the initiation of large, potentially tsunamogenic earthquakes such as the 1994 Mw= 7.8 tsunamogenic event.

LICSS - a chemical spreadsheet in microsoft excel

PubMed Central

2012-01-01

Background Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. Summary LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out. We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. Conclusions LICSS is an Excel-based chemical spreadsheet with a difference: • It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel • It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation • It is free and extensible LICSS is open source software and we hope sufficient detail is provided here to enable developers to add their own features and share with the community. PMID:22301088

LICSS - a chemical spreadsheet in microsoft excel.

PubMed

Lawson, Kevin R; Lawson, Jonty

2012-02-02

Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out.We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. LICSS is an Excel-based chemical spreadsheet with a difference:• It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel• It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation• It is free and extensibleLICSS is open source software and we hope sufficient detail is provided here to enable developers to add their own features and share with the community.

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

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

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

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/

Alteration of submarine basaltic glass from the Ontong Java Plateau: A STXM and TEM study

NASA Astrophysics Data System (ADS)

Benzerara, K.; Menguy, N.; Banerjee, N. R.; Tyliszczak, Tolek; Brown, G. E.; Guyot, F.

2007-08-01

Frequent observations of tubular to vermicular microchannels in altered basalt glass have led to increasing appreciation of a possible significant role of microbes in the low-temperature alteration of seafloor basalt. We have examined such microchannel alteration features at the nanoscale in basalt glass shards from the Ontong Java Plateau using a combination of focused ion beam milling, transmission electron microscopy and scanning transmission X-ray microscopy. Three types of materials were found in ultrathin cross-sections cut through the microchannels by FIB milling: fresh basalt glass, amorphous Si-rich rims surrounding the microchannels, and palagonite within the microchannels. X-ray absorption spectroscopy at the C K-edge and Fe L 2,3-edges showed the presence of organic carbon in association with carbonates within the microchannels and partial oxidation of iron in palagonite compared with basalt glass. Although these observations alone cannot discriminate between a biotic or abiotic origin for the microchannels, they provide new information on their mineralogical and chemical composition and thus better constrain the physical and chemical conditions prevailing during the alteration process.

Underwater Inspection of Navigation Structures with an Acoustic Camera

DTIC Science & Technology

2013-08-01

the camera with a slow angular speed while recording the images. 5. After the scanning has been performed, review recorded data to determine the...Core x86) or newer  2GB RAM  120GB disc space Operating system requirements  Windows XP, Vista, Windows 7, 32/64 bit Java requirements  Sun... Java JDK, Version 1.6, Update 16 or newer, for installation Limitations and tips for proper scanning  Best results are achieved when scanning in

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.

Velocity-depth ambiguity and the seismic structure of large igneous provinces: a case study from the Ontong Java Plateau

NASA Astrophysics Data System (ADS)

Korenaga, Jun

2011-05-01

The seismic structure of large igneous provinces provides unique constraints on the nature of their parental mantle, allowing us to investigate past mantle dynamics from present crustal structure. To exploit this crust-mantle connection, however, it is prerequisite to quantify the uncertainty of a crustal velocity model, as it could suffer from considerable velocity-depth ambiguity. In this contribution, a practical strategy is suggested to estimate the model uncertainty by explicitly exploring the degree of velocity-depth ambiguity in the model space. In addition, wide-angle seismic data collected over the Ontong Java Plateau are revisited to provide a worked example of the new approach. My analysis indicates that the crustal structure of this gigantic plateau is difficult to reconcile with the melting of a pyrolitic mantle, pointing to the possibility of large-scale compositional heterogeneity in the convecting mantle.

Influence of Coastal Upwelling on SST Trends along the South Coast of Java

PubMed Central

Varela, R.; Santos, F.; Gómez-Gesteira, M.; Álvarez, I.; Costoya, X.; Días, J. M.

2016-01-01

The south coast of Java has warmed at a much lower rate than adjacent ocean locations over the last three decades (1982–2015). This behavior can be observed during the upwelling season (July-October) and it is especially patent in August and September when upwelling attains the highest values. Although different warming rates (ocean-coast) had been previously observed in other areas around the world, this behavior was always linked to situations where upwelling increased or remained unchanged. South Java warming is observed at ocean locations and cooling near shore but under a scenario of decreasing upwelling (~30% in some cases). The origin of coastal cooling is due to changes in the vertical structure of the water column. A vein of subsurface water, which has cooled at a rate higher than 0.3°C per decade, is observed to enter from the northwestern part of the study area following the South Java Current. This water only manifests at surface near coast, where it is pumped up by coastal upwelling. PMID:27606676

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

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

PubMed

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

2005-01-01

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

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.

GIS learning tool for USA's tallest skyscrapers and their construction

NASA Astrophysics Data System (ADS)

Rajah Nagarajasetty, Kanaka Nethra

Urban development in the twenty-first century takes many forms, but for many none quite so interesting as the skyscraper. With swelling cities and growing concerns about the environment, vertical living has become the preferred way of life for millions of people around the world. But just how these tall buildings are designed, constructed and operated remains a mystery to many--even to those who live in them. The motivation behind this application is to build an interactive and one-stop Geographic Information systems (GIS) learning tool that will help users learn about structural facts and geography of tallest skyscrapers around the metro cities of USA. For purpose of this application development, any building more than 700ft (213m) is considered as one of the tallest skyscrapers. The points displayed on USA map are the metro cities hosting these skyscrapers. When users click on cities, a brief description about the city along with a link to the top three skyscrapers is displayed. The links of the skyscrapers opens a HTML page that has a photo gallery, embedded video, facts, structural information etc., in a web browser. Map Objects Java Objects (MOJO), a set of Java API's provided by ESRI, is used to display a map of the United States of America and skyscrapers locations in the form of points. Along with MOJO, other technical languages used to develop this application are HTML5, CSS3, JavaScript and Java Swing.

CHEMFLO-2000: INTERACTIVE SOFTWARE FOR PREDICTING AND VISUALIZING TRANSIENT WATER AND CHEMICAL MOVEMENT IN SOILS AND ASSOCIATED UNCERTAINTIES

EPA Science Inventory

An interactive Java applet and a stand-alone application program will be developed based on the CHEMFLO model developed in the mid-1980s and published as an EPA report (EPA/600/8-89/076). The model solves Richards Equation for transient water movement in unsaturated soils, and so...

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.

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.

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

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

PubMed

Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

2016-07-01

Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

Identification of the compositional changes in Orthosiphon stamineus leaves triggered by different drying techniques using 1 H NMR metabolomics.

PubMed

Pariyani, Raghunath; Ismail, Intan Safinar; Ahmad Azam, Amalina; Abas, Faridah; Shaari, Khozirah

2017-09-01

Java tea is a well-known herbal infusion prepared from the leaves of Orthosiphon stamineus (OS). The biological properties of tea are in direct correlation with the primary and secondary metabolite composition, which in turn largely depends on the choice of drying method. Herein, the impact of three commonly used drying methods, i.e. shade, microwave and freeze drying, on the metabolite composition and antioxidant activity of OS leaves was investigated using proton nuclear magnetic resonance ( 1 H NMR) spectroscopy combined with multivariate classification and regression analysis tools. A total of 31 constituents comprising primary and secondary metabolites belonging to the chemical classes of fatty acids, amino acids, sugars, terpenoids and phenolic compounds were identified. Shade-dried leaves were identified to possess the highest concentrations of bioactive secondary metabolites such as chlorogenic acid, caffeic acid, luteolin, orthosiphol and apigenin, followed by microwave-dried samples. Freeze-dried leaves had higher concentrations of choline, amino acids leucine, alanine and glutamine and sugars such as fructose and α-glucose, but contained the lowest levels of secondary metabolites. Metabolite profiling coupled with multivariate analysis identified shade drying as the best method to prepare OS leaves as Java tea or to include in traditional medicine preparation. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Global tectonic significance of the Solomon Islands and Ontong Java Plateau convergent zone

NASA Astrophysics Data System (ADS)

Mann, Paul; Taira, Asahiko

2004-10-01

Oceanic plateaus, areas of anomalously thick oceanic crust, cover about 3% of the Earth's seafloor and are thought to mark the surface location of mantle plume "heads". Hotspot tracks represent continuing magmatism associated with the remaining plume conduit or "tail". It is presently controversial whether voluminous and mafic oceanic plateau lithosphere is eventually accreted at subduction zones, and, therefore: (1) influences the eventual composition of continental crust and; (2) is responsible for significantly higher rates of continental growth than growth only by accretion of island arcs. The Ontong Java Plateau (OJP) of the southwestern Pacific Ocean is the largest and thickest oceanic plateau on Earth and the largest plateau currently converging on an island arc (Solomon Islands). For this reason, this convergent zone is a key area for understanding the fate of large and thick plateaus on reaching subduction zones. This volume consists of a series of four papers that summarize the results of joint US-Japan marine geophysical studies in 1995 and 1998 of the Solomon Islands-Ontong Java Plateau convergent zone. Marine geophysical data include single and multi-channel seismic reflection, ocean-bottom seismometer (OBS) refraction, gravity, magnetic, sidescan sonar, and earthquake studies. Objectives of this introductory paper include: (1) review of the significance of oceanic plateaus as potential contributors to continental crust; (2) review of the current theories on the fate of oceanic plateaus at subduction zones; (3) establish the present-day and Neogene tectonic setting of the Solomon Islands-Ontong Java Plateau convergent zone; (4) discuss the controversial sequence and timing of tectonic events surrounding Ontong Java Plateau-Solomon arc convergence; (5) present a series of tectonic reconstructions for the period 20 Ma (early Miocene) to the present-day in support of our proposed timing of major tectonic events affecting the Ontong Java Plateau-Solomon Islands convergent zone; and (6) compare the structural and deformational pattern observed in the Solomon Islands to ancient oceanic plateaus preserved in Precambrian and Phanerozoic orogenic belts. Our main conclusion of this study is that 80% of the crustal thickness of the Ontong Java Plateau is subducted beneath the Solomon island arc; only the uppermost basaltic and sedimentary part of the crust (˜7 km) is preserved on the overriding plate by subduction-accretion processes. This observation is consistent with the observed imbricate structural style of plateaus and seamount chains preserved in both Precambrian and Phanerozoic orogenic belts.

Dental cavities

MedlinePlus

... this page: //medlineplus.gov/ency/article/001055.htm Dental cavities To use the sharing features on this page, please enable JavaScript. Dental cavities are holes (or structural damage) in the ...

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.

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.

Implementation of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Performance and Scalability of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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

PubMed

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

2014-07-03

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

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

PubMed

Chandonia, John-Marc

2007-08-01

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

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.

PubMed

Weinbrand, Lina; Avihoo, Assaf; Barash, Danny

2013-11-15

In RNA design problems, it is plausible to assume that the user would be interested in preserving a particular RNA secondary structure motif, or fragment, for biological reasons. The preservation could be in structure or sequence, or both. Thus, the inverse RNA folding problem could benefit from considering fragment constraints. We have developed a new interactive Java application called RNA fragment-based inverse that allows users to insert an RNA secondary structure in dot-bracket notation. It then performs sequence design that conforms to the shape of the input secondary structure, the specified thermodynamic stability, the specified mutational robustness and the user-selected fragment after shape decomposition. In this shape-based design approach, specific RNA structural motifs with known biological functions are strictly enforced, while others can possess more flexibility in their structure in favor of preserving physical attributes and additional constraints. RNAfbinv is freely available for download on the web at http://www.cs.bgu.ac.il/~RNAexinv/RNAfbinv. The site contains a help file with an explanation regarding the exact use.

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

PubMed

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

2008-01-01

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

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.

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

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/

Congenital heart disease

MedlinePlus

... page: //medlineplus.gov/ency/article/001114.htm Congenital heart disease To use the sharing features on this page, please enable JavaScript. Congenital heart disease (CHD) is a problem with the heart's structure ...

Structure and Content Analysis for Vocational High School Website in Indonesia

NASA Astrophysics Data System (ADS)

Subagja, H.; Abdullah, A. G.; Trisno, B.; Nandiyanto, A. B. D.

2017-03-01

Statistics about the condition of the school’s website in Indonesia is still difficult. This study aims to determine website quality in terms of completeness of content’s criteria of Vocational High School (VHS) in West Java, Indonesia. The method used is the content analysis and survey. Content analysis is reviewing the documents comprising the general category, while the survey is a observation process to get the facts from 272 school websites. Aspects of the structure and content of school website are including institutional information, educators and education personnel, curriculum, student, infrastructure, school achievement, and public access. The results of this study showed the average quality of the VHS website in West Java is still low. The recommendations are needed to improve the quality of the school website.

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

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

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

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.

Magnetic properties of fishes from rivers near Semarang, Central Java

NASA Astrophysics Data System (ADS)

Khumaedi; Nurbaiti, U.; Setyaningsi, N. E.

2018-03-01

Magnetic properties, in the form of magnetic susceptibility (χ) and frequency-dependent susceptibility (χ fd) were measured on scores of samples made of fishes from river nearby Semarang, Central Java. Semarang is one of the major cities in Indonesia, where the river systems are very likely to be contaminated by anthropogenic activities. The objective of this study is to identify the presence of heavy metals in the fishes that will determine the suitability of these fishes for healthy food. The results show that magnetic susceptibility varies from -0.3 to 13.8 × 10-8 m3/kg, while the frequency-dependent susceptibility is less than 3% indicating the predominance of ferromagnetic minerals. Quantitative chemical analyses on four samples show consistently high concentration of Ca, while Fe, Hg, Cu, Pb, Cd, and Ni present a few in some of the samples. This finding shows that the fishes are suitable for the ongoing research on environmental magnetism.

libChEBI: an API for accessing the ChEBI database.

PubMed

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

2016-01-01

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

Airlift Operation Modeling Using Discrete Event Simulation (DES)

DTIC Science & Technology

2009-12-01

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

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

Friedman-Hill, Ernest

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

The Fragmented Manihiki Plateau - Key Region for Understanding the Break-up of the "Super" Large Igneous Province Ontong Java Nui

NASA Astrophysics Data System (ADS)

Hochmuth, K.; Gohl, K.; Uenzelmann-Neben, G.; Werner, R.

2014-12-01

The Manihiki Plateau of the western Pacific is one of the world - wide greatest Large Igneous Province (LIP) on oceanic crust. It is assumed that the Manihiki Plateau was emplaced as the centerpiece of the "Super-LIP" Ontong Java Nui by multiple volcanic phases during the Cretaceous Magnetic Quiet Period. The subsequent break-up of Ontong Java Nui led to fragmentation of the Manihiki Plateau into three sub-plateaus, which all exhibit individual relicts of the "Super-LIP" break-up. We examine two deep crustal seismic refraction/wide-angle reflection profiles crossing the two largest sub-plateaus of the Manihiki Plateau, the Western Plateaus and the High Plateau. Modeling of P- and S-wave velocities reveals surprising differences in the crustal structure between the two sub-plateaus. Whereas the High Plateau shows a constant crustal thickness of 20 km, relicts of multiple volcanic phases and break-up features at its margins, the model of the Western Plateaus reveals a crustal thickness decreasing from 17 km to only 9 km. There is only little evidence of secondary phases of volcanic activity. The main upper crustal structure on the Western Plateaus consists of fault systems and sedimentary basins. We infer that the High Plateau experienced phases of strong secondary volcanism, and that tectonic deformation was limited to its edges. The Western Plateaus, on the contrary, were deformed by crustal stretching and underwent only little to no secondary volcanism. This indicates that the two main sub-plateaus of the Manihiki Plateau experienced a different geological history and have played their individual parts in the break-up history of Ontong Java Nui.

Ecological wisdom of Hindu-Javanese community settlement in Cetho Hamlet, Lawu Mountains, Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Ikhsan, Fauzan Ali; Setioko, Bambang; Suprapti, Atiek

2017-12-01

Dwelling culture of Java community has a long history. In Javanese community point of view, Javanese culture is not a homogeneous entity. There is a diversity characteristic of a regional nature of Javanese culture, which is caused by differences in the natural environment on the island of Java. Dwelling Culture settled in the mountains is a variant form of Javanese culture that has its own uniqueness. This study aimed to describe the local values of the rural settlement structure of in Lawu mountains with Hindu-Javanese culture background. This study used a qualitative approach with case study strategy. The locus of research is in the Cetho hamlet on the slopes of Mount Lawu Karanganyar, Central Java. The results showed that local values in the neighborhoods of Cetho hamlet is based on the Memayu Hayuning Bawana philosophy. These concepts are abstracted into various aspects of settlements in Cetho hamlet such as aspects of dwelling house setting, water management, and ritual activities related to environmental management. Memayu Hayuning Bawana philosophy becomes a cultural space coloring the ecological action of the population of Cetho hamlet. The comprehensive motivation of ecological action ultimately leads to one final goal, namely the desire to maintain a harmonic atmosphere with the surroundings.

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.

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

Prediction of Caffeine Content in Java Preanger Coffee Beans by NIR Spectroscopy Using PLS and MLR Method

NASA Astrophysics Data System (ADS)

Budiastra, I. W.; Sutrisno; Widyotomo, S.; Ayu, P. C.

2018-05-01

Caffeine is one of important components in coffee that contributes to the coffee beverages flavor. Caffeine concentration in coffee bean is usually determined by chemical method which is time consuming and destructive method. A nondestructive method using NIR spectroscopy was successfully applied to determine the caffeine concentration of Arabica gayo coffee bean. In this study, NIR Spectroscopy was assessed to determine the caffeine concentration of java preanger coffee bean. A hundred samples, each consist of 96 g coffee beans were prepared for reflectance and chemical measurement. Reflectance of the sample was measured by FT-NIR spectrometer in the wavelength of 1000-2500 nm (10000-4000 cm-1) followed by determination of caffeine content using LCMS method. Calibration of NIR spectra and the caffeine content was carried out using PLS and MLR methods. Several spectra data processing was conducted to increase the accuracy of prediction. The result of the study showed that caffeine content could be determined by PLS model using 7 factors and spectra data processing of combination of the first derivative and MSC of spectra absorbance (r = 0.946; CV = 1.54 %; RPD = 2.28). A lower accuracy was obtained by MLR model consisted of three caffeine and other four absorption wavelengths (r = 0.683; CV = 3.31%; RPD = 1.18).

Development of a Web-Based Distributed Interactive Simulation (DIS) Environment Using JavaScript

DTIC Science & Technology

2014-09-01

scripting that let users change or interact with web content depending on user input, which is in contrast with server-side scripts such as PHP, Java and...transfer, DIS usually broadcasts or multicasts its PDUs based on UDP socket. 3. JavaScript JavaScript is the scripting language of the web, and all...IDE) for developing desktop, mobile and web applications with JAVA , C++, HTML5, JavaScript and more. b. Framework The DIS implementation of

Generalized Symbolic Execution for Model Checking and Testing

NASA Technical Reports Server (NTRS)

Khurshid, Sarfraz; Pasareanu, Corina; Visser, Willem; Kofmeyer, David (Technical Monitor)

2003-01-01

Modern software systems, which often are concurrent and manipulate complex data structures must be extremely reliable. We present a novel framework based on symbolic execution, for automated checking of such systems. We provide a two-fold generalization of traditional symbolic execution based approaches: one, we define a program instrumentation, which enables standard model checkers to perform symbolic execution; two, we give a novel symbolic execution algorithm that handles dynamically allocated structures (e.g., lists and trees), method preconditions (e.g., acyclicity of lists), data (e.g., integers and strings) and concurrency. The program instrumentation enables a model checker to automatically explore program heap configurations (using a systematic treatment of aliasing) and manipulate logical formulae on program data values (using a decision procedure). We illustrate two applications of our framework: checking correctness of multi-threaded programs that take inputs from unbounded domains with complex structure and generation of non-isomorphic test inputs that satisfy a testing criterion. Our implementation for Java uses the Java PathFinder model checker.

Molecular structure input on the web.

PubMed

Ertl, Peter

2010-02-02

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

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

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

Bringing Interactivity to the Web: The JAVA Solution.

ERIC Educational Resources Information Center

Knee, Richard H.; Cafolla, Ralph

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

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

PubMed Central

Jefferson, Emily R.; Walsh, Thomas P.; Roberts, Timothy J.; Barton, Geoffrey J.

2007-01-01

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: . PMID:17202171

Java, Indonesia

NASA Image and Video Library

1996-01-20

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

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

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

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

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

PubMed Central

Ježek, Petr; Mouček, Roman

2015-01-01

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

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

PubMed

Ježek, Petr; Mouček, Roman

2015-01-01

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

East Java Maritime Connectivity and Its Regional Development Support

NASA Astrophysics Data System (ADS)

Purboyo, H.; Ibad, M. Z.

2017-07-01

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

Using Java for distributed computing in the Gaia satellite data processing

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

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).

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

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.

Real-time Java simulations of multiple interference dielectric filters

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

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

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

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

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

Report of the Defense Science Board Task Force on Department of Defense Biological Safety and Security Program

DTIC Science & Technology

2009-05-01

Three (NAMRU-3) - Lima, Peru : Naval Medical Research Center Detachment (NMRCD) *These labs are co-located. To provide some measure of the scope and...Aceh, Indonesia and the more recent earthquakes in central Java and Peru . Edgewood Chemical Biological Center (ECBC) ECBC’s science and technology... diabetes , obesity, cancer, psychiatric disorders, problems of pregnancy, AIDS, hepatitis, malaria, parasitic infections, and a host of other

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

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

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.

New Prespective Paleogeography of East Java Basin; Implicationrespond to Oil and Gas Eksploration at Kujung Formation Carbonate Reservoar

NASA Astrophysics Data System (ADS)

Aprilana, C.; Premonowati; S, Hanif I.; Choirotunnisa; Shirly, A.; Utama, M. K.; Sinulingga, Y. R.; Syafitra, F.

2018-03-01

Paleogeography is one of critical points that always less considered by explorationist in the world. Almost all of the consideration is focused on trapping mechanism. Paleogeography is guidance in understanding both of physical and chemical of rock characteristic which will correlate with its depositional environment. Integration of various geological and geophysical data such as; tectonic, structural geology, stratigraphy, lithology, and biostratigraphy will lead us to a better understanding of rock characteristics. Six paleogeographic interpretations was made consist of; Early Tertiary (P5-56-55 ma), Middle Eocene (P14-41 ma), Late Oiligocene (P22-25.5 ma), Early Miocene (N7-16.5 ma), Middle Miocene (N9-14.5 ma), and Pleistocene (NN19-1.5 ma). That six paleogeographic interpretations are assumed represent the paleogeographic evolution of East Java Basin time after time. In Middle Eocene time, it would be more than hundred possibilities regarding the location where the formation deposited. This would be controlled by the existence of some local structural paleohighs and horsts which oriented NW-SE followed by their own sedimentary transportation path. With assumption that hydrocarbon generation was occurred in 15 Ma and the depth of maturation window lies on about 2,500 m depth. Therefore, the possibility of source rock maturation is high, due to almost of the clastics sediment of Ngimbang deposited into the series of grabens. The Kujung reef types simplified defines and categorize into; 1) Patch Reef 2) Berrier Reef 3) Pinnacle Reef Over Isolated Reef. Kujung Carbonates were deposited in Early Miocene when regional transgression occurred. The depositional environments were dominated by shallow marine littoral-sublittoral. Generally, the reservoir quality of this Kujung Carbonate shows fair to good quality, in range7-32% porosity, and 1-1400 mD permeability (internal SKK Migas data).

Case Designs for Ill-Structured Problems: Analysis and Implications for Practice

ERIC Educational Resources Information Center

Dabbagh, Nada; Blijd, Cecily Williams

2009-01-01

This study is a third in a series of studies that examined students' information seeking and problem solving behaviors while interacting with one of two types of web-based representations of an ill-structured instructional design case: hierarchical (tree-like) and heterarchical (network-like). A Java program was used to track students' hypermedia…

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.

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

Starlink Software Developments

NASA Astrophysics Data System (ADS)

Bly, M. J.; Giaretta, D.; Currie, M. J.; Taylor, M.

Some current and upcoming software developments from Starlink were demonstrated. These included invoking traditional Starlink applications via web services, the current version of the ORAC-DR reduction pipeline, and some new Java-based tools including Treeview, an interactive explorer of hierarchical data structures.

Pre-Clinical and Clinical Evaluation of High Resolution, Mobile Gamma Camera and Positron Imaging Devices

DTIC Science & Technology

2007-11-01

accuracy. FPGA ADC data acquisition is controlled by distributed Java -based software. Java -based server application sits on each of the acquisition...JNI ( Java Native Interface) is used to allow Java indirect control of the USB driver. Fig. 5. Photograph of mobile electronics rack...supplies with the monitor and keyboard. The server application on each of these machines is controlled by a remote client Java -based application

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.

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.

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

PubMed

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

2017-02-15

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

Java: An Explosion on the Internet.

ERIC Educational Resources Information Center

Read, Tim; Hall, Hazel

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

Microbial Diversity of Acidic Hot Spring (Kawah Hujan B) in Geothermal Field of Kamojang Area, West Java-Indonesia

PubMed Central

Aditiawati, Pingkan; Yohandini, Heni; Madayanti, Fida; Akhmaloka

2009-01-01

Microbial communities in an acidic hot spring, namely Kawah Hujan B, at Kamojang geothermal field, West Java-Indonesia was examined using culture dependent and culture independent strategies. Chemical analysis of the hot spring water showed a characteristic of acidic-sulfate geothermal activity that contained high sulfate concentrations and low pH values (pH 1.8 to 1.9). Microbial community present in the spring was characterized by 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) analysis. The majority of the sequences recovered from culture-independent method were closely related to Crenarchaeota and Proteobacteria phyla. However, detail comparison among the member of Crenarchaeota showing some sequences variation compared to that the published data especially on the hypervariable and variable regions. In addition, the sequences did not belong to certain genus. Meanwhile, the 16S Rdna sequences from culture-dependent samples revealed mostly close to Firmicute and gamma Proteobacteria. PMID:19440252

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

PubMed Central

O'Boyle, Noel M; Hutchison, Geoffrey R

2008-01-01

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

Microbial diversity of acidic hot spring (kawah hujan B) in geothermal field of kamojang area, west java-indonesia.

PubMed

Aditiawati, Pingkan; Yohandini, Heni; Madayanti, Fida; Akhmaloka

2009-01-01

Microbial communities in an acidic hot spring, namely Kawah Hujan B, at Kamojang geothermal field, West Java-Indonesia was examined using culture dependent and culture independent strategies. Chemical analysis of the hot spring water showed a characteristic of acidic-sulfate geothermal activity that contained high sulfate concentrations and low pH values (pH 1.8 to 1.9). Microbial community present in the spring was characterized by 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) analysis. The majority of the sequences recovered from culture-independent method were closely related to Crenarchaeota and Proteobacteria phyla. However, detail comparison among the member of Crenarchaeota showing some sequences variation compared to that the published data especially on the hypervariable and variable regions. In addition, the sequences did not belong to certain genus. Meanwhile, the 16S Rdna sequences from culture-dependent samples revealed mostly close to Firmicute and gamma Proteobacteria.

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.

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

PubMed

Karthikeyan, Muthukumarasamy; Vyas, Renu

2016-01-01

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

76 FR 63575 - Transportation Conformity Rule: MOVES Regional Grace Period Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-13

... written in FORTRAN and used simple text files for data input and output, MOVES2010a is written in JAVA and uses a relational database structure in MYSQL to handle input and output as data tables. These changes...

76 FR 63554 - Transportation Conformity Rule: MOVES Regional Grace Period Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-13

... written in FORTRAN and used simple text files for data input and output, MOVES2010a is written in JAVA and uses a relational database structure in MYSQL to handle input and output as data tables. These changes...

77 FR 11394 - Transportation Conformity Rule: MOVES Regional Grace Period Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-27

... written in FORTRAN and used simple text files for data input and output, MOVES is written in JAVA and uses a relational database structure in MYSQL to handle input and output as data tables.\\13\\ \\13\\ Some...

Accretionary nature of the crust of Central and East Java (Indonesia) revealed by local earthquake travel-time tomography

NASA Astrophysics Data System (ADS)

Haberland, Christian; Bohm, Mirjam; Asch, Günter

2014-12-01

Reassessment of travel time data from an exceptionally dense, amphibious, temporary seismic network on- and offshore Central and Eastern Java (MERAMEX) confirms the accretionary nature of the crust in this segment of the Sunda subduction zone (109.5-111.5E). Traveltime data of P- and S-waves of 244 local earthquakes were tomographically inverted, following a staggered inversion approach. The resolution of the inversion was inspected by utilizing synthetic recovery tests and analyzing the model resolution matrix. The resulting images show a highly asymmetrical crustal structure. The images can be interpreted to show a continental fragment of presumably Gondwana origin in the coastal area (east of 110E), which has been accreted to the Sundaland margin. An interlaced anomaly of high seismic velocities indicating mafic material can be interpreted to be the mantle part of the continental fragment, or part of obducted oceanic lithosphere. Lower than average crustal velocities of the Java crust are likely to reflect ophiolitic and metamorphic rocks of a subduction melange.

The jmzQuantML programming interface and validator for the mzQuantML data standard.

PubMed

Qi, Da; Krishna, Ritesh; Jones, Andrew R

2014-03-01

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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

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

Chandonia, John-Marc

2007-05-14

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

Scalable and Precise Abstraction of Programs for Trustworthy Software

DTIC Science & Technology

2017-01-01

calculus for core Java. • 14 months: A systematic abstraction of core Java. • 18 months: A security auditor for core Java. • 24 months: A contract... auditor for full Java. • 42 months: A web-deployed service for security auditing. Approved for Public Release; Distribution Unlimited 4 4.0 RESULTS

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…

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

NASA Astrophysics Data System (ADS)

Park, Minho; Fishwick, Paul A.

2002-07-01

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

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

PubMed

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

2010-01-01

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

High-Performance Java Codes for Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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

PubMed

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

1998-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

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.

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

Bower, G.

We summarize the current status and future developments of the North American Group's Java-based system for studying physics and detector design issues at a linear collider. The system is built around Java Analysis Studio (JAS) an experiment-independent Java-based utility for data analysis. Although the system is an integrated package running in JAS, many parts of it are also standalone Java utilities.

Priority setting in HIV/AIDS control in West Java Indonesia: an evaluation based on the accountability for reasonableness framework.

PubMed

Tromp, Noor; Prawiranegara, Rozar; Subhan Riparev, Harris; Siregar, Adiatma; Sunjaya, Deni; Baltussen, Rob

2015-04-01

Indonesia has insufficient resources to adequately respond to the HIV/AIDS epidemic, and thus faces a great challenge in prioritizing interventions. In many countries, such priority setting processes are typically ad hoc and not transparent leading to unfair decisions. Here, we evaluated the priority setting process in HIV/AIDS control in West Java province against the four conditions of the accountability for reasonableness (A4R) framework: relevance, publicity, appeals and revision, and enforcement. We reviewed government documents and conducted semi-structured qualitative interviews based on the A4R framework with 22 participants of the 5-year HIV/AIDS strategy development for 2008-13 (West Java province) and 2007-11 (Bandung). We found that criteria for priority setting were used implicitly and that the strategies included a wide range of programmes. Many stakeholders were involved in the process but their contribution could be improved and particularly the public and people living with HIV/AIDS could be better engaged. The use of appeal and publicity mechanisms could be more transparent and formally stated. Public regulations are not yet installed to ensure fair priority setting. To increase fairness in HIV/AIDS priority setting, West Java should make improvements on all four conditions of the A4R framework. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine © The Author 2014; all rights reserved.

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

NASA Astrophysics Data System (ADS)

Gaffar, Eddy Z.

2018-02-01

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

Anesthesia Basics

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

Asthma Diary

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

Pure JavaScript Storyline Layout Algorithm

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

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

Analysis of Ten Reverse Engineering Tools

NASA Astrophysics Data System (ADS)

Koskinen, Jussi; Lehmonen, Tero

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

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.

World Reference Center for Arboviruses.

DTIC Science & Technology

1984-01-01

viral antigen in Avian sera. .. . ... ....... . ... .. . ... . .......... 97 Effect of hibernation of EEE virus circulation and antibody Development...viruses were isolated from a variety of mosquito species collected on several different islands in the Indonesian archipelago (Sumatra, Kalimantan, Java ...vishnui Java 15 Jun 81 7180 Cx. tritaeniorhynchus Java 13 Jul 81 7887 Cx. tritaeniorhynchus Java 26-27 Jul 81 8442 Cx. tritaeniorhynchus Bali 10 Dec 80

An Interface Transformation Strategy for AF-IPPS

DTIC Science & Technology

2012-12-01

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

An efficient framework for Java data processing systems in HPC environments

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

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

PubMed

Mukhyala, Kiran; Masselot, Alexandre

2014-12-01

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

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

Cardiac Catheterization (For Teens)

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

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

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Senses and Your 8- to 12-Month-Old

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

A Preservice Mathematics Teacher's Beliefs about Teaching Mathematics with Technology

ERIC Educational Resources Information Center

Belbase, Shashidhar

2015-01-01

This paper analyzed a preservice mathematics teacher's beliefs about teaching mathematics with technology. The researcher used five semi-structured task-based interviews in the problematic contexts of teaching fraction multiplications with JavaBars, functions and limits, and geometric transformations with Geometer's Sketchpad, and statistical data…

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

DTIC Science & Technology

2008-09-01

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

Multi-National Information Sharing -- Cross Domain Collaborative Information Environment (CDCIE) Solution. Revision 4

DTIC Science & Technology

2005-04-12

Hardware, Database, and Operating System independence using Java • Enterprise-class Architecture using Java2 Enterprise Edition 1.4 • Standards based...portal applications. Compliance with the Java Specification Request for Portlet APIs (JSR-168) (Portlet API) and Web Services for Remote Portals...authentication and authorization • Portal Standards using Java Specification Request for Portlet APIs (JSR-168) (Portlet API) and Web Services for Remote

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

JNDMS Task Authorization 2 Report

DTIC Science & Technology

2013-10-01

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

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

Physical and Chemical Character of Fly Ash of Coal Fired Power Plant in Java

NASA Astrophysics Data System (ADS)

Triwulan; Priadana, K. A.; Ekaputri, J. J.; Bayuaji, R.

2017-11-01

Quality of fly ash is varying widely in the field, it depends on the combustion process and the quality of the basic ingredients, namely coal. It will affect the physical and mechanical properties of the concrete mixtures used. This study used 12 samples of fly ash. The physical and chemical properties and finesse modulus were analyzed. The fly ash was mixed with OPC (Ordinary Portland Cement) with the proportion of 20% fly ash and 80% OPC. The specimens were form with mortar dimension of 5cm x 5 cm. The test was affected by the correlation of fly ash fineness modulus to compressive strength, correlation density of fly ash to compressive strength, and correlation of carbon content to the compressive strength.

Petroleum system of Northwest Java basin based on gravity data analysis

NASA Astrophysics Data System (ADS)

Widianto, E.

2018-01-01

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

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.

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.

Comprehensive Chemical Fingerprinting of High-Quality Cocoa at Early Stages of Processing: Effectiveness of Combined Untargeted and Targeted Approaches for Classification and Discrimination.

PubMed

Magagna, Federico; Guglielmetti, Alessandro; Liberto, Erica; Reichenbach, Stephen E; Allegrucci, Elena; Gobino, Guido; Bicchi, Carlo; Cordero, Chiara

2017-08-02

This study investigates chemical information of volatile fractions of high-quality cocoa (Theobroma cacao L. Malvaceae) from different origins (Mexico, Ecuador, Venezuela, Columbia, Java, Trinidad, and Sao Tomè) produced for fine chocolate. This study explores the evolution of the entire pattern of volatiles in relation to cocoa processing (raw, roasted, steamed, and ground beans). Advanced chemical fingerprinting (e.g., combined untargeted and targeted fingerprinting) with comprehensive two-dimensional gas chromatography coupled with mass spectrometry allows advanced pattern recognition for classification, discrimination, and sensory-quality characterization. The entire data set is analyzed for 595 reliable two-dimensional peak regions, including 130 known analytes and 13 potent odorants. Multivariate analysis with unsupervised exploration (principal component analysis) and simple supervised discrimination methods (Fisher ratios and linear regression trees) reveal informative patterns of similarities and differences and identify characteristic compounds related to sample origin and manufacturing step.

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.

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

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

DTIC Science & Technology

2008-03-01

Machine [29]. OC4J applications support Java Servlets , Web services, and the following J2EE specific standards: Extensible Markup Language (XML...IMAP Internet Message Access Protocol IP Internet Protocol IT Information Technology xviii J2EE Java Enterprise Environment JSR 168 Java ...LDAP), World Wide Web Distributed Authoring and Versioning (WebDav), Java Specification Request 168 (JSR 168), and Web Services for Remote

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

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

Visualization Software for VisIT Java Client

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

Billings, Jay Jay; Smith, Robert W

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

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.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

Almost stochastic dominance for poverty level in Central Java Province

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Usability of HL7 and SNOMED CT standards in Java Persistence API environment.

PubMed

Antal, Gábor; Végh, Ádám Zoltán; Bilicki, Vilmos

2014-01-01

Due to the need for an efficient way of communication between the different stakeholders of healthcare (e.g. doctors, pharmacists, hospitals, patients etc.), the possibility of integrating different healthcare systems occurs. However, during the integration process several problems of heterogeneity might come up, which can turn integration into a difficult task. These problems motivated the development of healthcare information standards. The main goal of the HL7 family of standards is the standardization of communication between clinical systems and the unification of clinical document formats on the structural level. The SNOMED CT standard aims the unification of the healthcare terminology, thus the development of a standard on lexical level. The goal of this article is to introduce the usability of these two standards in Java Persistence API (JPA) environment, and to examine how standard-based system components can be efficiently generated. First, we shortly introduce the structure of the standards, their advantages and disadvantages. Then, we present an architecture design method, which can help to eliminate the possible structural drawbacks of the standards, and makes code generating tools applicable for the automatic production of certain system components.

Framework for architecture-independent run-time reconfigurable applications

NASA Astrophysics Data System (ADS)

Lehn, David I.; Hudson, Rhett D.; Athanas, Peter M.

2000-10-01

Configurable Computing Machines (CCMs) have emerged as a technology with the computational benefits of custom ASICs as well as the flexibility and reconfigurability of general-purpose microprocessors. Significant effort from the research community has focused on techniques to move this reconfigurability from a rapid application development tool to a run-time tool. This requires the ability to change the hardware design while the application is executing and is known as Run-Time Reconfiguration (RTR). Widespread acceptance of run-time reconfigurable custom computing depends upon the existence of high-level automated design tools. Such tools must reduce the designers effort to port applications between different platforms as the architecture, hardware, and software evolves. A Java implementation of a high-level application framework, called Janus, is presented here. In this environment, developers create Java classes that describe the structural behavior of an application. The framework allows hardware and software modules to be freely mixed and interchanged. A compilation phase of the development process analyzes the structure of the application and adapts it to the target platform. Janus is capable of structuring the run-time behavior of an application to take advantage of the memory and computational resources available.

jAMVLE, a New Integrated Molecular Visualization Learning Environment

ERIC Educational Resources Information Center

Bottomley, Steven; Chandler, David; Morgan, Eleanor; Helmerhorst, Erik

2006-01-01

A new computer-based molecular visualization tool has been developed for teaching, and learning, molecular structure. This java-based jmol Amalgamated Molecular Visualization Learning Environment (jAMVLE) is platform-independent, integrated, and interactive. It has an overall graphical user interface that is intuitive and easy to use. The…

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

Gunawan, Hendar; Puspito, Nanang T.; Ibrahim, Gunawan

Earthquake pose serious threat of live and properties for urban area near subduction zone offshore and active fault on land. Jakarta and Bandung is an example of big city that no system of Earthquake early warning (EEW) event very high urbanization, and has many important infra structure in the area. The capital city is potentially high risk ground shaking. EEW can be usefull tool for reducing earthquake hazard, if spatial relation between cities and earthquake source is favorable for such warning and their citizens are properly trained to response early warning message. An EEW and rapid response system can providemore » the critical information needed to minimized lost of live and property and direct rescue. Earthquake ground shaking with magnitude M>6.0 from zone of Megathrust, southern of West Java should potentially damage in the area of west java especially Bandung and Jakarta City. This research development of EEW parameter such as amplitude displacement (Pd), rapid magnitude determination (M) and Peak ground Velocity (PGV). We explore the practical approach to EEW with the use of Broadband seismogram signal. Time effective EEW which epicenter from megathrust zone has potential to provide EEW in the area of west java such as Jakarta first ground shaking more or less 60 second later and strong shaking 118 second after EEW Alarm on CISI Station. EEW notification at potentially damage in the area of west java can be predicted from the characteristic of Pd > 0.5 cm, M> 6 and PGV > 10 cm/sec. GIS as a tool for presentation of hazard mapping in the affected area.« less

BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs

PubMed Central

Micklem, Gos

2014-01-01

Summary: The DAGViewer BioJS component is a reusable JavaScript component made available as part of the BioJS project and intended to be used to display graphs of structured data, with a particular emphasis on Directed Acyclic Graphs (DAGs). It enables users to embed representations of graphs of data, such as ontologies or phylogenetic trees, in hyper-text documents (HTML). This component is generic, since it is capable (given the appropriate configuration) of displaying any kind of data that is organised as a graph. The features of this component which are useful for examining and filtering large and complex graphs are described. Availability: http://github.com/alexkalderimis/dag-viewer-biojs; http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.8303. PMID:24627804

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

PubMed

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

2017-01-01

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

Vulnerabilities in Bytecode Removed by Analysis, Nuanced Confinement and Diversification (VIBRANCE)

DTIC Science & Technology

2015-06-01

VIBRANCE tool starts with a vulnerable Java application and automatically hardens it against SQL injection, OS command injection, file path traversal...7 2.2 Java Front End...7 2.2.2 Java Byte Code Parser

Practical Application of Model Checking in Software Verification

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Skakkebaek, Jens Ulrik

1999-01-01

This paper presents our experiences in applying the JAVA PATHFINDER (J(sub PF)), a recently developed JAVA to SPIN translator, in the finding of synchronization bugs in a Chinese Chess game server application written in JAVA. We give an overview of J(sub PF) and the subset of JAVA that it supports and describe the abstraction and verification of the game server. Finally, we analyze the results of the effort. We argue that abstraction by under-approximation is necessary for abstracting sufficiently smaller models for verification purposes; that user guidance is crucial for effective abstraction; and that current model checkers do not conveniently support the computational models of software in general and JAVA in particular.

Software Assurance Measurement -- State of the Practice

DTIC Science & Technology

2013-11-01

quality and productivity. 30+ languages, C/C++, Java , .NET, Oracle, PeopleSoft, SAP, Siebel, Spring, Struts, Hibernate , and all major databases. ChecKing...NET 39 ActionScript 39 Ada 40 C/C++ 40 Java 41 JavaScript 42 Objective-C 42 Opa 42 Packages 42 Perl 42 PHP 42 Python 42 Formal Methods...Suite—A tool for Ada, C, C++, C#, and Java code that comprises various analyses such as architecture checking, interface analyses, and clone detection

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

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.

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.

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.

Real-time Java for flight applications: an update

NASA Technical Reports Server (NTRS)

Dvorak, D.

2003-01-01

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

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

ERIC Educational Resources Information Center

Gordon, Barbara

1996-01-01

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

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

PubMed

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

1976-09-01

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

Volcanoes, Central Java, Indonesia

NASA Technical Reports Server (NTRS)

1992-01-01

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

Volcanoes, Central Java, Indonesia

NASA Image and Video Library

1992-08-08

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

Java PathFinder: A Translator From Java to Promela

NASA Technical Reports Server (NTRS)

Havelund, Klaus

1999-01-01

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

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.

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

Java PathFinder User Guide

NASA Technical Reports Server (NTRS)

Havelund, Klaus

1999-01-01

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

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/.

JPARSS: A Java Parallel Network Package for Grid Computing

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

Chen, Jie; Akers, Walter; Chen, Ying

2002-03-01

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

Leveraging annotation-based modeling with Jump.

PubMed

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

2018-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2006-12-01

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

Open, Cross Platform Chemistry Application Unifying Structure Manipulation, External Tools, Databases and Visualization

DTIC Science & Technology

2012-11-27

with powerful analysis tools and an informatics approach leveraging best-of-breed NoSQL databases, in order to store, search and retrieve relevant...dictionaries, and JavaScript also has good support. The MongoDB project[15] was chosen as a scalable NoSQL data store for the cheminfor- matics components

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

NASA Astrophysics Data System (ADS)

Ervina, Rahmawati; Wasiq, Hidayat Jafron

2018-02-01

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

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

PubMed

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

Design and development of an interactive medical teleconsultation system over the World Wide Web.

PubMed

Bai, J; Zhang, Y; Dai, B

1998-06-01

The objective of the medical teleconsultation system presented in this paper is to demonstrate the use of the World Wide Web (WWW) for telemedicine and interactive medical information exchange. The system, which is developed based on Java, could provide several basic Java tools to fulfill the requirements of medical applications, including a file manager, data tool, bulletin board, and digital audio tool. The digital audio tool uses point-to-point structure to enable two physicians to communicate directly through voice. The others use multipoint structure. The file manager manages the medical images stored in the WWW information server, which come from a hospital database. The data tool supports cooperative operations on the medical data between the participating physicians. The bulletin board enables the users to discuss special cases by writing text on the board, send their personal or group diagnostic reports on the cases, and reorganize the reports and store them in its report file for later use. The system provides a hardware-independent platform for physicians to interact with one another as well as to access medical information over the WWW.

Environmental management and monitoring for education building development

NASA Astrophysics Data System (ADS)

Masri, R. M.

2018-05-01

The purpose of research were (1) a conceptual, functional model designed and implementation for environmental management and monitoring for education building development, (2) standard operational procedure made for management and monitoring for education building development, (3) assessed physic-chemical, biological, social-economic environmental components so that fulfilling sustainable development, (4) environmental management and monitoring program made for decreasing negative and increasing positive impact in education building development activities. Descriptive method is used for the research. Cibiru UPI Campus, Bandung, West Java, Indonesia was study location. The research was conducted on July 2016 to January 2017. Spatial and activities analysis were used to assess physic-chemical, biological, social-economic environmental components. Environmental management and monitoring for education building development could be decreasing water, air, soil pollution and environmental degradation in education building development activities.

Computing chemical organizations in biological networks.

PubMed

Centler, Florian; Kaleta, Christoph; di Fenizio, Pietro Speroni; Dittrich, Peter

2008-07-15

Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory of chemical organizations has recently been introduced as such a technique that links the topology of biochemical reaction network models to their dynamical repertoire. The network is decomposed into algebraically closed and self-maintaining subnetworks called organizations. They form a hierarchy representing all feasible system states including all steady states. We present three algorithms to compute the hierarchy of organizations for network models provided in SBML format. Two of them compute the complete organization hierarchy, while the third one uses heuristics to obtain a subset of all organizations for large models. While the constructive approach computes the hierarchy starting from the smallest organization in a bottom-up fashion, the flux-based approach employs self-maintaining flux distributions to determine organizations. A runtime comparison on 16 different network models of natural systems showed that none of the two exhaustive algorithms is superior in all cases. Studying a 'genome-scale' network model with 762 species and 1193 reactions, we demonstrate how the organization hierarchy helps to uncover the model structure and allows to evaluate the model's quality, for example by detecting components and subsystems of the model whose maintenance is not explained by the model. All data and a Java implementation that plugs into the Systems Biology Workbench is available from http://www.minet.uni-jena.de/csb/prj/ot/tools.

Mining collections of compounds with Screening Assistant 2

PubMed Central

2012-01-01

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

Mining collections of compounds with Screening Assistant 2.

PubMed

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

2012-08-31

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

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

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

Paintbrush of Discovery: Using Java Applets to Enhance Mathematics Education

ERIC Educational Resources Information Center

Eason, Ray; Heath, Garrett

2004-01-01

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

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

EPA Science Inventory

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

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

Malware Memory Analysis for Non-Specialists: Investigating Publicly Available Memory Image for the Stuxnet Worm

DTIC Science & Technology

2013-11-01

may be considered moderately suspicious. [20, 21, 22 and 23] PID 1580 (jqs.exe) is using port 5152, a port associated to with Java Quick Starter [26...spoolsv.exe 0x01000000 True False True \\WINDOWS\\system32\\spoolsv.exe 1580 jqs.exe 0x00400000 True False True \\Program Files\\ Java \\jre6\\bin\\jqs.exe 1664...Files\\ Java \\ Java Update\\jusched.exe 1816 VMUpgradeHelp er 0x00400000 True False True \\Program Files\\VMware\\VMware Tools\\VMUpgradeHelper.exe 1872

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

PubMed

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

2010-04-01

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

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

PubMed

Eng, J

1997-01-01

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

Java Programming Language

NASA Technical Reports Server (NTRS)

Shaykhian, Gholam Ali

2007-01-01

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

Tooth enamel surface micro-hardness with dual species Streptococcus biofilm after exposure to Java turmeric (Curcuma xanthorrhiza Roxb.) extract

NASA Astrophysics Data System (ADS)

Isjwara, F. R. G.; Hasanah, S. N.; Utami, Sri; Suniarti, D. F.

2017-08-01

Streptococcus biofilm on tooth surfaces can decrease mouth environment pH, thus causing enamel demineralization that can lead to dental caries. Java Turmeric extract has excellent antibacterial effects and can maintain S. mutans biofilm pH at neutral levels for 4 hours. To analyze the effect of Java Turmeric extract on tooth enamel micro-hardness, the Java Turmeric extract was added on enamel tooth samples with Streptococcus dual species biofilm (S. sanguinis and S. mutans). The micro-hardness of enamel was measured by Knoop Hardness Tester. Results showed that Curcuma xanthorrhiza Roxb. could not maintain tooth enamel surface micro-hardness. It is concluded that Java Turmeric extract ethanol could not inhibit the hardness of enamel with Streptococcus dual species biofilm.

A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1997-01-01

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

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.

Geo Techno Park potential at Arjuno-Welirang Volcano hosted geothermal area, Batu, East Java, Indonesia (Multi geophysical approach)

NASA Astrophysics Data System (ADS)

Maryanto, Sukir

2017-11-01

Arjuno Welirang Volcano Geothermal (AWVG) is located around Arjuno-Welirang Volcano in Malang, East Java, about 100 km southwest of Surabaya, the capital city of East Java province, and is still an undeveloped area of the geothermal field. The occurrence of solfatara and fumaroles with magmatic gasses indicated the existence of a volcanic geothermal system in the subsurface. A few hot springs are found in the Arjuno-Welirang volcanic complex, such as Padusan hot spring, Songgoriti hot spring, Kasinan hot spring, and Cangar hot spring. Multi geophysical observations in AWVG complex was carried out in order to explore the subsurface structure in supporting the plan of Geo Techno Park at the location. Gravity, Magnetic, Microearthquake, and Electrical Resistivity Tomography (ERT) methods were used to investigate the major and minor active faulting zones whether hot springs circulation occurs in these zones. The gravity methods allowed us to locate the subsurface structure and to evaluate their geometrical relationship base on density anomaly. Magnetic methods allow us to discriminate conductive areas which could correspond to an increase in thermal fluid circulation in the investigated sites. Micro-earthquakes using particle motion analysis to locate the focal depth related with hydrothermal activity and electrical resistivity tomography survey offers methods to locate more detail subsurface structure and geothermal fluids near the surface by identifying areas affected by the geothermal fluid. The magnetic and gravity anomaly indicates the subsurface structure of AWVG is composed of basalt rock, sulfide minerals, sandstone, and volcanic rock with high minor active fault structure as a medium for fluid circulation. While using micro-earthquake data in AWVG shown shallow focal depth range approximate 60 meters which indicates shallow hydrothermal circulation in AWVG. The geothermal fluid circulation zones along the fault structure resulted in some hot springs in a central and north-western part of AWVG detected by the Electrical Resistivity Tomography, appear to be well correlated with corresponding features derived from the gravity, magnetic, and micro-earthquake survey. We just ongoing process to develop Arjuno Welirang Volcano & Geothermal Research Center (AWVGRC) located at Universitas Brawijaya Agro Techno Park, Cangar in the flank of Arjuno Welirang volcano complex. Due to our initial observations, AWVG has a great potential for a pilot project of an educational geo technopark development area.

FastScript3D - A Companion to Java 3D

NASA Technical Reports Server (NTRS)

Koenig, Patti

2005-01-01

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

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

PubMed

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

2009-01-01

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

In Internet-Based Visualization System Study about Breakthrough Applet Security Restrictions

NASA Astrophysics Data System (ADS)

Chen, Jie; Huang, Yan

In the process of realization Internet-based visualization system of the protein molecules, system needs to allow users to use the system to observe the molecular structure of the local computer, that is, customers can generate the three-dimensional graphics from PDB file on the client computer. This requires Applet access to local file, related to the Applet security restrictions question. In this paper include two realization methods: 1.Use such as signature tools, key management tools and Policy Editor tools provided by the JDK to digital signature and authentication for Java Applet, breakthrough certain security restrictions in the browser. 2. Through the use of Servlet agent implement indirect access data methods, breakthrough the traditional Java Virtual Machine sandbox model restriction of Applet ability. The two ways can break through the Applet's security restrictions, but each has its own strengths.

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

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

Darby, John L.

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

The Functional Measurement Experiment Builder suite: two Java-based programs to generate and run functional measurement experiments.

PubMed

Mairesse, Olivier; Hofmans, Joeri; Theuns, Peter

2008-05-01

We propose a free, easy-to-use computer program that does not requires prior knowledge of computer programming to generate and run experiments using textual or pictorial stimuli. Although the FM Experiment Builder suite was initially programmed for building and conducting FM experiments, it can also be applied for non-FM experiments that necessitate randomized, single, or multifactorial designs. The program is highly configurable, allowing multilingual use and a wide range of different response formats. The outputs of the experiments are Microsoft Excel compatible .xls files that allow easy copy-paste of the results into Weiss's FM CalSTAT program (2006) or any other statistical package. Its Java-based structure is compatible with both Windows and Macintosh operating systems, and its compactness (< 1 MB) makes it easily distributable over the Internet.

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.

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.

Links between urbanization and sectoral shifts in employment in Java.

PubMed

Jones, G W

1984-12-01

The relationship between urbanization and changes in the employment structure in Indonesia is analyzed. In particular, the author examines whether changes in the occupational structure in rural areas can have any effect in slowing the general shift in economic emphasis to urban areas, whether nonagricultural economic activities can be developed in rural areas, and what policies are needed to assist the transformation of the rural employment sector. Data are primarily from Indonesian censuses, including the 1980 census.

Developmental Process Model for the Java Intelligent Tutoring System

ERIC Educational Resources Information Center

Sykes, Edward

2007-01-01

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

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…

Dynamic Learning Objects to Teach Java Programming Language

ERIC Educational Resources Information Center

Narasimhamurthy, Uma; Al Shawkani, Khuloud

2010-01-01

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

Geothermal and volcanism in west Java

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Subsurface Structure Interpretation Beneath of Mt. Pandan Based on Gravity Data

NASA Astrophysics Data System (ADS)

Santoso, D.; Wahyudi, E. J.; Alawiyah, S.; Nugraha, A. D.; Widiyantoro, S.; Kadir, W. G. A.; Supendi, P.; Wiyono, S.; Zulkafriza

2017-04-01

Mt. Pandan is one of the volcano that state as dormant volcano. On the other hand, Smyth et al. (2008) defined that Mt. Pandan is an active volcano. This volcano is apart a volcanic chain in Java island which is trending east-west along the island. This volcanic chain known as present day volcanic arc. Mt. Wilis is located in the south and it relatively much bigger compare to Mt. Pandan. There were earthquakes activity experienced in the surrounding Mt. Pandan area in the past several years. This event is interesting, because Mt. Pandan is not classify as the active volcano according to the list of volcanoes in Indonesia. On the otherhand Smyth et. al. (2008) mentioned that G. Pandan as modern volcanic which is located in Kendeng Zone of East Java. Gravity measurement around Mt. Pandan area was done in order to understand subsurface structure of Mt. Pandan. Gravity interpretation results shows that there is a low density structure beneath Mt. Pandan. It could be interpreted as existing of magma body below the surface. Some indication of submagmatic activities were found as hot spring and warm ground. Therefore it could be concluded that there is a possibility of magmatic activity below the Mt. Pandan.

Community Structure Of Coral Reefs In Saebus Island, Sumenep District, East Java

NASA Astrophysics Data System (ADS)

Rizmaadi, Mada; Riter, Johannes; Fatimah, Siti; Rifaldi, Riyan; Yoga, Arditho; Ramadhan, Fikri; Ambariyanto, Ambariyanto

2018-02-01

Increasing degradation coral reefs ecosystem has created many concerns. Reduction of this damage can only be done with good and proper management of coral reef ecosystem based on existing condition. The condition of coral reef ecosystem can be determined by assessing its community structure. This study investigates community structure of coral reef ecosystems around Saebus Island, Sumenep District, East Java, by using satellite imagery analysis and field observations. Satellite imagery analysis by Lyzenga methods was used to determine the observation stations and substrate distribution. Field observations were done by using Line Intercept Transect method at 4 stations, at the depth of 3 and 10 meters. The results showed that the percentage of coral reef coverage at the depth of 3 and 10 meters were 64.36% and 59.29%, respectively, and included in fine coverage category. This study found in total 25 genera from 13 families of corals at all stations. The most common species found were Acropora, Porites, and Pocillopora, while the least common species were Favites and Montastrea. Average value of Diversity, Uniformity and Dominancy indices were 2.94, 0.8 and 0.18 which include as medium, high, and low category, respectively. These results suggest that coral reef ecosystems around Saebus Island is in a good condition.

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

Wickstrom, Gregory Lloyd; Gale, Jason Carl; Ma, Kwok Kee

The Sandia Secure Processor (SSP) is a new native Java processor that has been specifically designed for embedded applications. The SSP's design is a system composed of a core Java processor that directly executes Java bytecodes, on-chip intelligent IO modules, and a suite of software tools for simulation and compiling executable binary files. The SSP is unique in that it provides a way to control real-time IO modules for embedded applications. The system software for the SSP is a 'class loader' that takes Java .class files (created with your favorite Java compiler), links them together, and compiles a binary. Themore » complete SSP system provides very powerful functionality with very light hardware requirements with the potential to be used in a wide variety of small-system embedded applications. This paper gives a detail description of the Sandia Secure Processor and its unique features.« less

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.

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.

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

ERIC Educational Resources Information Center

Karavirta, Ville; Shaffer, Clifford A.

2016-01-01

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

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…

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

ERIC Educational Resources Information Center

Askar, Petek; Davenport, David

2009-01-01

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

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.

JavaScript: Convenient Interactivity for the Class Web Page.

ERIC Educational Resources Information Center

Gray, Patricia

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

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

ERIC Educational Resources Information Center

Corder, Greg

2005-01-01

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

A Geostationary Earth Orbit Satellite Model Using Easy Java Simulation

ERIC Educational Resources Information Center

Wee, Loo Kang; Goh, Giam Hwee

2013-01-01

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

Muria Volcano, Island of Java, Indonesia

NASA Technical Reports Server (NTRS)

1991-01-01

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

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

ERIC Educational Resources Information Center

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

2013-01-01

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

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...

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

NASA Astrophysics Data System (ADS)

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

2014-08-01

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

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

Fiantis, Dian; Nelson, Malik; Van Ranst, Eric

Java Island, Indonesia with abundant amount of pyroclastic deposits is located in the very active and dynamic Pacific Ring of Fires. Studying the geochemical weathering indices of these pyroclastic deposits is important to get a clear picture about weathering profiles on deposits resulting from the eruption of Mt. Merapi. Immediately after the first phase of the eruption (March to June 2006), moist and leached pyroclastic deposits were collected. These pyroclastic deposits were found to be composed of volcanic glass, plagioclase feldspar in various proportions, orthopyroxene, clinopyroxene, olivine, amphibole, and titanomagnetite. Total elemental composition of the bulk samples (including trace elementsmore » and heavy metals) were determined by wet chemical methods and X-ray fluorescence (XRF) analyses. Weathering of the pyroclastic deposits was studied using various weathering indices. The Ruxton ratio, weathering index of Parker, Vought resudual index and chemical index of weathering of moist pyroclastic are lower than the leached sample but the alteration indices (chemical and plagioclase) are slightly higher in the moist compared to the leached pyroclastic deposits.« less

Model Checking JAVA Programs Using Java Pathfinder

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Pressburger, Thomas

2000-01-01

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

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

The 17 July 2006 Tsunami earthquake in West Java, Indonesia

USGS Publications Warehouse

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

2007-01-01

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

Characteristics of peri-urbanization of a secondary city: a challenge in recent urban development

NASA Astrophysics Data System (ADS)

Rahayu, P.; Mardiansjah, F. H.

2018-03-01

Urbanization process creates a tremendous spatial phenomenon since the last century. Especially for the country of the South, the phenomenon is still relevant to the situation today and the processes will still going until the foreseeable future. The metropolitan-based of urbanization process involves the development of peri-urban areas, which could be defined as transitional zones between city and rural areas characterized by integrated mixed-structures of agricultural and non-agricultural activities. This article reveals the characteristics of periurbanization process of an emerging secondary city in Java, which uses Surakarta, the second largest city in Central Java Province based on the population size, as the case. During the last ten years, there have been significant changes in peri-urban areas regarding urban population, land use, and urban activities that strengthening the contribution of the urban component into peri-urban system.

The pH ruler: a Java applet for developing interactive exercises on acids and bases.

PubMed

Barrette-Ng, Isabelle H

2011-07-01

In introductory biochemistry courses, it is often a struggle to teach the basic concepts of acid-base chemistry in a manner that is relevant to biological systems. To help students gain a more intuitive and visual understanding of abstract acid-base concepts, a simple graphical construct called the pH ruler Java applet was developed. The applet allows students to visualize the abundance of different protonation states of diprotic and triprotic amino acids at different pH values. Using the applet, the student can drag a widget on a slider bar to change the pH and observe in real time changes in the abundance of different ionization states of this amino acid. This tool provides a means for developing more complex inquiry-based, active-learning exercises to teach more advanced topics of biochemistry, such as protein purification, protein structure and enzyme mechanism.

Proper Plugin Protocols

DTIC Science & Technology

2011-12-28

specify collaboration constraints that occur in Java and XML frameworks and that the collaboration constraints from these frameworks matter in practice. (a...programming language boundaries, and Chapter 6 and Appendix A demonstrate that Fusion can specify constraints across both Java and XML in practice. (c...designed JUnit, Josh Bloch designed Java Collec- tions, and Krzysztof Cwalina designed the .NET Framework APIs. While all of these frameworks are very

Notice and Credits Page - NOAA's National Weather Service

Science.gov Websites

- Visolve is a software application (free for personal use) that transforms colors of the computer display Mac OS X 10.2 or later. (Purchase) - A 30-day free trial of eyePilot is available from eyePilot web site - http://www.colorhelper.com/ Java Java Virtual Machine - free download from java.com Adobe Reader

Tomcat, Oracle & XML Web Archive

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

Cothren, D. C.

2008-01-01

The TOX (Tomcat Oracle & XML) web archive is a foundation for development of HTTP-based applications using Tomcat (or some other servlet container) and an Oracle RDBMS. Use of TOX requires coding primarily in PL/SQL, JavaScript, and XSLT, but also in HTML, CSS and potentially Java. Coded in Java and PL/SQL itself, TOX provides the foundation for more complex applications to be built.

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

ERIC Educational Resources Information Center

Schmidt, Cecil

2007-01-01

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

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

Instrumentation of Java Bytecode for Runtime Analysis

NASA Technical Reports Server (NTRS)

Goldberg, Allen; Haveland, Klaus

2003-01-01

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

Java and its future in biomedical computing.

PubMed Central

Rodgers, R P

1996-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Creating Web-Based Scientific Applications Using Java Servlets

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Handle with care: the impact of using Java applets in Web-based studies on dropout and sample composition.

PubMed

Stieger, Stefan; Göritz, Anja S; Voracek, Martin

2011-05-01

In Web-based studies, Web browsers are used to display online questionnaires. If an online questionnaire relies on non-standard technologies (e.g., Java applets), it is often necessary to install a particular browser plug-in. This can lead to technically induced dropout because some participants lack the technological know-how or the willingness to install the plug-in. In two thematically identical online studies conducted across two time points in two different participant pools (N = 1,527 and 805), we analyzed whether using a Java applet produces dropout and distortion of demographics in the final sample. Dropout was significantly higher on the Java applet questionnaire page than on the preceding and subsequent questionnaire pages. Age-specific effects were found only in one sample (i.e., dropouts were older), whereas sex-specific effects were found in both samples (i.e., women dropped out more frequently than men on the Java applet page). These results additionally support the recommendation that using additional technologies (e.g., Java applets) can be dangerous in producing a sample that is biased toward both younger and male respondents.

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.

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

The r-Java 2.0 code: nuclear physics

NASA Astrophysics Data System (ADS)

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

2014-08-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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.

Static Extraction and Conformance Analysis of Hierarchical Runtime Architectural Structure

DTIC Science & Technology

2010-05-14

Example: CryptoDB 253 Architectural Component Java Class Note CustomerManager cryptodb.test.CustomerManager AKA “ crypto consumer” CustomerManager.Receipts...PROVIDERS PLAIN KEYID KEYMANAGEMENT KEYSTORAGE CRYPTO (+) (+) (+) (+) (+) (+) (+)(+) Figure 7.29: CryptoDB: Level-0 OOG with String objects...better understand this communication, we declared different domains for plain-text (PLAIN), encrypted ( CRYPTO ), alias identifier (ALIASID), and key

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…

Evaluating Environment, Erosion and Sedimentation Aspects in Coastal Area to Determine Priority Handling (A Case Study in Jepara Regency, northern Central Java, Indonesia)

NASA Astrophysics Data System (ADS)

Wahyudi, S. I.; Adi, H. P.

2018-04-01

Many areas of the northern coastal in Central Java, Indonesia, have been suffering from damage. One of the areas is Jepara, which has been experiencing this kind of damage for 7.6 kilometres from total 72 kilometres long beach. All damages are mostly caused by coastal erosion, sedimentation, environment and tidal flooding. Several efforts have been done, such as replanting mangroves, building revetment and groins, but it still could not mitigated the coastal damage. The purposes of this study are to map the coastal damages, to analyze handling priority and to determine coastal protection model. The method used are by identifying and plotting the coastal damage on the map, assessing score of each variable, and determining the handling priority and suitable coastal protection model. There are five levels of coastal damage used in this study, namely as light damage, medium, heavy, very heavy, and extremely heavy. Based on the priority assessment of coastal damage, it needs to be followed up by designing in detail and implementing through soft structure for example mangrove, sand nourishes and hard structure, such as breakwater, groins and revetment.

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).

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

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

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

PubMed

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

1997-12-01

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

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.

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

PubMed Central

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

2017-01-01

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

Using chemical organization theory for model checking

PubMed Central

Kaleta, Christoph; Richter, Stephan; Dittrich, Peter

2009-01-01

Motivation: The increasing number and complexity of biomodels makes automatic procedures for checking the models' properties and quality necessary. Approaches like elementary mode analysis, flux balance analysis, deficiency analysis and chemical organization theory (OT) require only the stoichiometric structure of the reaction network for derivation of valuable information. In formalisms like Systems Biology Markup Language (SBML), however, information about the stoichiometric coefficients required for an analysis of chemical organizations can be hidden in kinetic laws. Results: First, we introduce an algorithm that uncovers stoichiometric information that might be hidden in the kinetic laws of a reaction network. This allows us to apply OT to SBML models using modifiers. Second, using the new algorithm, we performed a large-scale analysis of the 185 models contained in the manually curated BioModels Database. We found that for 41 models (22%) the set of organizations changes when modifiers are considered correctly. We discuss one of these models in detail (BIOMD149, a combined model of the ERK- and Wnt-signaling pathways), whose set of organizations drastically changes when modifiers are considered. Third, we found inconsistencies in 5 models (3%) and identified their characteristics. Compared with flux-based methods, OT is able to identify those species and reactions more accurately [in 26 cases (14%)] that can be present in a long-term simulation of the model. We conclude that our approach is a valuable tool that helps to improve the consistency of biomodels and their repositories. Availability: All data and a JAVA applet to check SBML-models is available from http://www.minet.uni-jena.de/csb/prj/ot/tools Contact: dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19468053

RiboSketch: Versatile Visualization of Multi-stranded RNA and DNA Secondary Structure.

PubMed

Lu, Jacob S; Bindewald, Eckart; Kasprzak, Wojciech; Shapiro, Bruce A

2018-06-15

Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size, and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application. https://binkley2.ncifcrf.gov/users/bindewae/ribosketch_web.

Application of Semiparametric Spline Regression Model in Analyzing Factors that In uence Population Density in Central Java

NASA Astrophysics Data System (ADS)

Sumantari, Y. D.; Slamet, I.; Sugiyanto

2017-06-01

Semiparametric regression is a statistical analysis method that consists of parametric and nonparametric regression. There are various approach techniques in nonparametric regression. One of the approach techniques is spline. Central Java is one of the most densely populated province in Indonesia. Population density in this province can be modeled by semiparametric regression because it consists of parametric and nonparametric component. Therefore, the purpose of this paper is to determine the factors that in uence population density in Central Java using the semiparametric spline regression model. The result shows that the factors which in uence population density in Central Java is Family Planning (FP) active participants and district minimum wage.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2009-04-01

Landslides are important natural hazards occurring on mountainous area situated in the wet tropical climate like in Java, Indonesia. As a central of economic and government activity, Java become the most populated island in Indonesia and is increasing every year. This condition create population more vulnerable to hazard. Java is populated by 120 million inhabitants or equivalent with 60% of Indonesian population in only 6,9% of the total surface of Indonesia. Due to its geological setting, its topographical characteristics, and its climatic characteristics, Java is the most exposed regions to landslide hazard and closely related to several factors: (1) located on a subduction zone, 60% of Java is mountainous, with volcano-tectonic mountain chains and 36 active volcanoes out of the 129 in Indonesia, and these volcanic materials are intensively weathered (2) Java is under a humid tropical climate associated with heavy rainfall during the rainy season from October to April. On top of these "natural" conditions, the human activity is an additional factor of landslide occurrence, driven by a high demographic density The purpose of this paper was to collect and analyze spatial and temporal data concerning landslide hazard for the period 1981-2007 and to evaluate and analyze the characteristic and the behavior of landslide in Java. The results provides a new insight into our understanding of landslide hazard and characteristic in the humid tropics, and a basis for predicting future landslides and assessing related hazards at a regional scale. An overview of characteristic and behavior of landslides in Java is given. The result of this work would be valuable for decision makers and communities in the frame of future landslide risk reduction programs. Landslide inventory data was collected from internal database at the different institutions. The result is then georefenced. The temporal changes of landslide activities was done by examining the changes in number and frequency both annual and monthly level during the periods of 1981 - 2007. Simple statistical analysis was done to correlate landslide events, antecedent rainfall during 30 consecutive days and daily rainfall during the landslide day. Analysis the relationship between landslide events and their controlling factors (e.g. slope, geology, geomorphology and landuse) were carried out in GIS environment. The results show that the slope gradient has a good influence to landslides events. The number of landslides increases significantly from slopes inferior to 10° and from 30° to 40°. However, inverse correlation between landslides events occurs on slope steepness more than 40° when the landslide frequency tends to decline with an increasing of slope angle. The result from landuse analysis shows that most of landslides occur on dryland agriculture, followed by paddy fields and artificial. This data indicates that human activities play an important role on landslide occurrence. Dryland agriculture covers not only the lower part of land, but also reached middle and upper slopes; with terraces agriculture that often accelerate landslide triggering. During the period 1981-2007, the annual landslide frequency varies significantly, with an average of 49 events per year. Within a year, the number of landslides increases from June to November and decreases significantly from January to July. Statistically, both January and November are the most susceptible months for landslide generation, with respectively nine and seven events on average. This distribution is closely related to the rainfall monthly variations. Landslides in Java are unevenly distributed. Most landslides are concentrated in West Java Region, followed by Central Java and East Java. The overall landslide density in Java reached 1x10 events/km with the annual average was 3.6 x 10 event/km /year. The amount of annual precipitation is significantly higher in West Java than further East, decreasing with a constant W-E gradient. The minimum annual rainfall occurs in the northern part and in Far East Java, where few landslides can be spotted. Cumulative rainfalls are playing an important role on landslides triggering. Most of shallow landslides can be associated with antecedent rainfall, and rainfall superior on the day of landslide occurrence. There is an inverse relation between antecedent rainfalls and daily rainfall. Indeed heavy instantaneous rainfall can produce a landslide with the help of only low antecedent rainfall. On the contrary we encountered 11 cases of landslides with no rain on the triggering day, but with important antecedent rainfalls. Key words: rainfall induced landslide, spatio-temporal distribution, Java Island, Tropical Region.

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

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

DTIC Science & Technology

1997-06-01

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

Methods to Secure Databases Against Vulnerabilities

DTIC Science & Technology

2015-12-01

for several languages such as C, C++, PHP, Java and Python [16]. MySQL will work well with very large databases. The documentation references...using Eclipse and connected to each database management system using Python and Java drivers provided by MySQL , MongoDB, and Datastax (for Cassandra...tiers in Python and Java . Problem MySQL MongoDB Cassandra 1. Injection a. Tautologies Vulnerable Vulnerable Not Vulnerable b. Illegal query

Automatic Publication of a MIS Product to GeoNetwork: Case of the AIS Indexer

DTIC Science & Technology

2012-11-01

installation and configuration The following instructions are for installing and configuring the software packages Java 1.6 and MySQL 5.5 which are...An Automatic Identification System (AIS) reception indexer Java application was developed in the summer of 2011, based on the work of Lapinski and...release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT An Automatic Identification System (AIS) reception indexer Java application was

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

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…

Kleene Algebra and Bytecode Verification

DTIC Science & Technology

2016-04-27

computing the star (Kleene closure) of a matrix of transfer functions. In this paper we show how this general framework applies to the problem of Java ...bytecode verification. We show how to specify transfer functions arising in Java bytecode verification in such a way that the Kleene algebra operations...potentially improve the performance over the standard worklist algorithm when a small cutset can be found. Key words: Java , bytecode, verification, static

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

OGDD (Olive Genetic Diversity Database): a microsatellite markers' genotypes database of worldwide olive trees for cultivar identification and virgin olive oil traceability

PubMed Central

Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Ben Marzoug, Riadh; Rebai, Ahmed

2016-01-01

Olive (Olea europaea), whose importance is mainly due to nutritional and health features, is one of the most economically significant oil-producing trees in the Mediterranean region. Unfortunately, the increasing market demand towards virgin olive oil could often result in its adulteration with less expensive oils, which is a serious problem for the public and quality control evaluators of virgin olive oil. Therefore, to avoid frauds, olive cultivar identification and virgin olive oil authentication have become a major issue for the producers and consumers of quality control in the olive chain. Presently, genetic traceability using SSR is the cost effective and powerful marker technique that can be employed to resolve such problems. However, to identify an unknown monovarietal virgin olive oil cultivar, a reference system has become necessary. Thus, an Olive Genetic Diversity Database (OGDD) (http://www.bioinfo-cbs.org/ogdd/) is presented in this work. It is a genetic, morphologic and chemical database of worldwide olive tree and oil having a double function. In fact, besides being a reference system generated for the identification of unkown olive or virgin olive oil cultivars based on their microsatellite allele size(s), it provides users additional morphological and chemical information for each identified cultivar. Currently, OGDD is designed to enable users to easily retrieve and visualize biologically important information (SSR markers, and olive tree and oil characteristics of about 200 cultivars worldwide) using a set of efficient query interfaces and analysis tools. It can be accessed through 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. Database URL: http://www.bioinfo-cbs.org/ogdd/ PMID:26827236

Rayleigh-wave tomography of the Ontong-Java Plateau

NASA Astrophysics Data System (ADS)

Richardson, W. Philip; Okal, Emile A.; Van der Lee, Suzan

2000-02-01

The deep structure of the Ontong-Java Plateau (OJP) in the westcentral Pacific is investigated through a 2-year deployment of four PASSCAL seismic stations used in a passive tomographic experiment. Single-path inversions of 230 Rayleigh waveforms from 140 earthquakes mainly located in the Solomon Trench confirm the presence of an extremely thick crust, with an average depth to the Mohorovičić discontinuity of 33 km. The thickest crusts (38 km) are found in the southcentral part of the plateau, around 2°S, 157°E. Lesser values remaining much thicker than average oceanic crust (15-26 km) are found on either side of the main structure, suggesting that the OJP spills over into the Lyra Basin to the west. Such thick crustal structures are consistent with formation of the plateau at the Pacific-Phoenix ridge at 121 Ma, while its easternmost part may have formed later (90 Ma) on more mature lithosphere. Single-path inversions also reveal a strongly developed low-velocity zone at asthenospheric depths in the mantle. A three-dimensional tomographic inversion resolves a low-velocity root of the OJP extending as deep as 300 km, with shear velocity deficiencies of ˜5%, suggesting the presence of a keel, dragged along with the plateau as the latter moves as part of the drift of the Pacific plate over the mantle.

Transformation of Indonesian Natural Zeolite into Analcime Phase under Hydrothermal Condition

NASA Astrophysics Data System (ADS)

Lestari, W. W.; Hasanah, D. N.; Putra, R.; Mukti, R. R.; Nugrahaningtyas, K. D.

2018-04-01

Natural zeolite is abundantly available in Indonesia and well distributed especially in the volcano area like Java, Sumatera, and Sulawesi. So far, natural zeolite from Klaten, Central Java is one of the most interesting zeolites has been widely studied. This research aims to know the effect of seed-assisted synthesis under a hydrothermal condition at 120 °C for 24 hours of Klaten’s zeolite toward the structural change and phase transformation of the original structure. According to XRD and XRF analysis, seed-assisted synthesis through the addition of aluminosilicate mother solution has transformed Klaten’s zeolite which contains (mordenite and clinoptilolite) into analcime type with decreasing Si/Al ratio from 4.51 into 1.38. Morphological analysis using SEM showed the shape changes from irregular into spherical looks like takraw ball in the range of 0.3 to 0.7 micrometer. Based on FTIR data, structure of TO4 site (T = Si or Al) was observed in the range of 300-1300 cm-1 and the occupancy of Brønsted acid site as OH stretching band from silanol groups was detected at 3440-3650 cm-1. Nitrogen adsorption-desorption analysis confirmed that transformation Klaten’s zeolite into analcime type has decreased the surface area from 55.41 to 22.89 m2/g and showed inhomogeneous pore distribution which can be classified as micro-mesoporous aluminosilicate materials.

Semantic-Web Architecture for Electronic Discharge Summary Based on OWL 2.0 Standard.

PubMed

Tahmasebian, Shahram; Langarizadeh, Mostafa; Ghazisaeidi, Marjan; Safdari, Reza

2016-06-01

Patients' electronic medical record contains all information related to treatment processes during hospitalization. One of the most important documents in this record is the record summary. In this document, summary of the whole treatment process is presented which is used for subsequent treatments and other issues pertaining to the treatment. Using suitable architecture for this document, apart from the aforementioned points we can use it in other fields such as data mining or decision making based on the cases. In this study, at first, a model for patient's medical record summary has been suggested using semantic web-based architecture. Then, based on service-oriented architecture and using Java programming language, a software solution was designed and run in a way to generate medical record summary with this structure and at the end, new uses of this structure was explained. in this study a structure for medical record summaries along with corrective points within semantic web has been offered and a software running within Java along with special ontologies are provided. After discussing the project with the experts of medical/health data management and medical informatics as well as clinical experts, it became clear that suggested design for medical record summary apart from covering many issues currently faced in the medical records has also many advantages including its uses in research projects, decision making based on the cases etc.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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).

Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers.

PubMed Central

Selander, R K; Beltran, P; Smith, N H; Helmuth, R; Rubin, F A; Kopecko, D J; Ferris, K; Tall, B D; Cravioto, A; Musser, J M

1990-01-01

Multilocus enzyme electrophoresis was employed to measure chromosomal genotypic diversity and evolutionary relationships among 761 isolates of the serovars Salmonella typhi, S. paratyphi A, S. paratyphi B, S. paratyphi C, and S. sendai, which are human-adapted agents of enteric fever, and S. miami and S. java, which are serotypically similar to S. sendai and S. paratyphi B, respectively, but cause gastroenteritis in both humans and animals. To determine the phylogenetic positions of the clones of these forms within the context of the salmonellae of subspecies I, comparative data for 22 other common serovars were utilized. Except for S. paratyphi A and S. sendai, the analysis revealed no close phylogenetic relationships among clones of different human-adapted serovars, which implies convergence in host adaptation and virulence factors. Clones of S. miami are not allied with those of S. sendai or S. paratyphi A, being, instead, closely related to strains of S. panama. Clones of S. paratyphi B and S. java belong to a large phylogenetic complex that includes clones of S. typhimurium, S. heidelberg, S. saintpaul, and S. muenchen. Most strains of S. paratyphi B belong to a globally distributed clone that is highly polymorphic in biotype, bacteriophage type, and several other characters, whereas strains of S. java represent seven diverse lineages. The flagellar monophasic forms of S. java are genotypically more similar to clones of S. typhimurium than to other clones of S. java or S. paratyphi B. Clones of S. paratyphi C are related to those of S. choleraesuis. DNA probing with a segment of the viaB region specific for the Vi capsular antigen genes indicated that the frequent failure of isolates of S. paratyphi C to express Vi antigen is almost entirely attributable to regulatory processes rather than to an absence of the structural determinant genes themselves. Two clones of S. typhisuis are related to those of S. choleraesuis and S. paratyphi C, but a third clone is not. Although the clones of S. decatur and S. choleraesuis are serologically and biochemically similar, they are genotypically very distinct. Two clones of S. typhi were distinguished, one globally distributed and another apparently confined to Africa; both clones are distantly related to those of all other serovars studied. Images PMID:1973153

Internet Patient Records: new techniques

PubMed Central

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

2001-01-01

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

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

Applying a Service-Oriented Architecture to Operational Flight Program Development

DTIC Science & Technology

2007-09-01

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

ReSEARCH: A Requirements Search Engine: Progress Report 2

DTIC Science & Technology

2008-09-01

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

UAV Swarm Tactics: An Agent-Based Simulation and Markov Process Analysis

DTIC Science & Technology

2013-06-01

CRN Common Random Numbers CSV Comma Separated Values DoE Design of Experiment GLM Generalized Linear Model HVT High Value Target JAR Java ARchive JMF... Java Media Framework JRE Java runtime environment Mason Multi-Agent Simulator Of Networks MOE Measure Of Effectiveness MOP Measures Of Performance...with every set several times, and to write a CSV file with the results. Rather than scripting the agent behavior deterministically, the agents should

A Survey of Visualization Tools Assessed for Anomaly-Based Intrusion Detection Analysis

DTIC Science & Technology

2014-04-01

objective? • What vulnerabilities exist in the target system? • What damage or other consequences are likely? • What exploit scripts or other attack...languages C, R, and Python; no response capabilities. JUNG https://blogs.reucon.com/asterisk- java /tag/visualization/ Create custom layouts and can...annotate graphs, links, nodes with any Java data type. Must be familiar with coding in Java to call the routines; no monitoring or response

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

Cyber Intelligence Analysis Platform

DTIC Science & Technology

2014-04-01

inside a node. Moreover, by École Polytechnique de Montréal Page 6 of 18 adding one or two 10-Gigabit port(s) and/or fiber -channel ports enough... Java SDKs for the development of custom management tools. In any case, all these tools and SDKs would work with the vCenter Server. École...vSphere SDK for Java , http://communities.vmware.com/community/vmtn/developer/forums/java_toolkit xCAT main documentation page, http

Information Security Considerations for Applications Using Apache Accumulo

DTIC Science & Technology

2014-09-01

Distributed File System INSCOM United States Army Intelligence and Security Command JPA Java Persistence API JSON JavaScript Object Notation MAC Mandatory... MySQL [13]. BigTable can process 20 petabytes per day [14]. High degree of scalability on commodity hardware. NoSQL databases do not rely on highly...manipulation in relational databases. NoSQL databases each have a unique programming interface that uses a lower level procedural language (e.g., Java

Database Entity Persistence with Hibernate for the Network Connectivity Analysis Model

DTIC Science & Technology

2014-04-01

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

Faust: Flexible Acquistion and Understanding System for Text

DTIC Science & Technology

2013-07-01

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

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.

META-X Design Flow Tools

DTIC Science & Technology

2013-04-01

Forces can be computed at specific angular positions, and geometrical parameters can be evaluated. Much higher resolution models are required, along...composition engines (C#, C++, Python, Java ) Desert operates on the CyPhy model, converting from a design space alternative structure to a set of design...consists of scripts to execute dymola, post-processing of results to create metrics, and general management of the job sequence. An earlier version created

Single-crystal diffraction instrument TriCS at SINQ

NASA Astrophysics Data System (ADS)

Schefer, J.; Könnecke, M.; Murasik, A.; Czopnik, A.; Strässle, Th; Keller, P.; Schlumpf, N.

2000-03-01

The single-crystal diffractometer TriCS at the Swiss Continuous Spallation Source (SINQ) is presently in the commissioning phase. A two-dimensional wire detector produced by EMBL was delivered in March 1999. The instrument is presently tested with a single detector. First measurements on magnetic structures have been performed. The instrument is remotely controlled using JAVA-based software and a UNIX DEC-α host computer.

The Best of all Possible Worlds: Applying the Model Driven Architecture Approach to a JC3IEDM OWL Ontology Modeled in UML

DTIC Science & Technology

2014-04-25

EA’s Java application programming interface (API), the team built a tool called OWL2EA that can ingest an OWL file and generate the corresponding UML...ObjectItemStructure specification shown in Figure 10. Running this script in the relational database server MySQL creates the physical schema that

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

7 CFR 301.32-2 - Regulated articles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Oriental. Syzygium aquem Water apple, watery roseapple Peach. Syzygium cumini Java plum, jambolana Peach... samarangense Java apple Peach. Terminalia bellirica Myrobalan, belleric Peach. Terminalia catappa Tropical...

7 CFR 301.32-2 - Regulated articles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Oriental. Syzygium aquem Water apple, watery roseapple Peach. Syzygium cumini Java plum, jambolana Peach... samarangense Java apple Peach. Terminalia bellirica Myrobalan, belleric Peach. Terminalia catappa Tropical...

7 CFR 301.32-2 - Regulated articles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Oriental. Syzygium aquem Water apple, watery roseapple Peach. Syzygium cumini Java plum, jambolana Peach... samarangense Java apple Peach. Terminalia bellirica Myrobalan, belleric Peach. Terminalia catappa Tropical...

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.

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

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.

Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

PubMed

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

Novel Plasmids and Resistance Phenotypes in Yersinia pestis: Unique Plasmid Inventory of Strain Java 9 Mediates High Levels of Arsenic Resistance

PubMed Central

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L.

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium. PMID:22479347

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Extending DoD Modeling and Simulation with Web 2.0, Ajax and X3D

DTIC Science & Technology

2007-09-01

Supported by Gavin King, who created the well known and industry respected Hibernate , (O/R) Object Relational Mapping tool, which binds Java ...most likely a Hibernate derivative). The preceding is where eBay differs from a pure Java EE specification “by the book” implementation. A truly... Java language has come a long way in providing real world case studies and scalable solutions for the enterprise that are currently in production on

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

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

DTIC Science & Technology

2016-03-01

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

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

Identification of the terebrantian thrips (Insecta, Thysanoptera) associated with cultivated plants in Java, Indonesia

PubMed Central

Sartiami, Dewi; Mound, Laurence A.

2013-01-01

Abstract An illustrated identification key is provided to 49 species of Thysanoptera, Terebrantia that have been found in association with cultivated plants in Java. This is the first published identification system to this group of insects from Indonesia, and includes 15 species not previously recorded from Indonesia, and a further three species not previously recorded from Java. A table is provided indicating the plants from which thrips were taken. PMID:23794915

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.

Migrating Department of Defense (DoD) Web Service Based Applications to Mobile Computing Platforms

DTIC Science & Technology

2012-03-01

World Wide Web Consortium (W3C) Geolocation API to identify the device’s location and then center the map on the device. Finally, we modify the entry...THIS PAGE INTENTIONALLY LEFT BLANK xii List of Acronyms and Abbreviations API Application Programming Interface CSS Cascading Style Sheets CLIMO...Java API for XML Web Services Reference Implementation JS JavaScript JSNI JavaScript Native Interface METOC Meteorological and Oceanographic MAA Mobile

First geodetic measurement of convergence across the Java Trench

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

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.

Data mining for clustering naming of the village at Java Island

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

ISTP CDF Skeleton Editor

NASA Technical Reports Server (NTRS)

Chimiak, Reine; Harris, Bernard; Williams, Phillip

2013-01-01

Basic Common Data Format (CDF) tools (e.g., cdfedit) provide no specific support for creating International Solar-Terrestrial Physics/Space Physics Data Facility (ISTP/SPDF) standard files. While it is possible for someone who is familiar with the ISTP/SPDF metadata guidelines to create compliant files using just the basic tools, the process is error-prone and unreasonable for someone without ISTP/SPDF expertise. The key problem is the lack of a tool with specific support for creating files that comply with the ISTP/SPDF guidelines. There are basic CDF tools such as cdfedit and skeletoncdf for creating CDF files, but these have no specific support for creating ISTP/ SPDF compliant files. The SPDF ISTP CDF skeleton editor is a cross-platform, Java-based GUI editor program that allows someone with only a basic understanding of the ISTP/SPDF guidelines to easily create compliant files. The editor is a simple graphical user interface (GUI) application for creating and editing ISTP/SPDF guideline-compliant skeleton CDF files. The SPDF ISTP CDF skeleton editor consists of the following components: A swing-based Java GUI program, JavaHelp-based manual/ tutorial, Image/Icon files, and HTML Web page for distribution. The editor is available as a traditional Java desktop application as well as a Java Network Launching Protocol (JNLP) application. Once started, it functions like a typical Java GUI file editor application for creating/editing application-unique files.

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.

Management of Hazardous Waste in Indonesia

NASA Astrophysics Data System (ADS)

Widyatmoko, H.

2018-01-01

Indonesia needs to build four Treatment Centrals for 229,907 tons per year produced hazardous waste. But almost all hazardous waste treatment is managed by just one company at present, namely PT. PPLI (Prasada Pamunah Limbah Industri). This research is based on collected data which identifies payback period of 0.69 years and rate of return 85 %. PT PPLI is located within the Cileungsi District of the Bogor Regency of West Java Province. Records from nearest rainfall station at Cibinong indicate that annual average rainfall for the site is about 3,600 mm. It is situated on hilly terrain and is characterized by steep slopes as well as has a very complex geological structure. The Tertiary sequence was folded to form an assymetric anticline with axis trend in an East-West direction. Three major faults cut the middle of the site in a North-South direction with a vertical displacement of about 1.5 meters and a zone width of 1 meter. The high concentration of Chemical Oxygen Demand (COD) 2500 ppm in Secondary Leachate Collection System (SLCS) indicate a possible failure of the Primary Leachate Clection System (PLCS), which need correct action to prevent groundwater contamination.

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.

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

PubMed

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

2012-03-01

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

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.

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

PubMed

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

1996-01-01

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

Geographically weighted regression model on poverty indicator

NASA Astrophysics Data System (ADS)

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

2017-12-01

In this research, we applied geographically weighted regression (GWR) for analyzing the poverty in Central Java. We consider Gaussian Kernel as weighted function. The GWR uses the diagonal matrix resulted from calculating kernel Gaussian function as a weighted function in the regression model. The kernel weights is used to handle spatial effects on the data so that a model can be obtained for each location. The purpose of this paper is to model of poverty percentage data in Central Java province using GWR with Gaussian kernel weighted function and to determine the influencing factors in each regency/city in Central Java province. Based on the research, we obtained geographically weighted regression model with Gaussian kernel weighted function on poverty percentage data in Central Java province. We found that percentage of population working as farmers, population growth rate, percentage of households with regular sanitation, and BPJS beneficiaries are the variables that affect the percentage of poverty in Central Java province. In this research, we found the determination coefficient R2 are 68.64%. There are two categories of district which are influenced by different of significance factors.

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

NASA Astrophysics Data System (ADS)

Andriamanalimanana, Bruno R.

2004-08-01

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

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

NASA Astrophysics Data System (ADS)

Sarah, D.; Soebowo, E.

2018-02-01

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

Crustal structure in the southern part of Central Java based on analysis of tele-seismic receiver function using a neighbourhood algorithm

NASA Astrophysics Data System (ADS)

Ariyanto, P.; Syuhada; Rosid, S.; Anggono, T.; Januarti, Y.

2018-03-01

In this study, we applied receiver functions analysis to determine the crustal thickness, the ratio of Vp/Vs and the S wave velocity in the southern part of the Central Java. We selected tele-seismic data with magnitude more than 6 (M>6) and epicenter distance 30°-90° recorded from 3 broadband stations: UGM, YOGI, and WOJI station, as part of Indonesia-Geophone Network (IA-GE). Inversions were performed using nonlinear Neighborhood Algorithm (NA). We observed Ps phase conversion on the receiver functions corresponding to Moho depth at around 36-39 km. We also observed strong negative phase arrivals at around 10-12 s which might be associated with Indo-Australian subducting slab underneath the stations. The inversion results show the presence of low velocity zone with high Vp/Vs ratio (>1.78) in the middle crust around the study area which could be related to the Merapi-Lawu Anomaly (MLA).

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

Comparative morphological and morphometric description of the hominin calvaria from Bukuran (Sangiran, Central Java, Indonesia).

PubMed

Grimaud-Hervé, Dominique; Widianto, Harry; Détroit, Florent; Sémah, François

2012-11-01

We describe the hominin skull (called here "Bukuran") discovered in the lower Kabuh (or "Bapang") series near Sendangbusik, from the Bukuran area in the Sangiran dome. The fossil, heavily mineralized, consists of the parieto-occipital and the left temporal, and the frontal bones. When combined, those two cranial parts represent a rather complete and well-preserved calvaria. Its stratigraphic position was established after the discovery. A detailed description is presented of the morphological and metric features of the Bukuran calvaria, and comparisons are made with Asian Homo erectus from Indonesia and China. The estimated cranial capacity of Bukuran, the general shape of its cranial vault, its ectocranial structures, and its morphological and metrical characters are in the range of Asian Homo erectus, and show clear affinities with other Indonesian members of the species. We discuss the evolutionary status of the Bukuran calvaria and its implication for hominin history on Java. Copyright © 2012 Elsevier Ltd. All rights reserved.

Micro-seismic earthquakes characteristics at natural and exploited hydrothermal systems in West Java, Indonesia

NASA Astrophysics Data System (ADS)

Jousset, P. G.; Jaya, M. S.; Sule, R.; Diningrat, W.; Gassner, A.; Akbar, F.; Ryannugroho, R.; Hendryana, A.; Kusnadi, Y.; Syahbana, D.; Nugraha, A. D.; Umar, M.; Indrinanto, Y.; Erbas, K.

2013-12-01

The assessment of geothermal resources requires the understanding of the structure and the dynamics of geothermal reservoirs. We deployed a multidisciplinary geophysical network around geothermal areas in the south of Bandung, West Java, Indonesia. The first deployment included a network of 30 broadband and 4 short-period seismic stations with Güralp and Trillium sensors (0.008 - 100 Hz) since October 2012. In a second step, we extended the network in June 2013 with 16 short-period (1 Hz) seismometers. We describe the set-up of the seismic networks and discuss first observations and results. The co-existence of a large variety of intense surface manifestations like geysers, hot-steaming grounds, hot water pools, and active volcanoes suggest an intimate coupling between volcanic, tectonic and hydrothermal processes in this area. Preliminary location of earthquakes is performed using a non-linear algorithm, which allows us to define at least 3 seismic clusters. We discuss this seismic pattern within the geothermal fields.

Factors influencing non-adherence to tuberculosis treatment in Jepara, central Java, Indonesia.

PubMed

Rondags, Angelique; Himawan, Ari Budi; Metsemakers, Job Fm; Kristina, Tri Nur

2014-07-01

One of the most serious problems for tuberculosis (TB) control is non-adherence to TB treatment. We studied the factors influencing non-adherence to TB treatment in Indonesia to inform TB treatment adherence strategies. We con- ducted semi-structured interviews with non-adherent patients and key informants in Jepara, Central Java, Indonesia. Three major themes were found in reasons for non-adherence to TB treatment: 1) knowledge about TB, 2) knowledge about TB treatment and 3) choosing and changing a health care treatment facility. Respondents had an inadequate knowledge about TB and its treatment. Feeling healthy and having financial problems were the most common reasons for TB treatment non-adherence. Respondents sought treatment from many different health care providers, and often changed the treatment facility location. TB treatment adherence might improve by providing better education about the disease and its treatment to those undergoing treatment. Providing information about where to receive treatment and that treatment is free could also improve compliance.

Seismic imaging of a mid-lithospheric discontinuity beneath Ontong Java Plateau

NASA Astrophysics Data System (ADS)

Tharimena, Saikiran; Rychert, Catherine A.; Harmon, Nicholas

2016-09-01

Ontong Java Plateau (OJP) is a huge, completely submerged volcanic edifice that is hypothesized to have formed during large plume melting events ∼90 and 120 My ago. It is currently resisting subduction into the North Solomon trench. The size and buoyancy of the plateau along with its history of plume melting and current interaction with a subduction zone are all similar to the characteristics and hypothesized mechanisms of continent formation. However, the plateau is remote, and enigmatic, and its proto-continent potential is debated. We use SS precursors to image seismic discontinuity structure beneath Ontong Java Plateau. We image a velocity increase with depth at 28 ± 4 km consistent with the Moho. In addition, we image velocity decreases at 80 ± 5 km and 282 ± 7 km depth. Discontinuities at 60-100 km depth are frequently observed both beneath the oceans and the continents. However, the discontinuity at 282 km is anomalous in comparison to surrounding oceanic regions; in the context of previous results it may suggest a thick viscous root beneath OJP. If such a root exists, then the discontinuity at 80 km bears some similarity to the mid-lithospheric discontinuities (MLDs) observed beneath continents. One possibility is that plume melting events, similar to that which formed OJP, may cause discontinuities in the MLD depth range. Plume-plate interaction could be a mechanism for MLD formation in some continents in the Archean prior to the onset of subduction.

Launch Support Video Site

NASA Technical Reports Server (NTRS)

OFarrell, Zachary L.

2013-01-01

The goal of this project is to create a website that displays video, countdown clock, and event times to customers during launches, without needing to be connected to the internal operations network. The requirements of this project are to also minimize the delay in the clock and events to be less than two seconds. The two parts of this are the webpage, which will display the data and videos to the user, and a server to send clock and event data to the webpage. The webpage is written in HTML with CSS and JavaScript. The JavaScript is responsible for connecting to the server, receiving new clock data, and updating the webpage. JavaScript is used for this because it can send custom HTTP requests from the webpage, and provides the ability to update parts of the webpage without having to refresh the entire page. The server application will act as a relay between the operations network, and the open internet. On the operations network side, the application receives multicast packets that contain countdown clock and events data. It will then parse the data into current countdown times and events, and create a packet with that information that can be sent to webpages. The other part will accept HTTP requests from the webpage, and respond to them with current data. The server is written in C# with some C++ files used to define the structure of data packets. The videos for the webpage will be shown in an embedded player from UStream.

Scalable and Accurate SMT-Based Model Checking of Data Flow Systems

DTIC Science & Technology

2013-10-31

accessed from C, C++, Java, and OCaml , and provisions have been made to support other languages . CVC4 can be compiled and run on various flavors of...be accessed from C, C++, Java, and OCaml , and provisions have been made to support other languages . CVC4 can be compiled and run on various flavors of...C, C++, Java, and OCaml , and provisions have been made to support other languages . CVC4 can be compiled and run on various flavors of Linux, Mac OS

Integration of the MIP Command and Control Information Exchange Data Model into National Systems

DTIC Science & Technology

2005-06-01

Solutions for the Java programming language include Hibernate ( Hibernate , 2005), Java Data Objects (JDO, 2005), J2EE Container Managed Persistence (CMP) and... Java , C++, or UML classes in a first step. The semantical gap between the relational and the object-oriented world, also called O-R impedance, is a...cannot be achieved at the interfaces – it needs to be established in the core of national systems! References Hibernate (2005). www.hibernate.org. JDO

CrossTalk: The Journal of Defense Software Engineering. Volume 20, Number 9, September 2007

DTIC Science & Technology

2007-09-01

underlying application framework, e.g., Java Enter- prise Edition or .NET. This increases the risk that consumer Web services not based on the same...weaknesses and vulnera- bilities that are targeted by attackers and malicious code. For example, Apache Axis 2 enables a Java devel- oper to simply...load his/her Java objects into the Axis SOAP engine. At runtime, it is the SOAP engine that determines which incoming SOAP request messages should be

Strategy Planning Visualization Tool (SPVT) for the Air Operations Center (AOC). Volume 2: Information Operations (IO) Planning Enhancements

DTIC Science & Technology

2009-12-31

Status and Assessment data interfaces leverage the TBONE Services and data model. The services and supporting Java 2 Platform Enterprise Edition (J2EE...existing Java ™ and .Net developed “Fat Clients.” The IOPC-X design includes an Open Services Gateway Initiative (OSGi) compliant plug-in...J2EE Java 2 Platform Enterprise Edition JAOP Joint Air Operations Plan JAST JAOP AOD Status Tool JFACC Joint Forces Air Component Commander Data

JANIS-2: An Improved Version of the NEA Java-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, N.; Henriksson, H.; Nouri, A.; Nagel, P.; Dupont, E.

2005-05-01

JANIS (JAva-based Nuclear Information Software) is a display program designed to facilitate the visualisation and manipulation of nuclear data. Its objective is to allow the user of nuclear data to access numerical and graphical representations without prior knowledge of the storage format. It offers maximum flexibility for the comparison of different nuclear data sets. Features included in the latest release are described such as direct access to centralised databases through JAVA Servlet technology.

Graph Unification and Tangram Hypothesis Explanation Representation (GATHER) and System and Component Modeling Framework (SCMF)

DTIC Science & Technology

2008-08-01

services, DIDS and DMS, are deployable on the TanGrid system and are accessible via two APIs, a Java client and a servlet based interface. Additionally...but required the user to instantiate an IGraph object with several Java Maps containing the nodes, node attributes, edge types, and the connections...restrictions imposed by the bulk ingest process. Finally, once the bulk ingest process was available in the GraphUnification Java Archives (JAR), DC was

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

JANIS-2: An Improved Version of the NEA Java-based Nuclear Data Information System

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

Soppera, N.; Henriksson, H.; Nagel, P.

2005-05-24

JANIS (JAva-based Nuclear Information Software) is a display program designed to facilitate the visualisation and manipulation of nuclear data. Its objective is to allow the user of nuclear data to access numerical and graphical representations without prior knowledge of the storage format. It offers maximum flexibility for the comparison of different nuclear data sets. Features included in the latest release are described such as direct access to centralised databases through JAVA Servlet technology.

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.

2-Player Game With Uncertainty to Protect Mission Critical Information Over Blue Networks

DTIC Science & Technology

2009-04-01

Eclipse 233MHz 512MB 700MB JAVA 6 166MHz 64MB 98MB Key Focus Sensor Honeypot 1.5 GHz 512MB 500MB Distributed Data Pastry JAVA...defense, Pastry , run. JAVA 6 is an added plug-in that helps Eclipse software. There are many defenses that can be used to help alongside this project but...each defense to be used. Encryption : Steganos Privacy Suite 2008 Honeypots : Key Focus Sensor Distributed Data: Pastry 7    Table 2 Domain

Symbolic PathFinder: Symbolic Execution of Java Bytecode

NASA Technical Reports Server (NTRS)

Pasareanu, Corina S.; Rungta, Neha

2010-01-01

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

Verification Tools Secure Online Shopping, Banking

NASA Technical Reports Server (NTRS)

2010-01-01

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

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

ORA User’s Guide 2013

DTIC Science & Technology

2013-06-03

and a C++ computational backend . The most current version of ORA (3.0.8.5) software is available on the casos website: http://casos.cs.cmu.edu...optimizing a network’s design structure. ORA uses a Java interface for ease of use, and a C++ computational backend . The most current version of ORA...Eigenvector Centrality : Node most connected to other highly connected nodes. Assists in identifying those who can mobilize others Entity Class

Observation sand Results Gained from the Jade Project

DTIC Science & Technology

2002-05-04

project different dependency-based Center, 5095 Mawson Lakes (Adelaide) SA, Australia, email: models have been created that vary in their levels of...test eris Columna# T indenotesth n erfofmtests the Java programming language. Currently, exception han- of the respective test series. dling and...meets sentation in the debugging of software to reduce the problem error diagnosis in logic programs. In Proceedings 1 3 t h of structural faults in

Strategic Planning Implementation in Indonesia’s Transmigration Plan.

DTIC Science & Technology

1984-06-01

archipelago has a highly complex geolog - ical history . This effected the nation’s volcanic soil conditicns, numerous mountain systems, and a variety of...distinctive area caused by its geological structure. The islands of Java, Sumatra, and Kalimantan , together with the small islands in between, stand on the...continents, that of Asia and Australia. This formation has made the straits between the islands strategically important throughout history . because of

jSynthesizer: A Java based first-motion synthetic seismogram tool

NASA Astrophysics Data System (ADS)

Sullivan, Mark

2009-10-01

Both researchers and educators need software tools to create synthetic seismograms to model earthquake sources. We have developed a program that generates first-motion synthetic seismograms that is highly interactive and suited to the needs of both research and education audiences. Implemented in the Java programming language, our program is available for use on Windows, Mac OS X and Linux operating systems. Our program allows the user to input the fault parameters strike, dip and slip angle, numerically or graphically using a lower hemisphere equal-area stereographic projection of the focal sphere of the earthquake. This representation is familiar to geologists and seismologists as the standard way of displaying the orientation of a fault in space. The user is also able to enter the relative location of the seismograph and the depth and crustal velocity structure in the vicinity of the earthquake. The direct P wave along with reflections off of layer boundaries near the source are generated using a constant ray-parameter approximation. The instrument response functions used by the Worldwide Standardized Seismogram Network and the attenuation response of the Earth's mantle are generated in the frequency domain and applied to generate the synthetic seismogram. Planned enhancements to this program will allow the simultaneous generation of seismograms at many stations as well as more complicated crustal structures.

Medicare: Physician Compare

MedlinePlus

... application currently does not support browsers with "JavaScript" disabled. Please enable JavaScript and refresh the page to ... not support or have Cascading Style Sheets (CSS) disabled. For a more optimal experience viewing this application, ...

Medicare: Helpful Contacts

MedlinePlus

... not support or have Cascading Style Sheets (CSS) disabled. For a more optimal experience viewing this application, ... application currently does not support browsers with "JavaScript" disabled. Please enable JavaScript and refresh the page to ...

Java for flight software

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Find a Dialysis Facility

MedlinePlus

... not support or have Cascading Style Sheets (CSS) disabled. For a more optimal experience viewing this application, ... application currently does not support browsers with "JavaScript" disabled. Please enable JavaScript and refresh the page 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.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

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.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

PubMed

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

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.

Nematodes of amphibians from Java, Indonesia, with a description of
new species, Meteterakis wonosoboensis n. sp. (Nematoda : Heterakoidea).

PubMed

Purwaningsih, Endang; Dewi, Kartika; Hasegawa, Hideo

2015-06-24

During a survey on the parasites of amphibians of Indonesia, toads (30 Bufo melanostictus) and 246 frogs (213 Fejervarya cancrivora, 11 F. limnocharis, 22 Rana macrodon from West Java and 68 F. cancrivora from Central Java) were examined for parasitic nematodes. Three species of nematodes were found and described, i.e. Meteterakis wonosoboensis n. sp. from Fejervaria cancrivora; Meteterakis japonica from Bufo melanostictus, F. cancrivora and F. limnocharis; and Chabaudus sp. from F. cancrivora, F. limnocharis and Rana macrodon. Meteterakis wonosoboensis n. sp. is distinguished from other species of the genus by the length and shape of spicules, the number of caudal papillae, the presence of gubernaculum in male and the presence of vulval flap in female. Bufo melanostictus and Java are recorded as new host and locality for M. japonica, respectively.

Variations in Fe and S redox states in ocean island basalts

NASA Astrophysics Data System (ADS)

Brounce, M. N.; Peterson, M. E.; Stolper, E. M.; Eiler, J. M.

2016-12-01

The chemical and isotopic compositions of ocean island basalts (OIB) suggest that their mantle sources contain imprints of subducted sediments, altered oceanic crust, undegassed mantle, and/or residues of continental crust formation. By comparing the oxygen fugacities (fO2) of OIBs to the extent to which they contain these imprints, it may be possible to relate specific compositions to spatial and temporal variations in source fO2. To explore this, we present µ-XANES measurements of the oxidation states of Fe and S from pillow glass and olivine-hosted melt inclusions from the Reykjanes Ridge, Mauna Kea, Kilauea, Loihi, Hawaiian South Arch, Reunion Island, and the Ontong Java Plateau; we then compare these measurements with previous determinations of the chemical and isotopic compositions of these OIBs. Reykjanes Ridge and Ontong Java glasses have Fe and S redox states that are similar to MORBs; although these glasses show evidence for assimilation of seawater or crustal components, there is no relationship between indices of assimilation (18O/16O, Cl) and Fe or S redox states. This indicates that assimilation in these settings does not have a major effect on magmatic fO2. Mauna Kea and Kilauea glasses affected by S+H2O degassing have decreased Fe and S redox states, but the least degassed samples from both volcanoes are similar to each other and more oxidized than MORB, Reykjanes Ridge, and Ontong Java glasses. Loihi and South Arch glasses have not lost significant S and H2O to degassing, and they record fO2s similar to the least degassed Mauna Kea and Kilauea glasses. Olivine-hosted melt inclusions from Reunion range in Fe redox from similar to MORBs to more oxidized than Hawaiian volcanoes. These data demonstrate that OIBs are heterogeneous in Fe and S redox states. Although more data are needed for the various OIB end members, with the exception of the two most reduced glasses from Reunion, the data thus far suggest a rough positive correlation between 87Sr/86Sr ratios and Fe and S redox states. If this correlation holds up, it would be consistent with EMI and/or EMII end members having fO2s more oxidized than the upper mantle sources of MORBs, perhaps because these end members contain subducted sediments and/or oceanic crust that were previously oxidized during exposure to the H2O- and O2-rich conditions at Earth's surface.

Soil gas anomalies along the Watukosek fault system, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Sciarra, A.; Ruggiero, L.; Bigi, S.; Mazzini, A.

2017-12-01

Two soil gas surveys were carried out in the Sidoarjo district (East Java, Indonesia) to investigate the gas leaking properties along fractured zones that coincide with a strike-slip system in NE Java, the Watukosek Fault System. This structure has been the focus of attention since the beginning of the spectacular Lusi mud eruption on the 29th May 2006. This fault system appear to be a sinistral strike-slip system that originates from the Arjuno-Welirang volcanic complex, intersects the active Lusi eruption site displaying a system of antithetic faults, and extends towards the NE of Java where mud volcanic structures reside. In the Lusi region we completed two geochemical surveys (222Rn and 220Rn activity, CO2 and CH4 flux and concentration) along four profiles crossing the Watukosek fault system. In May 2015 two profiles ( 1.2 km long) were performed inside the 7 km2 embankment area framing the erupted mud breccia zone and across regions characterized by intense fracturing and surface deformation. In April 2017 two additional profiles ( 4 km long) were carried out in the northern and southern part outside the Lusi embankment mud eruption area, intersecting the direction of main Watukosek fault system. All the profiles highlight that the fractured zones have the highest 222Rn activity, CO2 and CH4 flux and concentration values. The relationship existing among the measured parameters suggest that the Watukosek fault system acts as a preferential pathway for active rise of deep fluids. In addition the longer profiles outside the embankment show very high average values of CO2 (5 - 8 %,v/v) and 222Rn (17 - 11.5 kBq/m3), while soil gas collected along the profiles inside the Lusi mud eruption are CH4-dominant (up to 4.5%,v/v).This suggests that inside the embankment area (i.e. covered by tens of meters thick deposits of erupted mud breccia) the seepage is overall methane-dominated. This is likely the result of microbial reactions ongoing in the organic-rich sediments producing shallow gas that gets mixed with deeper rising fluids. In contrasts profiles collected in areas not covered by the organic rich mud breccia, and that are crossing the main Watukosek fault system, have the highest 222Rn activity and CO2 concentration values. We suggest that at these localities the rise of deep fluids is not affected by shallower gas production.

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

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

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.

Web based tools for data manipulation, visualisation and validation with interactive georeferenced graphs

NASA Astrophysics Data System (ADS)

Ivankovic, D.; Dadic, V.

2009-04-01

Some of oceanographic parameters have to be manually inserted into database; some (for example data from CTD probe) are inserted from various files. All this parameters requires visualization, validation and manipulation from research vessel or scientific institution, and also public presentation. For these purposes is developed web based system, containing dynamic sql procedures and java applets. Technology background is Oracle 10g relational database, and Oracle application server. Web interfaces are developed using PL/SQL stored database procedures (mod PL/SQL). Additional parts for data visualization include use of Java applets and JavaScript. Mapping tool is Google maps API (javascript) and as alternative java applet. Graph is realized as dynamically generated web page containing java applet. Mapping tool and graph are georeferenced. That means that click on some part of graph, automatically initiate zoom or marker onto location where parameter was measured. This feature is very useful for data validation. Code for data manipulation and visualization are partially realized with dynamic SQL and that allow as to separate data definition and code for data manipulation. Adding new parameter in system requires only data definition and description without programming interface for this kind of data.

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.

Infrastructure for Rapid Development of Java GUI Programs

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

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.

Hierarchical time series bottom-up approach for forecast the export value in Central Java

NASA Astrophysics Data System (ADS)

Mahkya, D. A.; Ulama, B. S.; Suhartono

2017-10-01

The purpose of this study is Getting the best modeling and predicting the export value of Central Java using a Hierarchical Time Series. The export value is one variable injection in the economy of a country, meaning that if the export value of the country increases, the country’s economy will increase even more. Therefore, it is necessary appropriate modeling to predict the export value especially in Central Java. Export Value in Central Java are grouped into 21 commodities with each commodity has a different pattern. One approach that can be used time series is a hierarchical approach. Hierarchical Time Series is used Buttom-up. To Forecast the individual series at all levels using Autoregressive Integrated Moving Average (ARIMA), Radial Basis Function Neural Network (RBFNN), and Hybrid ARIMA-RBFNN. For the selection of the best models used Symmetric Mean Absolute Percentage Error (sMAPE). Results of the analysis showed that for the Export Value of Central Java, Bottom-up approach with Hybrid ARIMA-RBFNN modeling can be used for long-term predictions. As for the short and medium-term predictions, it can be used a bottom-up approach RBFNN modeling. Overall bottom-up approach with RBFNN modeling give the best result.

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.

Programming with non-heap memory in the real time specification for Java

NASA Technical Reports Server (NTRS)

Bollella, G.; Canham, T.; Carson, V.; Champlin, V.; Dvorak, D.; Giovannoni, B.; Indictor, M.; Meyer, K.; Reinholtz, A.; Murray, K.

2003-01-01

The Real-Time Specification for Java (RTSJ) provides facilities for deterministic, real-time execution in a language that is otherwise subject to variable latencies in memory allocation and garbage collection.

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.

JAVA PathFinder

NASA Technical Reports Server (NTRS)

Mehhtz, Peter

2005-01-01

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

First record of Puerulus mesodontus Chan, Ma & Chu, 2013 (Crustacea, Decapoda, Achelata, Palinuridae) from south of Java, Indonesia.

PubMed

Wardiatno, Yusli; Hakim, Agus Alim; Mashar, Ali; Butet, Nurlisa Alias; Adrianto, Luky; Farajallah, Achmad

2016-01-01

Three specimens of Puerulus mesodontus Chan, Ma & Chu, 2013 (Crustacea, Decapoda, Achelata, Palinuridae) were collected from Palabuhanratu Bay, southern Java, Indonesia. There is no previous record on the presence of the species in Indonesia. This finding represents the first record of this species in Java, Indonesia, and confirms that the species is present in the Indian Ocean. The morphological characters of the species are described. This paper contains a new distribution record of a lobster species from Indonesian waters.

Task Report for Task Authorization 1 for: Technology Demonstration of the Joint Network Defence and Management System (JNDMS) Project

DTIC Science & Technology

2009-01-30

tool written in Java to support the automated creation of simulated subnets. It can be run giving it a subnet, the number of hosts to create, the...network and can also be used to create subnets with specific profiles. Subnet Creator command line: > java –jar SubnetCreator.jar –j [path to client...command: > java –jar jss_client.jar com.mdacorporation.jndms.JSS.Client.JSSBatchClient [file] 5. Software: This is the output file that will store the

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

NASA Technical Reports Server (NTRS)

Staats, Matt

2009-01-01

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

Accommodating a growing population in Javanese agriculture.

PubMed

Booth, A

1985-08-01

An examination of how the island of Java, Indonesia, has accommodated population growth over the past 150 years by a process of agricultural development is presented. A brief review of the literature on the relationship between agricultural development and population growth is first provided. Next, the available data on land area, cultivated area, agricultural production, and employment in Java over the past century are reviewed. The relationship between agricultural development and population growth in Java is then analyzed in terms of the concepts and processes discussed in the theoretical literature.

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

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.

Deep Crustal Structure beneath Large Igneous Provinces and the Petrologic Evolution of Flood Basalts

NASA Astrophysics Data System (ADS)

Richards, Mark; Ridley, Victoria

2010-05-01

We present a review of seismological constraints on deep crustal structures underlying large igneous provinces (LIPs), largely from wide-angle seismic refraction surveys. The main purpose of this review is to ascertain whether this seismic evidence is consistent with, or contrary to, petrological models for the genesis of flood basalt lavas. Where high-quality data are available beneath continental flood basalt (CFB) provinces (Emeishan, Columbia River, Deccan, Siberia), high-velocity structures (Vp ~6.9-7.5 km/sec) are typically found immediately overlying the Moho in layers of order ~5-15 km thick. Oceanic plateau (OP) LIPs exhibit similar layers, with a conspicuous layer of very high crustal velocity (Vp~7.7 km/sec) beneath the enormous Ontong-Java plateau. These structures are similar to inferred ultramafic underplating structures seen beneath active hotspots such as Hawaii, the Marqueses, and La Reunion. Petrogenetic models for flood basalt volcanism based on hot plume melting beneath mature lithosphere suggest that these deep seismic structures may consist in large part of cumulate bodies of olivine and clinopyroxene which result from ponding and deep-crustal fractionation of ultramafic primary melts. Such fractionation is necessary to produce basalts with typical MgO contents of ~6-8%, as observed for the vast bulk of observed flood basalts, from primary melts with MgO contents of order ~15-18% (or greater) such as result from hot, deep melting beneath the lithosphere. The volumes of cumulate bodies and ultramafic intrusions in the lowermost crust, often described in the literature as "underplating," are comparable to those of the overlying basaltic formations, also consistent with petrological models. Further definition of the deep seismic structure beneath such prominent LIPs as the Ontong-Java Plateau could place better constraints on flood basalt petrogenesis by determining the relative volumes of ultramafic bodies and basaltic lavas, thereby better constraining the overall process of LIP emplacement.

Deep crustal structure beneath large igneous provinces and the petrologic evolution of flood basalts

NASA Astrophysics Data System (ADS)

Ridley, Victoria A.; Richards, Mark A.

2010-09-01

We present a review of seismological constraints on deep crustal structures underlying large igneous provinces (LIPs), largely from wide-angle seismic refraction surveys. The main purpose of this review is to ascertain whether this seismic evidence is consistent with, or contrary to, petrological models for the genesis of flood basalt lavas. Where high-quality data are available beneath continental flood basalt (CFB) provinces (Emeishan, Columbia River, Deccan, Siberia), high-velocity structures (Vp ˜ 6.9-7.5 km/sec) are typically found immediately overlying the Moho in layers of order ˜5-15 km thick. Oceanic plateau (OP) LIPs exhibit similar layers, with a conspicuous layer of very high crustal velocity (Vp ˜ 7.7 km/sec) beneath the enormous Ontong-Java plateau. These structures are similar to inferred ultramafic underplating structures seen beneath active hot spots such as Hawaii, the Marquesas, and La Reunion. Petrogenetic models for flood basalt volcanism based on hot plume melting beneath mature lithosphere suggest that these deep seismic structures may consist in large part of cumulate bodies of olivine and clinopyroxene which result from ponding and deep-crustal fractionation of ultramafic primary melts. Such fractionation is necessary to produce basalts with typical MgO contents of ˜6-8%, as observed for the vast bulk of observed flood basalts, from primary melts with MgO contents of order ˜15-18% (or greater) such as result from hot, deep melting beneath the lithosphere. The volumes of cumulate bodies and ultramafic intrusions in the lowermost crust, often described in the literature as "underplating," are comparable to those of the overlying basaltic formations, also consistent with petrological models. Further definition of the deep seismic structure beneath such prominent LIPs as the Ontong-Java Plateau could place better constraints on flood basalt petrogenesis by determining the relative volumes of ultramafic bodies and basaltic lavas, thereby better constraining the overall process of LIP emplacement.

Deep Crustal Structure beneath Large Igneous Provinces and the Petrologic Evolution of Flood Basalts

NASA Astrophysics Data System (ADS)

Richards, M. A.; Ridley, V. A.

2010-12-01

We present a review of seismological constraints on deep crustal structures underlying large igneous provinces (LIPs), largely from wide-angle seismic refraction surveys. The main purpose of this review is to ascertain whether this seismic evidence is consistent with, or contrary to, petrological models for the genesis of flood basalt lavas. Where high-quality data are available beneath continental flood basalt (CFB) provinces (Emeishan, Columbia River, Deccan, Siberia), high-velocity structures (Vp ~6.9-7.5 km/sec) are typically found immediately overlying the Moho in layers of order ~5-15 km thick. Oceanic plateau (OP) LIPs exhibit similar layers, with a conspicuous layer of very high crustal velocity (Vp~7.7 km/sec) beneath the enormous Ontong-Java plateau. These structures are similar to inferred ultramafic underplating structures seen beneath active hotspots such as Hawaii, the Marquesas, and La Reunion. Petrogenetic models for flood basalt volcanism based on hot plume melting beneath mature lithosphere suggest that these deep seismic structures may consist in large part of cumulate bodies of olivine and clinopyroxene which result from ponding and deep-crustal fractionation of ultramafic primary melts. Such fractionation is necessary to produce basalts with typical MgO contents of ~6-8%, as observed for the vast bulk of observed flood basalts, from primary melts with MgO contents of order ~15-18% (or greater) such as result from hot, deep melting beneath the lithosphere. The volumes of cumulate bodies and ultramafic intrusions in the lowermost crust, often described in the literature as “underplating,” are comparable to those of the overlying basaltic formations, also consistent with petrological models. Further definition of the deep seismic structure beneath such prominent LIPs as the Ontong-Java Plateau could place better constraints on flood basalt petrogenesis by determining the relative volumes of ultramafic bodies and basaltic lavas, thereby better constraining the overall process of LIP emplacement.

NGL Viewer: a web application for molecular visualization

PubMed Central

Rose, Alexander S.; Hildebrand, Peter W.

2015-01-01

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. ‘cartoon, spacefill, licorice’). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations. PMID:25925569

Dialysis Facility Compare: Information for Patients and Caregivers

MedlinePlus

... not support or have Cascading Style Sheets (CSS) disabled. For a more optimal experience viewing this application, ... application currently does not support browsers with "JavaScript" disabled. Please enable JavaScript and refresh the page to ...

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

USGS Publications Warehouse

Bishop, Michele G.

2000-01-01

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

A preliminary study of paleotsunami deposit along the south coast of East Java: Pacitan-Banyuwangi

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

Anugrah, Suci D.; Istiyanati; Zaim, Yahdi

Along the southern coast of East Java Indonesia, at a number of localities, it can be identified and attempted to assign the age of tsunami deposit. Laboratory analyses were conducted also to support this study such as Granulometry, Paleontology and radiometric dating analysis. The presence of tsunami 1994 deposit in the area of Pancer, Lampon, Prigi and Grajagan was found, as a result of 7.8 Magnitude Banyuwangi Earthquake. The radiometric dating analysis also identified some paleotsunami deposit of about 1921 and 1930 in the area of Prigi and Teleng. This paleotsunami is assumed to have a correlation with an earthquakemore » in the south of Java at the same time. An outcrop in the Prigi and Teleng strongly convinced the fact of an earthquake generated tsunami in the south of Java in the year of about 1921 and 1930.« less

Survey of Collaboration Technologies in Multi-level Security Environments

DTIC Science & Technology

2014-04-28

infrastructure or resources. In this research program, the security implications of the US Air Force GeoBase (the US The problem is that in many cases...design structure. ORA uses a Java interface for ease of use, and a C++ computational backend . The current version ORA1.2 software is available on the...information: culture, policy, governance, economics and resources, and technology and infrastructure . This plan, the DoD Information Sharing

Program Analysis Techniques for Efficient Software Model Checking

DTIC Science & Technology

2011-02-28

MIT Press, 1986. [29] D. Marinov, A . Andoni, D. Daniliuc, S . Khurshid, and M . Rinard. An evaluation of exhaustive testing for data structures...such as reading, writing, creating, or deleting a file or a directory) on a file system state s , it uses its analyses to identify other file system...ples of Programming Languages (POPL), January 2003. [6] C. Boyapati and M . Rinard. A parameterized type system for race-free Java programs. In

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

Oligocene to Recent tectonic history of the Central Solomon intra-arc basin as determined from marine seismic reflection data and compilation of onland geology

NASA Astrophysics Data System (ADS)

Cowley, Shane; Mann, Paul; Coffin, M. F.; Shipley, Thomas H.

2004-10-01

Systematic analysis of a grid of 3450 km of multichannel seismic reflection lines from the Solomon Islands constrains the late Tertiary sedimentary and tectonic history of the Solomon Island arc and its convergent interaction with the Cretaceous Ontong Java oceanic plateau (OJP). The OJP, the largest oceanic plateau on Earth, subducted beneath the northern edge of the Solomon arc in the late Neogene, but the timing and consequences of this obliquely convergent event and its role in the subduction polarity reversal process remain poorly constrained. The Central Solomon intra-arc basin (CSB), which developed in Oligocene to Recent time above the Solomon arc, provides a valuable record of the tectonic environment prior to and accompanying the OJP convergent event and the subsequent arc polarity reversal. Recognition of regionally extensive stratigraphic sequences—whose ages can be inferred from marine sedimentary sections exposed onland in the Solomon Islands—indicate four distinct tectonic phases affecting the Solomon Island arc. Phase 1: Late Oligocene-Late Miocene rifting of the northeast-facing Solomon Island arc produced basal, normal-fault-controlled, asymmetrical sequences of the CSB; the proto-North Solomon trench was probably much closer to the CSB and is inferred to coincide with the trace of the present-day Kia-Kaipito-Korigole (KKK) fault zone; this protracted period of intra-arc extension shows no evidence for interruption by an early Miocene period of convergent "soft docking" of the Ontong Java Plateau as proposed by previous workers. Phase 2: Late Miocene-Pliocene oblique convergence of the Ontong Java Plateau at the proto-North Solomon trench (KKK fault zone) and folding of the CSB and formation of the Malaita accretionary prism (MAP); the highly oblique and diachronous convergence between the Ontong Java plateau and the Solomon arc terminates intra-arc extension first in the southeast (Russell subbasin of the CSB) during the Late Miocene and later during the Pliocene in the northwest (Shortland subbasin of the CSB); folds in the CSB form by inversion of normal faults formed during Phase 1; Phinney et al. [Sequence stratigraphy, structural style, and age of deformation of the Malaita accretionary prism (Solomon arc-Ontong Java Plateau convergent zone)] show a coeval pattern of southeast to northwest younging in folding and faulting of the MAP. Phase 3: Late Pliocene-early Pleistocene arc polarity reversal and subduction initiation at the San Cristobal trench. Effects of this event in the CSB include the formation of a chain of volcanoes above the subducting Australia plate at the San Cristobal trench, the formation of the broad synclinal structure of the CSB with evidence for truncation at the uplifted flanks, and widespread occurrence of slides and "seismites" (deposits formed by seismic shaking). Phase 4: Pleistocene to Recent continued shortening and synclinal subsidence of the CSB. Continued Australia-Pacific oblique plate convergence has led to deepening of the submarine, elongate basin axis of the synclinal CSB and uplift of the dual chain of the islands on its flanks.

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.

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.

DemQSAR: predicting human volume of distribution and clearance of drugs

NASA Astrophysics Data System (ADS)

Demir-Kavuk, Ozgur; Bentzien, Jörg; Muegge, Ingo; Knapp, Ernst-Walter

2011-12-01

In silico methods characterizing molecular compounds with respect to pharmacologically relevant properties can accelerate the identification of new drugs and reduce their development costs. Quantitative structure-activity/-property relationship (QSAR/QSPR) correlate structure and physico-chemical properties of molecular compounds with a specific functional activity/property under study. Typically a large number of molecular features are generated for the compounds. In many cases the number of generated features exceeds the number of molecular compounds with known property values that are available for learning. Machine learning methods tend to overfit the training data in such situations, i.e. the method adjusts to very specific features of the training data, which are not characteristic for the considered property. This problem can be alleviated by diminishing the influence of unimportant, redundant or even misleading features. A better strategy is to eliminate such features completely. Ideally, a molecular property can be described by a small number of features that are chemically interpretable. The purpose of the present contribution is to provide a predictive modeling approach, which combines feature generation, feature selection, model building and control of overtraining into a single application called DemQSAR. DemQSAR is used to predict human volume of distribution (VDss) and human clearance (CL). To control overtraining, quadratic and linear regularization terms were employed. A recursive feature selection approach is used to reduce the number of descriptors. The prediction performance is as good as the best predictions reported in the recent literature. The example presented here demonstrates that DemQSAR can generate a model that uses very few features while maintaining high predictive power. A standalone DemQSAR Java application for model building of any user defined property as well as a web interface for the prediction of human VDss and CL is available on the webpage of DemPRED: http://agknapp.chemie.fu-berlin.de/dempred/.

DemQSAR: predicting human volume of distribution and clearance of drugs.

PubMed

Demir-Kavuk, Ozgur; Bentzien, Jörg; Muegge, Ingo; Knapp, Ernst-Walter

2011-12-01

In silico methods characterizing molecular compounds with respect to pharmacologically relevant properties can accelerate the identification of new drugs and reduce their development costs. Quantitative structure-activity/-property relationship (QSAR/QSPR) correlate structure and physico-chemical properties of molecular compounds with a specific functional activity/property under study. Typically a large number of molecular features are generated for the compounds. In many cases the number of generated features exceeds the number of molecular compounds with known property values that are available for learning. Machine learning methods tend to overfit the training data in such situations, i.e. the method adjusts to very specific features of the training data, which are not characteristic for the considered property. This problem can be alleviated by diminishing the influence of unimportant, redundant or even misleading features. A better strategy is to eliminate such features completely. Ideally, a molecular property can be described by a small number of features that are chemically interpretable. The purpose of the present contribution is to provide a predictive modeling approach, which combines feature generation, feature selection, model building and control of overtraining into a single application called DemQSAR. DemQSAR is used to predict human volume of distribution (VD(ss)) and human clearance (CL). To control overtraining, quadratic and linear regularization terms were employed. A recursive feature selection approach is used to reduce the number of descriptors. The prediction performance is as good as the best predictions reported in the recent literature. The example presented here demonstrates that DemQSAR can generate a model that uses very few features while maintaining high predictive power. A standalone DemQSAR Java application for model building of any user defined property as well as a web interface for the prediction of human VD(ss) and CL is available on the webpage of DemPRED: http://agknapp.chemie.fu-berlin.de/dempred/ .

Java for flight software

NASA Technical Reports Server (NTRS)

Benowitz, E.; Niessner, A.

2003-01-01

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

HEP data analysis using jHepWork and Java.

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

Chekanov, S.; High Energy Physics

2009-03-23

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

DNS Rebinding Attacks

DTIC Science & Technology

2009-09-01

active scripting, file downloads, installation of desktop items, signed and unsigned ActiveX controls, Java permissions, launching applications and...files in an IFRAME, running ActiveX controls and plug-ins, and scripting of Java applets [49]. This security measure is very effective against DNS

OAS :: Office of the Inspector General

Science.gov Websites

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75 FR 26846 - Unblocking of Three Specially Designated Nationals Pursuant to Executive Order 13224

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-12

.... ``ABU SA'AD''; a.k.a. ``ABU SAAD''; a.k.a. ``FREEDOM FIGHTER''); DOB 17 Feb 1971; POB Madiun, East Java..., Lamongan district, East Java province, Indonesian; nationality Indonesia (individual) [SDGT]. SAMUDRA, Imam...

Chemical landscape analysis with the OpenTox framework.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2012-01-01

The Structure-Activity Relationships (SAR) landscape and activity cliffs concepts have their origins in medicinal chemistry and receptor-ligand interactions modelling. While intuitive, the definition of an activity cliff as a "pair of structurally similar compounds with large differences in potency" is commonly recognized as ambiguous. This paper proposes a new and efficient method for identifying activity cliffs and visualization of activity landscapes. The activity cliffs definition could be improved to reflect not the cliff steepness alone, but also the rate of the change of the steepness. The method requires explicitly setting similarity and activity difference thresholds, but provides means to explore multiple thresholds and to visualize in a single map how the thresholds affect the activity cliff identification. The identification of the activity cliffs is addressed by reformulating the problem as a statistical one, by introducing a probabilistic measure, namely, calculating the likelihood of a compound having large activity difference compared to other compounds, while being highly similar to them. The likelihood is effectively a quantification of a SAS Map with defined thresholds. Calculating the likelihood relies on four counts only, and does not require the pairwise matrix storage. This is a significant advantage, especially when processing large datasets. The method generates a list of individual compounds, ranked according to the likelihood of their involvement in the formation of activity cliffs, and goes beyond characterizing cliffs by structure pairs only. The visualisation is implemented by considering the activity plane fixed and analysing the irregularities of the similarity itself. It provides a convenient analogy to a topographic map and may help identifying the most appropriate similarity representation for each specific SAR space. The proposed method has been applied to several datasets, representing different biological activities. Finally, the method is implemented as part of an existing open source Ambit package and could be accessed via an OpenTox API compliant web service and via an interactive application, running within a modern, JavaScript enabled web browser. Combined with the functionalities already offered by the OpenTox framework, like data sharing and remote calculations, it could be a useful tool for exploring chemical landscapes online.

Utilizing Internet Technologies in Observatory Control Systems

NASA Astrophysics Data System (ADS)

Cording, Dean

2002-12-01

The 'Internet boom' of the past few years has spurred the development of a number of technologies to provide services such as secure communications, reliable messaging, information publishing and application distribution for commercial applications. Over the same period, a new generation of computer languages have also developed to provide object oriented design and development, improved reliability, and cross platform compatibility. Whilst the business models of the 'dot.com' era proved to be largely unviable, the technologies that they were based upon have survived and have matured to the point were they can now be utilized to build secure, robust and complete observatory control control systems. This paper will describe how Electro Optic Systems has utilized these technologies in the development of its third generation Robotic Observatory Control System (ROCS). ROCS provides an extremely flexible configuration capability within a control system structure to provide truly autonomous robotic observatory operation including observation scheduling. ROCS was built using Internet technologies such as Java, Java Messaging Service (JMS), Lightweight Directory Access Protocol (LDAP), Secure Sockets Layer (SSL), eXtendible Markup Language (XML), Hypertext Transport Protocol (HTTP) and Java WebStart. ROCS was designed to be capable of controlling all aspects of an observatory and be able to be reconfigured to handle changing equipment configurations or user requirements without the need for an expert computer programmer. ROCS consists of many small components, each designed to perform a specific task, with the configuration of the system specified using a simple meta language. The use of small components facilitates testing and makes it possible to prove that the system is correct.

Drought Vulnerability Mapping with Geomorphological Approach in Yogyakarta Special Region (DIY) and Central Java

NASA Astrophysics Data System (ADS)

Sudaryatno

2016-11-01

This study aims to determine the level of vulnerability of the geomorphologic drought that occurred in Central Java and Yogyakarta Special Region. This study examines geomorphologic drought. Parameters used were slope, drainage, Available Water Capacity (AWC), permeability, landform, and land use. Landsat 8 and SRTM data were used for the extraction of physical parameters, such as slope, drainage, landform, and land use. The method used in this study is scoring and weighting. Query results were used for data classification by overlaying drought geomorphologic parameters. The expected outcome of this research is to map the geomorphologic drought vulnerability on Central Java and Yogyakarta Special Region. Drought vulnerability was divided into wet, normal and dry classes. Distribution of the dry class is frequent. Some of the dry classes are distributed on the steep till extremely steep slope region and on the structural and karsts landform. This was related to AWC value where region with high AWC contributed to the poor drainage of the soil, such as at Kulonprogo, Purworejo, Kebumen, Blora, Wonogiri, Purbalingga, Pekalongan, Jepara and Kudus regency. Normal classes are distributed on the sloping till steep slope, have moderate till well-drained soil and low AWC, such as at Gunung Kidul, Pati, Temanggung regency, and Magelang city. Wet classes are distributed on the flat or almost flat and sloping region. Most of the wet classes are distributed on volcanic hills and coastal area. Those regions are well-drained and the land uses are mostly for settlement and farming, such as at Sleman, Yogyakarta city, Klaten, Bantul, and Wonosobo regency.

Tomographic imaging of Central Java, Indonesia: Preliminary result of joint inversion of the MERAMEX and MCGA earthquake data

NASA Astrophysics Data System (ADS)

Rohadi, Supriyanto; Widiyantoro, Sri; Nugraha, Andri Dian; Masturyono

2013-09-01

The realization of local earthquake tomography is usually conducted by removing distant events outside the study region, because these events may increase errors. In this study, tomographic inversion has been conducted using the travel time data of local and regional events in order to improve the structural resolution, especially for deep structures. We used the local MERapi Amphibious EXperiments (MERAMEX) data catalog that consists of 292 events from May to October 2004. The additional new data of regional events in the Java region were taken from the Meteorological, Climatological, and Geophysical Agency (MCGA) of Indonesia, which consist of 882 events, having at least 10 recording phases at each seismographic station from April 2009 to February 2011. We have conducted joint inversions of the combined data sets using double-difference tomography to invert for velocity structures and to conduct hypocenter relocation simultaneously. The checkerboard test results of Vp and Vs structures demonstrate a significantly improved spatial resolution from the shallow crust down to a depth of 165 km. Our tomographic inversions reveal a low velocity anomaly beneath the Lawu - Merapi zone, which is consistent with the results from previous studies. A strong velocity anomaly zone with low Vp, low Vs and low Vp/Vs is also identified between Cilacap and Banyumas. We interpret this anomaly as a fluid content material with large aspect ratio or sediment layer. This anomaly zone is in a good agreement with the existence of a large dome containing sediment in this area as proposed by previous geological studies. A low velocity anomaly zone is also detected in Kebumen, where it may be related to the extensional oceanic basin toward the land.

Tomographic imaging of Central Java, Indonesia: Preliminary result of joint inversion of the MERAMEX and MCGA earthquake data

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

Rohadi, Supriyanto; Widiyantoro, Sri; Nugraha, Andri Dian

The realization of local earthquake tomography is usually conducted by removing distant events outside the study region, because these events may increase errors. In this study, tomographic inversion has been conducted using the travel time data of local and regional events in order to improve the structural resolution, especially for deep structures. We used the local MERapi Amphibious EXperiments (MERAMEX) data catalog that consists of 292 events from May to October 2004. The additional new data of regional events in the Java region were taken from the Meteorological, Climatological, and Geophysical Agency (MCGA) of Indonesia, which consist of 882 events,more » having at least 10 recording phases at each seismographic station from April 2009 to February 2011. We have conducted joint inversions of the combined data sets using double-difference tomography to invert for velocity structures and to conduct hypocenter relocation simultaneously. The checkerboard test results of Vp and Vs structures demonstrate a significantly improved spatial resolution from the shallow crust down to a depth of 165 km. Our tomographic inversions reveal a low velocity anomaly beneath the Lawu - Merapi zone, which is consistent with the results from previous studies. A strong velocity anomaly zone with low Vp, low Vs and low Vp/Vs is also identified between Cilacap and Banyumas. We interpret this anomaly as a fluid content material with large aspect ratio or sediment layer. This anomaly zone is in a good agreement with the existence of a large dome containing sediment in this area as proposed by previous geological studies. A low velocity anomaly zone is also detected in Kebumen, where it may be related to the extensional oceanic basin toward the land.« less