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…

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

PubMed

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

2012-01-01

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

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.

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…

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.…

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 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

Teaching Introductory Programming to IS Students: Java Problems and Pitfalls

ERIC Educational Resources Information Center

Pendergast, Mark O.

2006-01-01

This paper examines the impact the use of the Java programming language has had on the way our students learn to program and the success they achieve. The importance of a properly constructed first course in programming cannot be overstated. A course well experienced will leave students with good programming habits, the ability to learn on their…

Shuttle Data Center File-Processing Tool in Java

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Miller, Walter H.

2006-01-01

A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

A comparison of common programming languages used in bioinformatics.

PubMed

Fourment, Mathieu; Gillings, Michael R

2008-02-05

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

A comparison of common programming languages used in bioinformatics

PubMed Central

Fourment, Mathieu; Gillings, Michael R

2008-01-01

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

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)

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.

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.

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

PubMed

Bakhtiari, M

2012-06-01

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

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

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.

What about a Simple Language? Analyzing the Difficulties in Learning to Program

ERIC Educational Resources Information Center

Mannila, Linda; Peltomaki, Mia; Salakoski, Tapio

2006-01-01

In this paper, we present the results from a two-part study. We analyze 60 programs written by novice programmers aged 16-19 after their first programming course, in either Java or Python. The aim is to find difficulties independent of the language used, and such originating from the language. Second, we analyze the transition from a…

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

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.

Aspect-Oriented Subprogram Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

The Rational Sequence computer program described elsewhere includes a subprogram that utilizes the capability for aspect-oriented programming when that capability is present. This subprogram is denoted the Rational Sequence (AspectJ) component because it uses AspectJ, which is an extension of the Java programming language that introduces aspect-oriented programming techniques into the language

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.

A Counterexample Guided Abstraction Refinement Framework for Verifying Concurrent C Programs

DTIC Science & Technology

2005-05-24

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

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

JaxoDraw: A graphical user interface for drawing Feynman diagrams

NASA Astrophysics Data System (ADS)

Binosi, D.; Theußl, L.

2004-08-01

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

Update on PISCES

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

Innovative Active Networking Services

DTIC Science & Technology

2004-03-01

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

DAVE-ML Utility Programs

NASA Technical Reports Server (NTRS)

Jackson, Bruce

2006-01-01

DAVEtools is a set of Java archives that embodies tools for manipulating flight-dynamics models that have been encoded in dynamic aerospace vehicle exchange markup language (DAVE-ML). [DAVE-ML is an application program, written in Extensible Markup Language (XML), for encoding complete computational models of the dynamics of aircraft and spacecraft.

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.

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.

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

Hard Real-Time: C++ Versus RTSJ

NASA Technical Reports Server (NTRS)

Dvorak, Daniel L.; Reinholtz, William K.

2004-01-01

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

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

Exploring the Synergies between the Object Oriented Paradigm and Mathematics: A Java Led Approach

ERIC Educational Resources Information Center

Conrad, Marc; French, Tim

2004-01-01

While the object oriented paradigm and its instantiation within programming languages such as Java has become a ubiquitous part of both the commercial and educational landscapes, its usage as a visualization technique within mathematics undergraduate programmes of study has perhaps been somewhat underestimated. By regarding the object oriented…

Large-Scale Dynamic Observation Planning for Unmanned Surface Vessels

DTIC Science & Technology

2007-06-01

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

Toward Managing & Automating CyberCIEGE Scenario Definition File Creation

DTIC Science & Technology

2004-03-01

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

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

Cultural and social change of foreign students in Indonesia: The influence of Javanese Culture in Teaching Indonesian to Speakers of Other Languages (TISOL)

NASA Astrophysics Data System (ADS)

Saddhono, Kundharu

2018-03-01

Teaching Indonesian to Speakers of Other Languages (TISOL) program is increasingly in demand by people in various parts of the world. Foreign students learn a lot of Indonesian language in major cities in Indonesia. The purpose of this study is to explain the cultural and social changes of foreign students in Indonesia, especially in Java, which is following TISOL program. This study focused on the influence of Javanese culture on foreign students studying Indonesian in Java. Research method used is descriptive qualitative with ethnography approach. This research was conducted in TISOL program organized by in Central Java, East Java, and Yogyakarta. Sources of data used are documents and informants. The sampling technique used is purposive sampling. Purposive sampling is considered more capable to obtain complete data in the face of various realities. Data collection techniques are done by reviewing documents or records using content analysis techniques. Other techniques used are interview techniques with some students and lecturers to get data about the factors that affect the cultural and social changes of foreign students in Indonesia. Also, interviews were also conducted with teachers to request a different process in TISOL. The most common way used to improve validity in qualitative research is the triangulation technique. In this study used triangulation theory, triangulation method, and review of informants. The results show that using Javanese culture is very influential in the cultural and social changes of foreign students in Indonesia. Students become more enthusiastic and active in responding to learning in TISOL that is influenced by Javanese culture. The change comes from internal and external students. This change helps foreign students to understand Indonesian language and culture more comprehensively.

Development of a Night Vision Goggle Heads-Up Display for Paratrooper Guidance

DTIC Science & Technology

2008-06-01

and GPS data [MIC07]. requiring altitude, position, velocity, acceleration, and angular rates for navigation or control. An internal GPS receiver...Language There are several programming languages that provide the operating capabilities for this program. Languages like JAVA and C# provide an...acceleration, and angular rates. Figure 3.6 illustrates the MIDG hardware’s input and output data. The sensor actually generates the INS data, which is

An Interactive Decision Support System for Scheduling Fighter Pilot Training

DTIC Science & Technology

2002-03-26

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

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.

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

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.

So Wide a Web, So Little Time.

ERIC Educational Resources Information Center

McConville, David; And Others

1996-01-01

Discusses new trends in the World Wide Web. Highlights include multimedia; digitized audio-visual files; compression technology; telephony; virtual reality modeling language (VRML); open architecture; and advantages of Java, an object-oriented programming language, including platform independence, distributed development, and pay-per-use software.…

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.

[A design of software for management of hospital equipment maintenance process].

PubMed

Xie, Haiyuan; Liu, Yiqing

2010-03-01

According to the circumstance of hospital equipment maintenance, we designed a computer program for management of hospital equipment maintenance process by Java programming language. This program can control the maintenance process, increase the efficiency; and be able to fix the equipment location.

GUI and Object Oriented Programming in COBOL.

ERIC Educational Resources Information Center

Lorents, Alden C.

Various schools are struggling with the introduction of Object Oriented (OO) programming concepts and GUI (graphical user interfaces) within the traditional COBOL sequence. OO programming has been introduced in some of the curricula with languages such as C++, Smalltalk, and Java. Introducing OO programming into a typical COBOL sequence presents…

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.

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.

Declarative language design for interactive visualization.

PubMed

Heer, Jeffrey; Bostock, Michael

2010-01-01

We investigate the design of declarative, domain-specific languages for constructing interactive visualizations. By separating specification from execution, declarative languages can simplify development, enable unobtrusive optimization, and support retargeting across platforms. We describe the design of the Protovis specification language and its implementation within an object-oriented, statically-typed programming language (Java). We demonstrate how to support rich visualizations without requiring a toolkit-specific data model and extend Protovis to enable declarative specification of animated transitions. To support cross-platform deployment, we introduce rendering and event-handling infrastructures decoupled from the runtime platform, letting designers retarget visualization specifications (e.g., from desktop to mobile phone) with reduced effort. We also explore optimizations such as runtime compilation of visualization specifications, parallelized execution, and hardware-accelerated rendering. We present benchmark studies measuring the performance gains provided by these optimizations and compare performance to existing Java-based visualization tools, demonstrating scalability improvements exceeding an order of magnitude.

Experience in the application of Java Technologies in telemedicine

PubMed Central

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

2002-01-01

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

Experience in the application of Java Technologies in telemedicine.

PubMed

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

2002-09-17

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

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.

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

Wagner, Robert; Rivers, Wilmer

any single computer program for seismic data analysis will not have all the capabilities needed to study reference events, since hese detailed studies will be highly specialized. It may be necessary to develop and test new algorithms, and then these special ;odes must be integrated with existing software to use their conventional data-processing routines. We have investigated two neans of establishing communications between the legacy and new codes: CORBA and XML/SOAP Web services. We have nvestigated making new Java code communicate with a legacy C-language program, geotool, running under Linux. Both methods vere successful, but both were difficult to implement.more » C programs on UNIX/Linux are poorly supported for Web services, compared vith the Java and .NET languages and platforms. Easier-to-use middleware will be required for scientists to construct distributed applications as easily as stand-alone ones. Considerable difficulty was encountered in modifying geotool, and this problem shows he need to use component-based user interfaces instead of large C-language codes where changes to one part of the program nay introduce side effects into other parts. We have nevertheless made bug fixes and enhancements to that legacy program, but t remains difficult to expand it through communications with external software.« less

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.

Specification and Error Pattern Based Program Monitoring

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Analytical scheme calculations of angular momentum coupling and recoupling coefficients

NASA Astrophysics Data System (ADS)

Deveikis, A.; Kuznecovas, A.

2007-03-01

We investigate the Scheme programming language opportunities to analytically calculate the Clebsch-Gordan coefficients, Wigner 6j and 9j symbols, and general recoupling coefficients that are used in the quantum theory of angular momentum. The considered coefficients are calculated by a direct evaluation of the sum formulas. The calculation results for large values of quantum angular momenta were compared with analogous calculations with FORTRAN and Java programming languages.

Java Mission Evaluation Workstation System

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

A Survey of Quantum Programming Languages: History, Methods, and Tools

DTIC Science & Technology

2008-01-01

and entanglement , to achieve computational solutions to certain problems in less time (fewer computational cycles) than is possible using classical...superposition of quantum bits, entanglement , destructive measurement, and the no-cloning theorem. These differences must be thoroughly understood and even...computers using well-known languages such as C, C++, Java, and rapid prototyping languages such as Maple, Mathematica, and Matlab . A good on-line

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

Scientific Programming Using Java and C: A Remote Sensing Example

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

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.

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

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

NASA Astrophysics Data System (ADS)

Cha, Moon Hoe

2007-02-01

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

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

PubMed

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

2006-10-01

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

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.

Programming models for energy-aware systems

NASA Astrophysics Data System (ADS)

Zhu, Haitao

Energy efficiency is an important goal of modern computing, with direct impact on system operational cost, reliability, usability and environmental sustainability. This dissertation describes the design and implementation of two innovative programming languages for constructing energy-aware systems. First, it introduces ET, a strongly typed programming language to promote and facilitate energy-aware programming, with a novel type system design called Energy Types. Energy Types is built upon a key insight into today's energy-efficient systems and applications: despite the popular perception that energy and power can only be described in joules and watts, real-world energy management is often based on discrete phases and modes, which in turn can be reasoned about by type systems very effectively. A phase characterizes a distinct pattern of program workload, and a mode represents an energy state the program is expected to execute in. Energy Types is designed to reason about energy phases and energy modes, bringing programmers into the optimization of energy management. Second, the dissertation develops Eco, an energy-aware programming language centering around sustainability. A sustainable program built from Eco is able to adaptively adjusts its own behaviors to stay on a given energy budget, avoiding both deficit that would lead to battery drain or CPU overheating, and surplus that could have been used to improve the quality of the program output. Sustainability is viewed as a form of supply and demand matching, and a sustainable program consistently maintains the equilibrium between supply and demand. ET is implemented as a prototyped compiler for smartphone programming on Android, and Eco is implemented as a minimal extension to Java. Programming practices and benchmarking experiments in these two new languages showed that ET can lead to significant energy savings for Android Apps and Eco can efficiently promote battery awareness and temperature awareness in real-world Java programs.

Visualization of Real-Time Data

NASA Technical Reports Server (NTRS)

Stansifer, Ryan; Engrand, Peter

1996-01-01

In this project we explored various approaches to presenting real-time data from the numerous systems monitored on the space shuttle to computer users. We examined the approach that several projects at the Kennedy Space Center (KSC) used to accomplish this. We undertook to build a prototype system to demonstrate that the Internet and the Java programming language could be used to present the real-time data conveniently. Several Java programs were developed that presented real-time data in different forms including one form that emulated the display screens of the PC GOAL system which is familiar to many at KSC. Also, we developed several communications programs to supply the data continuously. Furthermore, a framework was created using the World Wide Web (WWW) to organize the collection and presentation of the real-time data. We believe our demonstration project shows the great flexibility of the approach. We had no particular use of the data in mind, instead we wanted the most general and the least complex framework possible. People who wish to view data need only know how to use a WWW browser and the address (the URL). People wanting to build WWW documents containing real-time data need only know the values of a few parameters, they do not need to program in Java or any other language. These are stunning advantages over more monolithic systems.

Applications of Java and Vector Graphics to Astrophysical Visualization

NASA Astrophysics Data System (ADS)

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

2002-12-01

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

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

Productive High Performance Parallel Programming with Auto-tuned Domain-Specific Embedded Languages

DTIC Science & Technology

2013-01-02

Compilation JVM Java Virtual Machine KB Kilobyte KDT Knowledge Discovery Toolbox LAPACK Linear Algebra Package LLVM Low-Level Virtual Machine LOC Lines...different starting points. Leo Meyerovich also helped solidify some of the ideas here in discussions during Par Lab retreats. I would also like to thank...multi-timestep computations by blocking in both time and space. 88 Implementation Output Approx DSL Type Language Language Parallelism LoC Graphite

Ground Support Software for Spaceborne Instrumentation

NASA Technical Reports Server (NTRS)

Anicich, Vincent; Thorpe, rob; Fletcher, Greg; Waite, Hunter; Xu, Hykua; Walter, Erin; Frick, Kristie; Farris, Greg; Gell, Dave; Furman, Jufy;

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

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

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.

Ancient Egypt

NASA Astrophysics Data System (ADS)

Swamy, Ashwin Balegar

This thesis involves development of an interactive GIS (Geographic Information System) based application, which gives information about the ancient history of Egypt. The astonishing architecture, the strange burial rituals and their civilization were some of the intriguing questions that motivated me towards developing this application. The application is a historical timeline starting from 3100 BC, leading up to 664 BC, focusing on the evolution of the Egyptian dynasties. The tool holds information regarding some of the famous monuments which were constructed during that era and also about the civilizations that co-existed. It also provides details about the religions followed by their kings. It also includes the languages spoken during those periods. The tool is developed using JAVA, a programing language and MOJO (Map Objects Java Objects) a product of ESRI (Environmental Science Research Institute) to create map objects, to provide geographic information. JAVA Swing is used for designing the user interface. HTML (Hyper Text Markup Language) pages are created to provide the user with more information related to the historic period. CSS (Cascade Style Sheets) and JAVA Scripts are used with HTML5 to achieve creative display of content. The tool is kept simple and easy for the user to interact with. The tool also includes pictures and videos for the user to get a feel of the historic period. The application is built to motivate people to know more about one of the prominent and ancient civilization of the Mediterranean world.

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

Enabling On-Demand Database Computing with MIT SuperCloud Database Management System

DTIC Science & Technology

2015-09-15

arc.liv.ac.uk/trac/SGE) provides these services and is independent of programming language (C, Fortran, Java , Matlab, etc) or parallel programming...a MySQL database to store DNS records. The DNS records are controlled via a simple web service interface that allows records to be created

Internet Distribution of Spacecraft Telemetry Data

NASA Technical Reports Server (NTRS)

Specht, Ted; Noble, David

2006-01-01

Remote Access Multi-mission Processing and Analysis Ground Environment (RAMPAGE) is a Java-language server computer program that enables near-real-time display of spacecraft telemetry data on any authorized client computer that has access to the Internet and is equipped with Web-browser software. In addition to providing a variety of displays of the latest available telemetry data, RAMPAGE can deliver notification of an alarm by electronic mail. Subscribers can then use RAMPAGE displays to determine the state of the spacecraft and formulate a response to the alarm, if necessary. A user can query spacecraft mission data in either binary or comma-separated-value format by use of a Web form or a Practical Extraction and Reporting Language (PERL) script to automate the query process. RAMPAGE runs on Linux and Solaris server computers in the Ground Data System (GDS) of NASA's Jet Propulsion Laboratory and includes components designed specifically to make it compatible with legacy GDS software. The client/server architecture of RAMPAGE and the use of the Java programming language make it possible to utilize a variety of competitive server and client computers, thereby also helping to minimize costs.

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).

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

RACER: Effective Race Detection Using AspectJ

NASA Technical Reports Server (NTRS)

Bodden, Eric; Havelund, Klaus

2008-01-01

The limits of coding with joint constraints on detected and undetected error rates Programming errors occur frequently in large software systems, and even more so if these systems are concurrent. In the past, researchers have developed specialized programs to aid programmers detecting concurrent programming errors such as deadlocks, livelocks, starvation and data races. In this work we propose a language extension to the aspect-oriented programming language AspectJ, in the form of three new built-in pointcuts, lock(), unlock() and may be Shared(), which allow programmers to monitor program events where locks are granted or handed back, and where values are accessed that may be shared amongst multiple Java threads. We decide thread-locality using a static thread-local objects analysis developed by others. Using the three new primitive pointcuts, researchers can directly implement efficient monitoring algorithms to detect concurrent programming errors online. As an example, we expose a new algorithm which we call RACER, an adoption of the well-known ERASER algorithm to the memory model of Java. We implemented the new pointcuts as an extension to the Aspect Bench Compiler, implemented the RACER algorithm using this language extension and then applied the algorithm to the NASA K9 Rover Executive. Our experiments proved our implementation very effective. In the Rover Executive RACER finds 70 data races. Only one of these races was previously known.We further applied the algorithm to two other multi-threaded programs written by Computer Science researchers, in which we found races as well.

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

Buttler, D J

The Java Metadata Facility is introduced by Java Specification Request (JSR) 175 [1], and incorporated into the Java language specification [2] in version 1.5 of the language. The specification allows annotations on Java program elements: classes, interfaces, methods, and fields. Annotations give programmers a uniform way to add metadata to program elements that can be used by code checkers, code generators, or other compile-time or runtime components. Annotations are defined by annotation types. These are defined the same way as interfaces, but with the symbol {at} preceding the interface keyword. There are additional restrictions on defining annotation types: (1) Theymore » cannot be generic; (2) They cannot extend other annotation types or interfaces; (3) Methods cannot have any parameters; (4) Methods cannot have type parameters; (5) Methods cannot throw exceptions; and (6) The return type of methods of an annotation type must be a primitive, a String, a Class, an annotation type, or an array, where the type of the array is restricted to one of the four allowed types. See [2] for additional restrictions and syntax. The methods of an annotation type define the elements that may be used to parameterize the annotation in code. Annotation types may have default values for any of its elements. For example, an annotation that specifies a defect report could initialize an element defining the defect outcome submitted. Annotations may also have zero elements. This could be used to indicate serializability for a class (as opposed to the current Serializability interface).« less

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.

COVERT: A Framework for Finding Buffer Overflows in C Programs via Software Verification

DTIC Science & Technology

2010-08-01

is greater than the allocated size of B. In the case of a type-safe language or a language with runtime bounds checking (such as Java), an overflow...leads either to a (compile-time) type error or a (runtime) exception. In such languages , a buffer overflow can lead to a denial of service attack (i.e...of current and legacy software is written in unsafe languages (such as C or C++) that allow buffers to be overflowed with impunity. For reasons such as

Task Description Language

NASA Technical Reports Server (NTRS)

Simmons, Reid; Apfelbaum, David

2005-01-01

Task Description Language (TDL) is an extension of the C++ programming language that enables programmers to quickly and easily write complex, concurrent computer programs for controlling real-time autonomous systems, including robots and spacecraft. TDL is based on earlier work (circa 1984 through 1989) on the Task Control Architecture (TCA). TDL provides syntactic support for hierarchical task-level control functions, including task decomposition, synchronization, execution monitoring, and exception handling. A Java-language-based compiler transforms TDL programs into pure C++ code that includes calls to a platform-independent task-control-management (TCM) library. TDL has been used to control and coordinate multiple heterogeneous robots in projects sponsored by NASA and the Defense Advanced Research Projects Agency (DARPA). It has also been used in Brazil to control an autonomous airship and in Canada to control a robotic manipulator.

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.

An Examination of Job Skills Posted on Internet Databases: Implications for Information Systems Degree Programs.

ERIC Educational Resources Information Center

Liu, Xia; Liu, Lai C.; Koong, Kai S.; Lu, June

2003-01-01

Analysis of 300 information technology job postings in two Internet databases identified the following skill categories: programming languages (Java, C/C++, and Visual Basic were most frequent); website development (57% sought SQL and HTML skills); databases (nearly 50% required Oracle); networks (only Windows NT or wide-area/local-area networks);…

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

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

Wu, C

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

WaveJava: Wavelet-based network computing

NASA Astrophysics Data System (ADS)

Ma, Kun; Jiao, Licheng; Shi, Zhuoer

1997-04-01

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

Automated Verification of Design Patterns with LePUS3

NASA Technical Reports Server (NTRS)

Nicholson, Jonathan; Gasparis, Epameinondas; Eden, Ammon H.; Kazman, Rick

2009-01-01

Specification and [visual] modelling languages are expected to combine strong abstraction mechanisms with rigour, scalability, and parsimony. LePUS3 is a visual, object-oriented design description language axiomatized in a decidable subset of the first-order predicate logic. We demonstrate how LePUS3 is used to formally specify a structural design pattern and prove ( verify ) whether any JavaTM 1.4 program satisfies that specification. We also show how LePUS3 specifications (charts) are composed and how they are verified fully automatically in the Two-Tier Programming Toolkit.

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/

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

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

The 10 Hottest Technologies in Telecom.

ERIC Educational Resources Information Center

Flanagan, Patrick

1996-01-01

Synthesizes opinions of experts regarding technologies deemed most likely to enter the telecommunications mainstream by 1998, including: (1) the Java programming language; (2) voice- over frame relay; (3) virtual local area networks (LANs); (4) cable modems; (5) gigabit LANs; (6) Internet appliances; (7) personal satellite phones; (8) intranets;…

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

A comparative study of programming languages for next-generation astrodynamics systems

NASA Astrophysics Data System (ADS)

Eichhorn, Helge; Cano, Juan Luis; McLean, Frazer; Anderl, Reiner

2018-03-01

Due to the computationally intensive nature of astrodynamics tasks, astrodynamicists have relied on compiled programming languages such as Fortran for the development of astrodynamics software. Interpreted languages such as Python, on the other hand, offer higher flexibility and development speed thereby increasing the productivity of the programmer. While interpreted languages are generally slower than compiled languages, recent developments such as just-in-time (JIT) compilers or transpilers have been able to close this speed gap significantly. Another important factor for the usefulness of a programming language is its wider ecosystem which consists of the available open-source packages and development tools such as integrated development environments or debuggers. This study compares three compiled languages and three interpreted languages, which were selected based on their popularity within the scientific programming community and technical merit. The three compiled candidate languages are Fortran, C++, and Java. Python, Matlab, and Julia were selected as the interpreted candidate languages. All six languages are assessed and compared to each other based on their features, performance, and ease-of-use through the implementation of idiomatic solutions to classical astrodynamics problems. We show that compiled languages still provide the best performance for astrodynamics applications, but JIT-compiled dynamic languages have reached a competitive level of speed and offer an attractive compromise between numerical performance and programmer productivity.

A Moderate Constructivist E-Learning Instructional Model Evaluated on Computer Specialists

ERIC Educational Resources Information Center

Alonso, Fernando; Manrique, Daniel; Vines, Jose M.

2009-01-01

This paper presents a novel instructional model for e-learning and an evaluation study to determine the effectiveness of this model for teaching Java language programming to information technology specialists working for the Spanish Public Administration. This is a general-purpose model that combines objectivist and constructivist learning…

The Competitive Edge: Expanded Access Drives Vendors.

ERIC Educational Resources Information Center

Pepin, Theresa; And Others

1997-01-01

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

Virtually Exploring A Pillar Of Experimental Physics: The Hertz Experiment

NASA Astrophysics Data System (ADS)

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

2008-05-01

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

Polymorphous Computing Architectures

DTIC Science & Technology

2007-12-12

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

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

The Effectiveness of Using Learning Management Systems and Collaborative Tool in Web-Based Teaching of Programming Languages

ERIC Educational Resources Information Center

Cavus, Nadire; Uzunboylu, Huseyin; Ibrahim, Dogan

2006-01-01

This paper is about a pilot study which has been carried out at the Near East University during the 2004/5 Fall Semester using the Moodle LMS [learning management system] together with GREWPtool collaborative editor. The system has been tested with 36 students taking the Java and the Pascal programming courses. The results of the pilot study…

The state of the Java universe

ScienceCinema

Gosling, James

2018-05-22

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

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/

JavaScript DNA translator: DNA-aligned protein translations.

PubMed

Perry, William L

2002-12-01

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

A Visual Editor in Java for View

NASA Technical Reports Server (NTRS)

Stansifer, Ryan

2000-01-01

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

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

NASA Astrophysics Data System (ADS)

Wang, Manyi; Liu, Chaoshun; Gao, Wei

2014-10-01

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

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

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

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.

Towards a Certified Lightweight Array Bound Checker for Java Bytecode

NASA Technical Reports Server (NTRS)

Pichardie, David

2009-01-01

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

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.

Hierarchical programming for data storage and visualization

USGS Publications Warehouse

Donovan, John M.; Smith, Peter E.; ,

2001-01-01

Graphics software is an essential tool for interpreting, analyzing, and presenting data from multidimensional hydrodynamic models used in estuarine and coastal ocean studies. The post-processing of time-varying three-dimensional model output presents unique requirements for data visualization because of the large volume of data that can be generated and the multitude of time scales that must be examined. Such data can relate to estuarine or coastal ocean environments and come from numerical models or field instruments. One useful software tool for the display, editing, visualization, and printing of graphical data is the Gr application, written by the first author for use in U.S. Geological Survey San Francisco Bay Program. The Gr application has been made available to the public via the Internet since the year 2000. The Gr application is written in the Java (Sun Microsystems, Nov. 29, 2001) programming language and uses the Extensible Markup Language standard for hierarchical data storage. Gr presents a hierarchy of objects to the user that can be edited using a common interface. Java's object-oriented capabilities allow Gr to treat data, graphics, and tools equally and to save them all to a single XML file.

KB3D Reference Manual. Version 1.a

NASA Technical Reports Server (NTRS)

Munoz, Cesar; Siminiceanu, Radu; Carreno, Victor A.; Dowek, Gilles

2005-01-01

This paper is a reference manual describing the implementation of the KB3D conflict detection and resolution algorithm. The algorithm has been implemented in the Java and C++ programming languages. The reference manual gives a short overview of the detection and resolution functions, the structural implementation of the program, inputs and outputs to the program, and describes how the program is used. Inputs to the program can be rectangular coordinates or geodesic coordinates. The reference manual also gives examples of conflict scenarios and the resolution outputs the program produces.

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

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

NASA Astrophysics Data System (ADS)

Gutfreund, Yechezkal-Shimon; Nicol, John R.

1997-01-01

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

Biomolecules in the Computer: Jmol to the Rescue

ERIC Educational Resources Information Center

Herraez, Angel

2006-01-01

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

Developing Multimedia Courseware for the Internet's Java versus Shockwave.

ERIC Educational Resources Information Center

Majchrzak, Tina L.

1996-01-01

Describes and compares two methods for developing multimedia courseware for use on the Internet: an authoring tool called Shockwave, and an object-oriented language called Java. Topics include vector graphics, browsers, interaction with network protocols, data security, multithreading, and computer languages versus development environments. (LRW)

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

Enabling Data Fusion via a Common Data Model and Programming Interface

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Wilson, A.

2011-12-01

Much progress has been made in scientific data interoperability, especially in the areas of metadata and discovery. However, while a data user may have improved techniques for finding data, there is often a large chasm to span when it comes to acquiring the desired subsets of various datasets and integrating them into a data processing environment. Some tools such as OPeNDAP servers and the Unidata Common Data Model (CDM) have introduced improved abstractions for accessing data via a common interface, but they alone do not go far enough to enable fusion of data from multidisciplinary sources. Although data from various scientific disciplines may represent semantically similar concepts (e.g. time series), the user may face widely varying structural representations of the data (e.g. row versus column oriented), not to mention radically different storage formats. It is not enough to convert data to a common format. The key to fusing scientific data is to represent each dataset with consistent sampling. This can best be done by using a data model that expresses the functional relationship that each dataset represents. The domain of those functions determines how the data can be combined. The Visualization for Algorithm Development (VisAD) Java API has provided a sophisticated data model for representing the functional nature of scientific datasets for well over a decade. Because VisAD is largely designed for its visualization capabilities, the data model can be cumbersome to use for numerical computation, especially for those not comfortable with Java. Although both VisAD and the implementation of the CDM are written in Java, neither defines a pure Java interface that others could implement and program to, further limiting potential for interoperability. In this talk, we will present a solution for data integration based on a simple discipline-agnostic scientific data model and programming interface that enables a dataset to be defined in terms of three variable types: Scalar (a), Tuple (a,b), and Function (a -> b). These basic building blocks can be combined and nested to represent any arbitrarily complex dataset. For example, a time series of surface temperature and pressure could be represented as: time -> ((lon,lat) -> (T,P)). Our data model is expressed in UML and can be implemented in numerous programming languages. We will demonstrate an implementation of our data model and interface using the Scala programming language. Given its functional programming constructs, sophisticated type system, and other language features, Scala enables us to construct complex data structures that can be manipulated using natural mathematical expressions while taking advantage of the language's ability to operate on collections in parallel. This API will be applied to the problem of assimilating various measurements of the solar spectrum and other proxies from multiple sources to construct a composite Lyman-alpha irradiance dataset.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

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

2011-01-01

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

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

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

2010-01-01

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

Real-Time Payload Control and Monitoring on the World Wide Web

NASA Technical Reports Server (NTRS)

Sun, Charles; Windrem, May; Givens, John J. (Technical Monitor)

1998-01-01

World Wide Web (W3) technologies such as the Hypertext Transfer Protocol (HTTP) and the Java object-oriented programming environment offer a powerful, yet relatively inexpensive, framework for distributed application software development. This paper describes the design of a real-time payload control and monitoring system that was developed with W3 technologies at NASA Ames Research Center. Based on Java Development Toolkit (JDK) 1.1, the system uses an event-driven "publish and subscribe" approach to inter-process communication and graphical user-interface construction. A C Language Integrated Production System (CLIPS) compatible inference engine provides the back-end intelligent data processing capability, while Oracle Relational Database Management System (RDBMS) provides the data management function. Preliminary evaluation shows acceptable performance for some classes of payloads, with Java's portability and multimedia support identified as the most significant benefit.

Applying Jlint to Space Exploration Software

NASA Technical Reports Server (NTRS)

Artho, Cyrille; Havelund, Klaus

2004-01-01

Java is a very successful programming language which is also becoming widespread in embedded systems, where software correctness is critical. Jlint is a simple but highly efficient static analyzer that checks a Java program for several common errors, such as null pointer exceptions, and overflow errors. It also includes checks for multi-threading problems, such as deadlocks and data races. The case study described here shows the effectiveness of Jlint in find-false positives in the multi-threading warnings gives an insight into design patterns commonly used in multi-threaded code. The results show that a few analysis techniques are sufficient to avoid almost all false positives. These techniques include investigating all possible callers and a few code idioms. Verifying the correct application of these patterns is still crucial, because their correct usage is not trivial.

Generic, Type-Safe and Object Oriented Computer Algebra Software

NASA Astrophysics Data System (ADS)

Kredel, Heinz; Jolly, Raphael

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

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.

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus

PubMed Central

Comeau, Donald C.; Liu, Haibin; Islamaj Doğan, Rezarta; Wilbur, W. John

2014-01-01

BioC is a new format and associated code libraries for sharing text and annotations. We have implemented BioC natural language preprocessing pipelines in two popular programming languages: C++ and Java. The current implementations interface with the well-known MedPost and Stanford natural language processing tool sets. The pipeline functionality includes sentence segmentation, tokenization, part-of-speech tagging, lemmatization and sentence parsing. These pipelines can be easily integrated along with other BioC programs into any BioC compliant text mining systems. As an application, we converted the NCBI disease corpus to BioC format, and the pipelines have successfully run on this corpus to demonstrate their functionality. Code and data can be downloaded from http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net PMID:24935050

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

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Wilson, A.

2012-12-01

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

Legacy model integration for enhancing hydrologic interdisciplinary research

NASA Astrophysics Data System (ADS)

Dozier, A.; Arabi, M.; David, O.

2013-12-01

Many challenges are introduced to interdisciplinary research in and around the hydrologic science community due to advances in computing technology and modeling capabilities in different programming languages, across different platforms and frameworks by researchers in a variety of fields with a variety of experience in computer programming. Many new hydrologic models as well as optimization, parameter estimation, and uncertainty characterization techniques are developed in scripting languages such as Matlab, R, Python, or in newer languages such as Java and the .Net languages, whereas many legacy models have been written in FORTRAN and C, which complicates inter-model communication for two-way feedbacks. However, most hydrologic researchers and industry personnel have little knowledge of the computing technologies that are available to address the model integration process. Therefore, the goal of this study is to address these new challenges by utilizing a novel approach based on a publish-subscribe-type system to enhance modeling capabilities of legacy socio-economic, hydrologic, and ecologic software. Enhancements include massive parallelization of executions and access to legacy model variables at any point during the simulation process by another program without having to compile all the models together into an inseparable 'super-model'. Thus, this study provides two-way feedback mechanisms between multiple different process models that can be written in various programming languages and can run on different machines and operating systems. Additionally, a level of abstraction is given to the model integration process that allows researchers and other technical personnel to perform more detailed and interactive modeling, visualization, optimization, calibration, and uncertainty analysis without requiring deep understanding of inter-process communication. To be compatible, a program must be written in a programming language with bindings to a common implementation of the message passing interface (MPI), which includes FORTRAN, C, Java, the .NET languages, Python, R, Matlab, and many others. The system is tested on a longstanding legacy hydrologic model, the Soil and Water Assessment Tool (SWAT), to observe and enhance speed-up capabilities for various optimization, parameter estimation, and model uncertainty characterization techniques, which is particularly important for computationally intensive hydrologic simulations. Initial results indicate that the legacy extension system significantly decreases developer time, computation time, and the cost of purchasing commercial parallel processing licenses, while enhancing interdisciplinary research by providing detailed two-way feedback mechanisms between various process models with minimal changes to legacy code.

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

NASA Astrophysics Data System (ADS)

Sventek, Joe

1998-12-01

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

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

Java Library for Input and Output of Image Data and Metadata

NASA Technical Reports Server (NTRS)

Deen, Robert; Levoe, Steven

2003-01-01

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

Strategies for Teaching Object-Oriented Concepts with Java

ERIC Educational Resources Information Center

Sicilia, Miguel-Angel

2006-01-01

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

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.

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.

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

QSPIN: A High Level Java API for Quantum Computing Experimentation

NASA Technical Reports Server (NTRS)

Barth, Tim

2017-01-01

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

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus.

PubMed

Comeau, Donald C; Liu, Haibin; Islamaj Doğan, Rezarta; Wilbur, W John

2014-01-01

BioC is a new format and associated code libraries for sharing text and annotations. We have implemented BioC natural language preprocessing pipelines in two popular programming languages: C++ and Java. The current implementations interface with the well-known MedPost and Stanford natural language processing tool sets. The pipeline functionality includes sentence segmentation, tokenization, part-of-speech tagging, lemmatization and sentence parsing. These pipelines can be easily integrated along with other BioC programs into any BioC compliant text mining systems. As an application, we converted the NCBI disease corpus to BioC format, and the pipelines have successfully run on this corpus to demonstrate their functionality. Code and data can be downloaded from http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net. © The Author(s) 2014. Published by Oxford University Press.

BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

PubMed

Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

2015-06-02

Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

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

Schaumberg, Andrew

The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the “omics.jar” file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on amore » server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the “help” command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args« less

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.

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

DTIC Science & Technology

2001-12-01

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

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

NASA Astrophysics Data System (ADS)

Cen, Haifeng

2017-04-01

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

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set.

PubMed

Alvare, Graham Gm; Roche-Lima, Abiel; Fristensky, Brian

2012-11-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces.

X-Windows PVT Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

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

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

PubMed

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

2006-12-01

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

Cross-language Babel structs—making scientific interfaces more efficient

NASA Astrophysics Data System (ADS)

Prantl, Adrian; Ebner, Dietmar; Epperly, Thomas G. W.

2013-01-01

Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture, it is employed in a wide range of scientific applications where it is used to connect components written in different programming languages. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in (mono-lingual) scientific application programming interfaces (APIs); they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific codes can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++, Fortran 2003/2008 and Chapel, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90/95, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data to compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods. A case study shows how structs can help simplify the interfaces of scientific codes significantly.

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

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.

Block Architecture Problem with Depth First Search Solution and Its Application

NASA Astrophysics Data System (ADS)

Rahim, Robbi; Abdullah, Dahlan; Simarmata, Janner; Pranolo, Andri; Saleh Ahmar, Ansari; Hidayat, Rahmat; Napitupulu, Darmawan; Nurdiyanto, Heri; Febriadi, Bayu; Zamzami, Z.

2018-01-01

Searching is a common process performed by many computer users, Raita algorithm is one algorithm that can be used to match and find information in accordance with the patterns entered. Raita algorithm applied to the file search application using java programming language and the results obtained from the testing process of the file search quickly and with accurate results and support many data types.

Searching Process with Raita Algorithm and its Application

NASA Astrophysics Data System (ADS)

Rahim, Robbi; Saleh Ahmar, Ansari; Abdullah, Dahlan; Hartama, Dedy; Napitupulu, Darmawan; Putera Utama Siahaan, Andysah; Hasan Siregar, Muhammad Noor; Nasution, Nurliana; Sundari, Siti; Sriadhi, S.

2018-04-01

Searching is a common process performed by many computer users, Raita algorithm is one algorithm that can be used to match and find information in accordance with the patterns entered. Raita algorithm applied to the file search application using java programming language and the results obtained from the testing process of the file search quickly and with accurate results and support many data types.

A Model of Research Paper Writing Instructional Materials for Academic Writing Course: "Needs & Documents Analysis and Model Design"

ERIC Educational Resources Information Center

Ghufron, M. Ali; Saleh, Mursid; Warsono; Sofwan, Ahmad

2016-01-01

This study aimed at designing a model of instructional materials for Academic Writing Course focusing on research paper writing. The model was designed based on the Curriculum at the English Education Study Program, Faculty of Language and Art Education of IKIP PGRI Bojonegoro, East Java, Indonesia. This model was developed in order to improve…

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

NASA Astrophysics Data System (ADS)

Zhou, Yuping; Zhang, Qi

2018-04-01

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

Internet-based system for simulation-based medical planning for cardiovascular disease.

PubMed

Steele, Brooke N; Draney, Mary T; Ku, Joy P; Taylor, Charles A

2003-06-01

Current practice in vascular surgery utilizes only diagnostic and empirical data to plan treatments, which does not enable quantitative a priori prediction of the outcomes of interventions. We have previously described simulation-based medical planning methods to model blood flow in arteries and plan medical treatments based on physiologic models. An important consideration for the design of these patient-specific modeling systems is the accessibility to physicians with modest computational resources. We describe a simulation-based medical planning environment developed for the World Wide Web (WWW) using the Virtual Reality Modeling Language (VRML) and the Java programming language.

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

DTIC Science & Technology

2008-07-01

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

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

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.

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

PubMed

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

2014-06-14

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

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

NASA Astrophysics Data System (ADS)

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

2013-07-01

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

Test-driven programming

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2013-12-01

In this paper, are presented some possibilities concerning the implementation of a test-driven development as a programming method. Here is offered a different point of view for creation of advanced programming techniques (build tests before programming source with all necessary software tools and modules respectively). Therefore, this nontraditional approach for easier programmer's work through building tests at first is preferable way of software development. This approach allows comparatively simple programming (applied with different object-oriented programming languages as for example JAVA, XML, PYTHON etc.). It is predictable way to develop software tools and to provide help about creating better software that is also easier to maintain. Test-driven programming is able to replace more complicated casual paradigms, used by many programmers.

Instrument Remote Control via the Astronomical Instrument Markup Language

NASA Technical Reports Server (NTRS)

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

1998-01-01

The Instrument Remote Control (IRC) project ongoing at NASA's Goddard Space Flight Center's (GSFC) Information Systems Center (ISC) supports NASA's mission by defining an adaptive intranet-based framework that provides robust interactive and distributed control and monitoring of remote instruments. An astronomical IRC architecture that combines the platform-independent processing capabilities of Java with the power of Extensible Markup Language (XML) to express hierarchical data in an equally platform-independent, as well as human readable manner, has been developed. This architecture is implemented using a variety of XML support tools and Application Programming Interfaces (API) written in Java. IRC will enable trusted astronomers from around the world to easily access infrared instruments (e.g., telescopes, cameras, and spectrometers) located in remote, inhospitable environments, such as the South Pole, a high Chilean mountaintop, or an airborne observatory aboard a Boeing 747. Using IRC's frameworks, an astronomer or other scientist can easily define the type of onboard instrument, control the instrument remotely, and return monitoring data all through the intranet. The Astronomical Instrument Markup Language (AIML) is the first implementation of the more general Instrument Markup Language (IML). The key aspects of our approach to instrument description and control applies to many domains, from medical instruments to machine assembly lines. The concepts behind AIML apply equally well to the description and control of instruments in general. IRC enables us to apply our techniques to several instruments, preferably from different observatories.

GIS tool to locate major Sikh temples in USA

NASA Astrophysics Data System (ADS)

Sharma, Saumya

This tool is a GIS based interactive and graphical user interface tool, which locates the major Sikh temples of USA on a map. This tool is using Java programming language along with MOJO (Map Object Java Object) provided by ESRI that is the organization that provides the GIS software. It also includes some of the integration with Google's API's like Google Translator API. This application will tell users about the origin of Sikhism in India and USA, the major Sikh temples in each state of USA, location, name and detail information through their website. The primary purpose of this application is to make people aware about this religion and culture. This tool will also measure the distance between two temple points in a map and display the result in miles and kilometers. Also, there is an added support to convert each temple's website language from English to Punjabi or any other language using a language convertor tool so that people from different nationalities can understand their culture. By clicking on each point on a map, a new window will pop up showing the picture of the temple and a hyperlink that will redirect to the website of that particular temple .It will also contain links to their dance, music, history, and also a help menu to guide the users to use the software efficiently.

Cross-Platform Development Techniques for Mobile Devices

DTIC Science & Technology

2013-09-01

many other platforms including Windows, Blackberry , and Symbian. Each of these platforms has their own distinct architecture and programming language...sales of iPhones and the increasing use of Android-based devices have forced less successful competitors such as Microsoft, Blackberry , and Symbian... Blackberry and Windows Phone are planned [12] in this tool’s attempt to reuse code with a unified JavaScript API while at the same time supporting unique

Stata Hybrids: Updates and Ideas

NASA Technical Reports Server (NTRS)

Fieldler, James

2014-01-01

At last year's Stata conference I presented two projects for using Python with Stata: a plugin that embeds the Python programming language within Stata and code for using Stata data sets in Python. In this talk I will describe some small improvements being made to these projects, and I will present other ideas for combining tools with Stata. Some of these ideas use Python, some use JavaScript and a web browser.

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

ERIC Educational Resources Information Center

Godbee, Sara; de Jong, Mark

2007-01-01

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

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set

PubMed Central

Alvare, Graham GM; Roche-Lima, Abiel; Fristensky, Brian

2016-01-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces. PMID:27818582

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

Polyglot Programming in Applications Used for Genetic Data Analysis

PubMed Central

Nowak, Robert M.

2014-01-01

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

Polyglot programming in applications used for genetic data analysis.

PubMed

Nowak, Robert M

2014-01-01

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

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

[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.

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.

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

Gosling, James

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

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

PubMed

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

2016-01-01

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

ScaMo: Realisation of an OO-functional DSL for cross platform mobile applications development

NASA Astrophysics Data System (ADS)

Macos, Dragan; Solymosi, Andreas

2013-10-01

The software market is dynamically changing: the Internet is going mobile, the software applications are shifting from the desktop hardware onto the mobile devices. The largest markets are the mobile applications for iOS, Android and Windows Phone and for the purpose the typical programming languages include Objective-C, Java and C ♯. The realization of the native applications implies the integration of the developed software into the environments of mentioned mobile operating systems to enable the access to different hardware components of the devices: GPS module, display, GSM module, etc. This paper deals with the definition and possible implementation of an environment for the automatic application generation for multiple mobile platforms. It is based on a DSL for mobile application development, which includes the programming language Scala and a DSL defined in Scala. As part of a multi-stage cross-compiling algorithm, this language is translated into the language of the affected mobile platform. The advantage of our method lies in the expressiveness of the defined language and the transparent source code translation between different languages, which implies, for example, the advantages of debugging and development of the generated code.

Dynamic XML-based exchange of relational data: application to the Human Brain Project.

PubMed

Tang, Zhengming; Kadiyska, Yana; Li, Hao; Suciu, Dan; Brinkley, James F

2003-01-01

This paper discusses an approach to exporting relational data in XML format for data exchange over the web. We describe the first real-world application of SilkRoute, a middleware program that dynamically converts existing relational data to a user-defined XML DTD. The application, called XBrain, wraps SilkRoute in a Java Server Pages framework, thus permitting a web-based XQuery interface to a legacy relational database. The application is demonstrated as a query interface to the University of Washington Brain Project's Language Map Experiment Management System, which is used to manage data about language organization in the brain.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

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

2010-10-15

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

Global Language Identities and Ideologies in an Indonesian University Context

ERIC Educational Resources Information Center

Zentz, Lauren

2012-01-01

This ethnographic study of language use and English language learners in Central Java, Indonesia examines globalization processes within and beyond language; processes of language shift and change in language ecologies; and critical and comprehensive approaches to the teaching of English around the world. From my position as teacher-researcher and…

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

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

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

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

PubMed

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

2017-06-01

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

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

PubMed Central

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

2017-01-01

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

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

PubMed Central

2009-01-01

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

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

PubMed

Lee, Yoon-Hwan

2009-12-20

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

Foundations of the Bandera Abstraction Tools

NASA Technical Reports Server (NTRS)

Hatcliff, John; Dwyer, Matthew B.; Pasareanu, Corina S.; Robby

2003-01-01

Current research is demonstrating that model-checking and other forms of automated finite-state verification can be effective for checking properties of software systems. Due to the exponential costs associated with model-checking, multiple forms of abstraction are often necessary to obtain system models that are tractable for automated checking. The Bandera Tool Set provides multiple forms of automated support for compiling concurrent Java software systems to models that can be supplied to several different model-checking tools. In this paper, we describe the foundations of Bandera's data abstraction mechanism which is used to reduce the cardinality (and the program's state-space) of data domains in software to be model-checked. From a technical standpoint, the form of data abstraction used in Bandera is simple, and it is based on classical presentations of abstract interpretation. We describe the mechanisms that Bandera provides for declaring abstractions, for attaching abstractions to programs, and for generating abstracted programs and properties. The contributions of this work are the design and implementation of various forms of tool support required for effective application of data abstraction to software components written in a programming language like Java which has a rich set of linguistic features.

The ENSDF Java Package

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

Sonzogni, A.A.

2005-05-24

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

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

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-01-01

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

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.

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

Simulation Tools for Power Electronics Courses Based on Java Technologies

ERIC Educational Resources Information Center

Canesin, Carlos A.; Goncalves, Flavio A. S.; Sampaio, Leonardo P.

2010-01-01

This paper presents interactive power electronics educational tools. These interactive tools make use of the benefits of Java language to provide a dynamic and interactive approach to simulating steady-state ideal rectifiers (uncontrolled and controlled; single-phase and three-phase). Additionally, this paper discusses the development and use of…

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.

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

NASA Astrophysics Data System (ADS)

Chu, A.

2016-12-01

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

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…

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

Visualization and Interaction in Research, Teaching, and Scientific Communication

NASA Astrophysics Data System (ADS)

Ammon, C. J.

2017-12-01

Modern computing provides many tools for exploring observations, numerical calculations, and theoretical relationships. The number of options is, in fact, almost overwhelming. But the choices provide those with modest programming skills opportunities to create unique views of scientific information and to develop deeper insights into their data, their computations, and the underlying theoretical data-model relationships. I present simple examples of using animation and human-computer interaction to explore scientific data and scientific-analysis approaches. I illustrate how valuable a little programming ability can free scientists from the constraints of existing tools and can facilitate the development of deeper appreciation data and models. I present examples from a suite of programming languages ranging from C to JavaScript including the Wolfram Language. JavaScript is valuable for sharing tools and insight (hopefully) with others because it is integrated into one of the most powerful communication tools in human history, the web browser. Although too much of that power is often spent on distracting advertisements, the underlying computation and graphics engines are efficient, flexible, and almost universally available in desktop and mobile computing platforms. Many are working to fulfill the browser's potential to become the most effective tool for interactive study. Open-source frameworks for visualizing everything from algorithms to data are available, but advance rapidly. One strategy for dealing with swiftly changing tools is to adopt common, open data formats that are easily adapted (often by framework or tool developers). I illustrate the use of animation and interaction in research and teaching with examples from earthquake seismology.

Modular Chemical Descriptor Language (MCDL): Stereochemical modules

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

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

2011-01-01

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

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

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.

Utilizing Linked Open Data Sources for Automatic Generation of Semantic Metadata

NASA Astrophysics Data System (ADS)

Nummiaho, Antti; Vainikainen, Sari; Melin, Magnus

In this paper we present an application that can be used to automatically generate semantic metadata for tags given as simple keywords. The application that we have implemented in Java programming language creates the semantic metadata by linking the tags to concepts in different semantic knowledge bases (CrunchBase, DBpedia, Freebase, KOKO, Opencyc, Umbel and/or WordNet). The steps that our application takes in doing so include detecting possible languages, finding spelling suggestions and finding meanings from amongst the proper nouns and common nouns separately. Currently, our application supports English, Finnish and Swedish words, but other languages could be included easily if the required lexical tools (spellcheckers, etc.) are available. The created semantic metadata can be of great use in, e.g., finding and combining similar contents, creating recommendations and targeting advertisements.

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

PubMed

Dallakian, Pavel; Haider, Norbert

2011-02-01

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

Java-based cryptosystem for PACS and tele-imaging

NASA Astrophysics Data System (ADS)

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

1998-07-01

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

Building a genome database using an object-oriented approach.

PubMed

Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

2002-01-01

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

Barg, M. I.; Stobie, E. B.; Ferro, A. J.; O'Neil, E. J.

In the spring of 2000, at the request of the ADASS Program Organizing Committee (POC), we began organizing information from previous ADASS conferences in an effort to create a centralized database. The beginnings of this database originated from data (invited speakers, participants, papers, etc.) extracted from HyperText Markup Language (HTML) documents from past ADASS host sites. Unfortunately, not all HTML documents are well formed and parsing them proved to be an iterative process. It was evident at the beginning that if these Web documents were organized in a standardized way, such as XML (Extensible Markup Language), the processing of this information across the Web could be automated, more efficient, and less error prone. This paper will briefly review the many programming tools available for processing XML, including Java, Perl and Python, and will explore the mapping of relational data from our MySQL database to XML.

Development of computer-assisted instruction application for statistical data analysis android platform as learning resource

NASA Astrophysics Data System (ADS)

Hendikawati, P.; Arifudin, R.; Zahid, M. Z.

2018-03-01

This study aims to design an android Statistics Data Analysis application that can be accessed through mobile devices to making it easier for users to access. The Statistics Data Analysis application includes various topics of basic statistical along with a parametric statistics data analysis application. The output of this application system is parametric statistics data analysis that can be used for students, lecturers, and users who need the results of statistical calculations quickly and easily understood. Android application development is created using Java programming language. The server programming language uses PHP with the Code Igniter framework, and the database used MySQL. The system development methodology used is the Waterfall methodology with the stages of analysis, design, coding, testing, and implementation and system maintenance. This statistical data analysis application is expected to support statistical lecturing activities and make students easier to understand the statistical analysis of mobile devices.

HYDRA Hyperspectral Data Research Application Tom Rink and Tom Whittaker

NASA Astrophysics Data System (ADS)

Rink, T.; Whittaker, T.

2005-12-01

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

Thoth: Software for data visualization & statistics

NASA Astrophysics Data System (ADS)

Laher, R. R.

2016-10-01

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

Cassini Archive Tracking System

NASA Technical Reports Server (NTRS)

Conner, Diane; Sayfi, Elias; Tinio, Adrian

2006-01-01

The Cassini Archive Tracking System (CATS) is a computer program that enables tracking of scientific data transfers from originators to the Planetary Data System (PDS) archives. Without CATS, there is no systematic means of locating products in the archive process or ensuring their completeness. By keeping a database of transfer communications and status, CATS enables the Cassini Project and the PDS to efficiently and accurately report on archive status. More importantly, problem areas are easily identified through customized reports that can be generated on the fly from any Web-enabled computer. A Web-browser interface and clearly defined authorization scheme provide safe distributed access to the system, where users can perform functions such as create customized reports, record a transfer, and respond to a transfer. CATS ensures that Cassini provides complete science archives to the PDS on schedule and that those archives are available to the science community by the PDS. The three-tier architecture is loosely coupled and designed for simple adaptation to multimission use. Written in the Java programming language, it is portable and can be run on any Java-enabled Web server.

Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models.

PubMed

Jardine, Bartholomew; Raymond, Gary M; Bassingthwaighte, James B

2015-01-01

The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) ( http://www.physiome.org/jsim/) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle in writing complex models for physiological processes is the large amount of time it takes to model the myriad processes taking place simultaneously in cells, tissues, and organs. MPC replaces this task with code-generating algorithms that take model code from several different existing models and produce model code for a new JSim model. This is particularly useful during multi-scale model development where many variants are to be configured and tested against data. MPC encodes and preserves information about how a model is built from its simpler model modules, allowing the researcher to quickly substitute or update modules for hypothesis testing. MPC is implemented in Java and requires JSim to use its output. MPC source code and documentation are available at http://www.physiome.org/software/MPC/.

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.

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…

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

PubMed

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

2007-05-15

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

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

NASA Astrophysics Data System (ADS)

Frantzeskou, Georgia; Stamatatos, Efstathios; Gritzalis, Stefanos

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

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.

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…

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

NASA Astrophysics Data System (ADS)

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

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

Bad Breath - Multiple Languages

MedlinePlus

... List of All Topics All Bad Breath - Multiple Languages To use the sharing features on this page, please enable JavaScript. Chinese, Traditional ( ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 23 May 2018

Arthritis - Multiple Languages

MedlinePlus

... XYZ List of All Topics All Arthritis - Multiple Languages To use the sharing features on this page, please enable JavaScript. Chinese, Simplified ( ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 31 May 2018

Abortion - Multiple Languages

MedlinePlus

... XYZ List of All Topics All Abortion - Multiple Languages To use the sharing features on this page, please enable JavaScript. Chinese, Simplified ( ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 12 October 2017

Calcium - Multiple Languages

MedlinePlus

... XYZ List of All Topics All Calcium - Multiple Languages To use the sharing features on this page, please enable JavaScript. Chinese, Traditional ( ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 31 May 2018

Aspect-Oriented Monitoring of C Programs

NASA Technical Reports Server (NTRS)

Havelund, Klaus; VanWyk, Eric

2008-01-01

The paper presents current work on extending ASPECTC with state machines, resulting in a framework for aspect-oriented monitoring of C programs. Such a framework can be used for testing purposes, or it can be part of a fault protection strategy. The long term goal is to explore the synergy between the fields of runtime verification, focused on program monitoring, and aspect-oriented programming, focused on more general program development issues. The work is inspired by the observation that most work in this direction has been done for JAVA, partly due to the lack of easily accessible extensible compiler frameworks for C. The work is performed using the SILVER extensible attribute grammar compiler framework, in which C has been defined as a host language. Our work consists of extending C with ASPECTC, and subsequently to extend ASPECTC with state machines.

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.

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

PubMed Central

2011-01-01

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

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.

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

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,…

Anal Disorders - Multiple Languages

MedlinePlus

... List of All Topics All Anal Disorders - Multiple Languages To use the sharing features on this page, please enable JavaScript. French (français) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 3 May 2018

Cholera - Multiple Languages

MedlinePlus

... XYZ List of All Topics All Cholera - Multiple Languages To use the sharing features on this page, please enable JavaScript. Spanish (español) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 25 April 2018

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

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

A Rule-Based System Implementing a Method for Translating FOL Formulas into NL Sentences

NASA Astrophysics Data System (ADS)

Mpagouli, Aikaterini; Hatzilygeroudis, Ioannis

In this paper, we mainly present the implementation of a system that translates first order logic (FOL) formulas into natural language (NL) sentences. The motivation comes from an intelligent tutoring system teaching logic as a knowledge representation language, where it is used as a means for feedback to the students-users. FOL to NL conversion is achieved by using a rule-based approach, where we exploit the pattern matching capabilities of rules. So, the system consists of rule-based modules corresponding to the phases of our translation methodology. Facts are used in a lexicon providing lexical and grammatical information that helps in producing the NL sentences. The whole system is implemented in Jess, a java-implemented rule-based programming tool. Experimental results confirm the success of our choices.

DPADL: An Action Language for Data Processing Domains

NASA Technical Reports Server (NTRS)

Golden, Keith; Clancy, Daniel (Technical Monitor)

2002-01-01

This paper presents DPADL (Data Processing Action Description Language), a language for describing planning domains that involve data processing. DPADL is a declarative object-oriented language that supports constraints and embedded Java code, object creation and copying, explicit inputs and outputs for actions, and metadata descriptions of existing and desired data. DPADL is supported by the IMAGEbot system, which will provide automation for an ecosystem forecasting system called TOPS.

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…

Bile Duct Diseases - Multiple Languages

MedlinePlus

... of All Topics All Bile Duct Diseases - Multiple Languages To use the sharing features on this page, please enable JavaScript. French (français) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 7 May 2018

[Development of a System to Use Patient's Information Which is Required at the Radiological Department].

PubMed

Satoh, Akihiro

2016-04-01

The purpose of this study is to develop a new system to get and share some data of a patient which are required for a radiological examination not using an electronic medical chart or a radiological information system (RIS), and also to demonstrate that this system is operated on cloud technology. I used Java Enterprise Edition (Java EE) as a programing language and MySQL as a server software, and I used two laptops as hardware for client computer and server computer. For cloud computing, I hired a server of Google App Engine for Java (GAE). As a result, I could get some data of the patient required at his/her examination instantly using this system. This system also helps to improve the efficiency of examination. For example, it has been useful when I want to decide radiographic condition or to create CT images such as multi-planar reconstruction (MPR) or volume rendering (VR). When it comes to cloud computing, the GAE was used experimentally due to some legal restrictions. From the above points it is clear that this system has played an important role in radiological examinations, but there has been still few things which I have to resolve for cloud computing.

Event Reconstruction for Many-core Architectures using Java

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

Graf, Norman A.; /SLAC

Although Moore's Law remains technically valid, the performance enhancements in computing which traditionally resulted from increased CPU speeds ended years ago. Chip manufacturers have chosen to increase the number of core CPUs per chip instead of increasing clock speed. Unfortunately, these extra CPUs do not automatically result in improvements in simulation or reconstruction times. To take advantage of this extra computing power requires changing how software is written. Event reconstruction is globally serial, in the sense that raw data has to be unpacked first, channels have to be clustered to produce hits before those hits are identified as belonging tomore » a track or shower, tracks have to be found and fit before they are vertexed, etc. However, many of the individual procedures along the reconstruction chain are intrinsically independent and are perfect candidates for optimization using multi-core architecture. Threading is perhaps the simplest approach to parallelizing a program and Java includes a powerful threading facility built into the language. We have developed a fast and flexible reconstruction package (org.lcsim) written in Java that has been used for numerous physics and detector optimization studies. In this paper we present the results of our studies on optimizing the performance of this toolkit using multiple threads on many-core architectures.« less

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Warehouses information system design and development

NASA Astrophysics Data System (ADS)

Darajatun, R. A.; Sukanta

2017-12-01

Materials/goods handling industry is fundamental for companies to ensure the smooth running of their warehouses. Efficiency and organization within every aspect of the business is essential in order to gain a competitive advantage. The purpose of this research is design and development of Kanban of inventory storage and delivery system. Application aims to facilitate inventory stock checks to be more efficient and effective. Users easily input finished goods from production department, warehouse, customer, and also suppliers. Master data designed as complete as possible to be prepared applications used in a variety of process logistic warehouse variations. The author uses Java programming language to develop the application, which is used for building Java Web applications, while the database used is MySQL. System development methodology that I use is the Waterfall methodology. Waterfall methodology has several stages of the Analysis, System Design, Implementation, Integration, Operation and Maintenance. In the process of collecting data the author uses the method of observation, interviews, and literature.

Bronchial Disorders - Multiple Languages

MedlinePlus

... List of All Topics All Bronchial Disorders - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 2 May 2018

Cholesterol - Multiple Languages

MedlinePlus

... XYZ List of All Topics All Cholesterol - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 1 May 2018

Blood Thinners - Multiple Languages

MedlinePlus

... List of All Topics All Blood Thinners - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 7 February 2018

Advance Directives - Multiple Languages

MedlinePlus

... List of All Topics All Advance Directives - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 7 December 2017

Breathing Problems - Multiple Languages

MedlinePlus

... List of All Topics All Breathing Problems - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 2 May 2018

Bullying - Multiple Languages

MedlinePlus

... XYZ List of All Topics All Bullying - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 28 February 2018

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

JAVA CLASSES FOR NONPROCEDURAL VARIOGRAM MONITORING

EPA Science Inventory

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

Blood Transfusion and Donation - Multiple Languages

MedlinePlus

... All Topics All Blood Transfusion and Donation - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 30 April 2018

Asthma in Children - Multiple Languages

MedlinePlus

... of All Topics All Asthma in Children - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 23 May 2018

Biodefense and Bioterrorism - Multiple Languages

MedlinePlus

... of All Topics All Biodefense and Bioterrorism - Multiple Languages To use the sharing features on this page, please enable JavaScript. Arabic (العربية) ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated on 17 January 2018

GOBASE—a database of mitochondrial and chloroplast information

PubMed Central

O'Brien, Emmet A.; Badidi, Elarbi; Barbasiewicz, Ania; deSousa, Cristina; Lang, B. Franz; Burger, Gertraud

2003-01-01

GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130 000 mitochondrial sequences, an increase of 37% over the previous release, and more than 30 000 chloroplast sequences in a new auxiliary database. To handle this flood of new data, we have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html. PMID:12519975

Automatic visualization of 3D geometry contained in online databases

NASA Astrophysics Data System (ADS)

Zhang, Jie; John, Nigel W.

2003-04-01

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

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

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

NASA Astrophysics Data System (ADS)

Hernandez, Christopher

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

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

NASA Astrophysics Data System (ADS)

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

2014-10-01

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

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

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.

The Importance of Artificial Intelligence for Naval Intelligence Training Simulations

DTIC Science & Technology

2006-09-01

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

Measuring the Effects of Virtual Pair Programming in an Introductory Programming Java Course

ERIC Educational Resources Information Center

Zacharis, N. Z.

2011-01-01

This study investigated the effectiveness of virtual pair programming (VPP) on student performance and satisfaction in an introductory Java course. Students used online tools that integrated desktop sharing and real-time communication, and the metrics examined showed that VPP is an acceptable alternative to individual programming experience.…

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

SIP: A Web-Based Astronomical Image Processing Program

NASA Astrophysics Data System (ADS)

Simonetti, J. H.

1999-12-01

I have written an astronomical image processing and analysis program designed to run over the internet in a Java-compatible web browser. The program, Sky Image Processor (SIP), is accessible at the SIP webpage (http://www.phys.vt.edu/SIP). Since nothing is installed on the user's machine, there is no need to download upgrades; the latest version of the program is always instantly available. Furthermore, the Java programming language is designed to work on any computer platform (any machine and operating system). The program could be used with students in web-based instruction or in a computer laboratory setting; it may also be of use in some research or outreach applications. While SIP is similar to other image processing programs, it is unique in some important respects. For example, SIP can load images from the user's machine or from the Web. An instructor can put images on a web server for students to load and analyze on their own personal computer. Or, the instructor can inform the students of images to load from any other web server. Furthermore, since SIP was written with students in mind, the philosophy is to present the user with the most basic tools necessary to process and analyze astronomical images. Images can be combined (by addition, subtraction, multiplication, or division), multiplied by a constant, smoothed, cropped, flipped, rotated, and so on. Statistics can be gathered for pixels within a box drawn by the user. Basic tools are available for gathering data from an image which can be used for performing simple differential photometry, or astrometry. Therefore, students can learn how astronomical image processing works. Since SIP is not part of a commercial CCD camera package, the program is written to handle the most common denominator image file, the FITS format.

Configuration Tool for the Trusted Computing Exemplar Project

DTIC Science & Technology

2009-12-01

languages were examined: Microsoft .NET [8], Apple Cocoa (Objective-C) [9], wxPython [10], and Java [11]. Since every language has its pros and...languages using the criteria described above. Based on the developer’s limited experience and knowledge of Microsoft .NET and Apple Cocoa (Objective...became a tabbed panel within a separate window panel. Figure 9 depicts this evolution of the conceptual design. In Figure 9, the table column

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

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.

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

PubMed Central

Buerstedde, Jean-Marie; Prill, Florian

2001-01-01

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

Monitoring and Acquisition Real-time System (MARS)

NASA Technical Reports Server (NTRS)

Holland, Corbin

2013-01-01

MARS is a graphical user interface (GUI) written in MATLAB and Java, allowing the user to configure and control the Scalable Parallel Architecture for Real-Time Acquisition and Analysis (SPARTAA) data acquisition system. SPARTAA not only acquires data, but also allows for complex algorithms to be applied to the acquired data in real time. The MARS client allows the user to set up and configure all settings regarding the data channels attached to the system, as well as have complete control over starting and stopping data acquisition. It provides a unique "Test" programming environment, allowing the user to create tests consisting of a series of alarms, each of which contains any number of data channels. Each alarm is configured with a particular algorithm, determining the type of processing that will be applied on each data channel and tested against a defined threshold. Tests can be uploaded to SPARTAA, thereby teaching it how to process the data. The uniqueness of MARS is in its capability to be adaptable easily to many test configurations. MARS sends and receives protocols via TCP/IP, which allows for quick integration into almost any test environment. The use of MATLAB and Java as the programming languages allows for developers to integrate the software across multiple operating platforms.

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.

An Accessible User Interface for Geoscience and Programming

NASA Astrophysics Data System (ADS)

Sevre, E. O.; Lee, S.

2012-12-01

The goal of this research is to develop an interface that will simplify user interaction with software for scientists. The motivating factor of the research is to develop tools that assist scientists with limited motor skills with the efficient generation and use of software tools. Reliance on computers and programming is increasing in the world of geology, and it is increasingly important for geologists and geophysicists to have the computational resources to use advanced software and edit programs for their research. I have developed a prototype of a program to help geophysicists write programs using a simple interface that requires only simple single-mouse-clicks to input code. It is my goal to minimize the amount of typing necessary to create simple programs and scripts to increase accessibility for people with disabilities limiting fine motor skills. This interface can be adapted for various programming and scripting languages. Using this interface will simplify development of code for C/C++, Java, and GMT, and can be expanded to support any other text based programming language. The interface is designed around the concept of maximizing the amount of code that can be written using a minimum number of clicks and typing. The screen is split into two sections: a list of click-commands is on the left hand side, and a text area is on the right hand side. When the user clicks on a command on the left hand side the applicable code is automatically inserted at the insertion point in the text area. Currently in the C/C++ interface, there are commands for common code segments that are often used, such as for loops, comments, print statements, and structured code creation. The primary goal is to provide an interface that will work across many devices for developing code. A simple prototype has been developed for the iPad. Due to the limited number of devices that an iOS application can be used with, the code has been re-written in Java to run on a wider range of devices. Currently, the software works in a prototype mode, and it is our goal to further development to create software that can benefit a wide range of people working in geosciences, which will make code development practical and accessible for a wider audience of scientists. By using an interface like this, it reduces potential for errors by reusing known working code.

Parallel programming with Easy Java Simulations

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Pattern Analysis of El Nino and La Nina Phenomenon Based on Sea Surface Temperature (SST) and Rainfall Intensity using Oceanic Nino Index (ONI) in West Java Area

NASA Astrophysics Data System (ADS)

Prasetyo, Yudo; Nabilah, Farras

2017-12-01

Climate change occurs in 1998-2016 brings significant alteration in the earth surface. It is affects an extremely anomaly temperature such as El Nino and La Nina or mostly known as ENSO (El Nino Southern Oscillation). West Java is one of the regions in Indonesia that encounters the impact of this phenomenon. Climate change due to ENSO also affects food production and other commodities. In this research, processing data method is conducted using programming language to process SST data and rainfall data from 1998 to 2016. The data are sea surface temperature from NOAA satellite, SST Reynolds (Sea Surface Temperature) and daily rainfall temperature from TRMM satellite. Data examination is done using analysis of rainfall spatial pattern and sea surface temperature (SST) where is affected by El Nino and La Nina phenomenon. This research results distribution map of SST and rainfall for each season to find out the impacts of El Nino and La Nina around West Java. El Nino and La Nina in Java Sea are occurring every August to February. During El Nino, sea surface temperature is between 27°C - 28°C with average temperature on 27.71°C. Rainfall intensity is 1.0 mm/day - 2.0 mm/day and the average are 1.63 mm/day. During La Nina, sea surface temperature is between 29°C - 30°C with average temperature on 29.06°C. Rainfall intensity is 9.0 mm/day - 10 mm/day, and the average is 9.74 mm/day. The correlation between rainfall and SST is 0,413 which is expresses a fairly strong correlation between parameters. The conclusion is, during La Nina SST and rainfall increase. While during El Nino SST and rainfall decrease. Hopefully this research could be a guideline to plan disaster mitigation in West Java region that is related extreme climate change.

Application-Program-Installer Builder

NASA Technical Reports Server (NTRS)

Wolgast, Paul; Demore, Martha; Lowik, Paul

2007-01-01

A computer program builds application programming interfaces (APIs) and related software components for installing and uninstalling application programs in any of a variety of computers and operating systems that support the Java programming language in its binary form. This program is partly similar in function to commercial (e.g., Install-Shield) software. This program is intended to enable satisfaction of a quasi-industry-standard set of requirements for a set of APIs that would enable such installation and uninstallation and that would avoid the pitfalls that are commonly encountered during installation of software. The requirements include the following: 1) Properly detecting prerequisites to an application program before performing the installation; 2) Properly registering component requirements; 3) Correctly measuring the required hard-disk space, including accounting for prerequisite components that have already been installed; and 4) Correctly uninstalling an application program. Correct uninstallation includes (1) detecting whether any component of the program to be removed is required by another program, (2) not removing that component, and (3) deleting references to requirements of the to-be-removed program for components of other programs so that those components can be properly removed at a later time.

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

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.

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

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

A Telemetry Browser Built with Java Components

NASA Astrophysics Data System (ADS)

Poupart, E.

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

Programmed Instruction for Teaching Java: Consideration of Learn Unit Frequency and Rule-Test Performance

ERIC Educational Resources Information Center

Emurian, Henry H.

2007-01-01

At the beginning of a Java computer programming course, nine students in an undergraduate class and nine students in a graduate class completed a web-based programmed instruction tutoring system that taught a simple computer program. All students exited the tutor with an identical level of skill, at least as determined by the tutor's required…

Toward a Practical Type Theory for Recursive Modules

DTIC Science & Technology

2001-03-01

Carnegie Mellon University Pittsburgh, PA 15213 Abstract Module systems for languages with complex type systems, such as Standard ML, often lack the...Project: Advanced Languages for Systems Software”, ARPA Order No. C533, issued by ESC/ENS under Contract No. F19628-95-C-0050. The views and conclusions...power of a module system lies in the flexibility of its facility for expressing dependencies between modular components. Some languages (such as Java

Configuration Tool Prototype for the Trusted Computing Exemplar Project

DTIC Science & Technology

2009-12-01

languages were examined: Microsoft .NET [8], Apple Cocoa (Objective-C) [9], wxPython [10], and Java [11]. Since every language has its pros and...languages using the criteria described above. Based on the developer’s limited experience and knowledge of Microsoft .NET and Apple Cocoa (Objective...a tabbed panel within a separate window panel. Figure 9 depicts this evolution of the conceptual design. In Figure 9, the table column headers are

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

[Temperature Measurement with Bluetooth under Android Platform].

PubMed

Wang, Shuai; Shen, Hao; Luo, Changze

2015-03-01

To realize the real-time transmission of temperature data and display using the platform of intelligent mobile phone and bluetooth. Application of Arduino Uno R3 in temperature data acquisition of digital temperature sensor DS18B20 acquisition, through the HC-05 bluetooth transmits the data to the intelligent smart phone Android system, realizes transmission of temperature data. Using Java language to write applications program under Android development environment, can achieve real-time temperature data display, storage and drawing temperature fluctuations drawn graphics. Temperature sensor is experimentally tested to meet the body temperature measurement precision and accuracy. This paper can provide a reference for other smart phone mobile medical product development.

Security Behavior Observatory: Infrastructure for Long-term Monitoring of Client Machines

DTIC Science & Technology

2014-07-14

desired data. In Wmdows, this is most often a .NET language (e.g., C#, PowerShell), a command-line batch script, or Java . 3) Least privilege: To ensure...modules are written in Java , and thus should be easily-portable to any OS. B. Deployment There are several high-level requirements the SBO must meet...practically feasible with such solutions. Instead, one researcher with access to all the clients’ keys (stored in an isolated and secured MySQL database

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

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

1999-02-01

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

Platform-independent software for medical image processing on the Internet

NASA Astrophysics Data System (ADS)

Mancuso, Michael E.; Pathak, Sayan D.; Kim, Yongmin

1997-05-01

We have developed a software tool for image processing over the Internet. The tool is a general purpose, easy to use, flexible, platform independent image processing software package with functions most commonly used in medical image processing.It provides for processing of medical images located wither remotely on the Internet or locally. The software was written in Java - the new programming language developed by Sun Microsystems. It was compiled and tested using Microsoft's Visual Java 1.0 and Microsoft's Just in Time Compiler 1.00.6211. The software is simple and easy to use. In order to use the tool, the user needs to download the software from our site before he/she runs it using any Java interpreter, such as those supplied by Sun, Symantec, Borland or Microsoft. Future versions of the operating systems supplied by Sun, Microsoft, Apple, IBM, and others will include Java interpreters. The software is then able to access and process any image on the iNternet or on the local computer. Using a 512 X 512 X 8-bit image, a 3 X 3 convolution took 0.88 seconds on an Intel Pentium Pro PC running at 200 MHz with 64 Mbytes of memory. A window/level operation took 0.38 seconds while a 3 X 3 median filter took 0.71 seconds. These performance numbers demonstrate the feasibility of using this software interactively on desktop computes. Our software tool supports various image processing techniques commonly used in medical image processing and can run without the need of any specialized hardware. It can become an easily accessible resource over the Internet to promote the learning and of understanding image processing algorithms. Also, it could facilitate sharing of medical image databases and collaboration amongst researchers and clinicians, regardless of location.

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.

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

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

Charles A. Wemple; Joshua J. Cogliati

2005-04-01

A univel geometry, neutral particle Monte Carlo transport code, written entirely in the Java programming language, is under development for medical radiotherapy applications. The code uses ENDF-VI based continuous energy cross section data in a flexible XML format. Full neutron-photon coupling, including detailed photon production and photonuclear reactions, is included. Charged particle equilibrium is assumed within the patient model so that detailed transport of electrons produced by photon interactions may be neglected. External beam and internal distributed source descriptions for mixed neutron-photon sources are allowed. Flux and dose tallies are performed on a univel basis. A four-tap, shift-register-sequence random numbermore » generator is used. Initial verification and validation testing of the basic neutron transport routines is underway. The searchlight problem was chosen as a suitable first application because of the simplicity of the physical model. Results show excellent agreement with analytic solutions. Computation times for similar numbers of histories are comparable to other neutron MC codes written in C and FORTRAN.« less

SoyFN: a knowledge database of soybean functional networks.

PubMed

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

2014-01-01

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

Addressing Dynamic Issues of Program Model Checking

NASA Technical Reports Server (NTRS)

Lerda, Flavio; Visser, Willem

2001-01-01

Model checking real programs has recently become an active research area. Programs however exhibit two characteristics that make model checking difficult: the complexity of their state and the dynamic nature of many programs. Here we address both these issues within the context of the Java PathFinder (JPF) model checker. Firstly, we will show how the state of a Java program can be encoded efficiently and how this encoding can be exploited to improve model checking. Next we show how to use symmetry reductions to alleviate some of the problems introduced by the dynamic nature of Java programs. Lastly, we show how distributed model checking of a dynamic program can be achieved, and furthermore, how dynamic partitions of the state space can improve model checking. We support all our findings with results from applying these techniques within the JPF model checker.

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.

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.

SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

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

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…

An integrated domain specific language for post-processing and visualizing electrophysiological signals in Java.

PubMed

Strasser, T; Peters, T; Jagle, H; Zrenner, E; Wilke, R

2010-01-01

Electrophysiology of vision - especially the electroretinogram (ERG) - is used as a non-invasive way for functional testing of the visual system. The ERG is a combined electrical response generated by neural and non-neuronal cells in the retina in response to light stimulation. This response can be recorded and used for diagnosis of numerous disorders. For both clinical practice and clinical trials it is important to process those signals in an accurate and fast way and to provide the results as structured, consistent reports. Therefore, we developed a freely available and open-source framework in Java (http://www.eye.uni-tuebingen.de/project/idsI4sigproc). The framework is focused on an easy integration with existing applications. By leveraging well-established software patterns like pipes-and-filters and fluent interfaces as well as by designing the application programming interfaces (API) as an integrated domain specific language (DSL) the overall framework provides a smooth learning curve. Additionally, it already contains several processing methods and visualization features and can be extended easily by implementing the provided interfaces. In this way, not only can new processing methods be added but the framework can also be adopted for other areas of signal processing. This article describes in detail the structure and implementation of the framework and demonstrate its application through the software package used in clinical practice and clinical trials at the University Eye Hospital Tuebingen one of the largest departments in the field of visual electrophysiology in Europe.

Rubus: A compiler for seamless and extensible parallelism.

PubMed

Adnan, Muhammad; Aslam, Faisal; Nawaz, Zubair; Sarwar, Syed Mansoor

2017-01-01

Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming. To this end, languages like CUDA and OpenCL have been introduced, which can be used to write code with parallelism. The main shortcoming of these languages is that programmer needs to specify all the complex details manually in order to parallelize the code across multiple cores. Therefore, the code written in these languages is difficult to understand, debug and maintain. Furthermore, to parallelize legacy code can require rewriting a significant portion of code in CUDA or OpenCL, which can consume significant time and resources. Thus, the amount of parallelism achieved is proportional to the skills of the programmer and the time spent in code optimizations. This paper proposes a new open source compiler, Rubus, to achieve seamless parallelism. The Rubus compiler relieves the programmer from manually specifying the low-level details. It analyses and transforms a sequential program into a parallel program automatically, without any user intervention. This achieves massive speedup and better utilization of the underlying hardware without a programmer's expertise in parallel programming. For five different benchmarks, on average a speedup of 34.54 times has been achieved by Rubus as compared to Java on a basic GPU having only 96 cores. Whereas, for a matrix multiplication benchmark the average execution speedup of 84 times has been achieved by Rubus on the same GPU. Moreover, Rubus achieves this performance without drastically increasing the memory footprint of a program.

Rubus: A compiler for seamless and extensible parallelism

PubMed Central

Adnan, Muhammad; Aslam, Faisal; Sarwar, Syed Mansoor

2017-01-01

Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming. To this end, languages like CUDA and OpenCL have been introduced, which can be used to write code with parallelism. The main shortcoming of these languages is that programmer needs to specify all the complex details manually in order to parallelize the code across multiple cores. Therefore, the code written in these languages is difficult to understand, debug and maintain. Furthermore, to parallelize legacy code can require rewriting a significant portion of code in CUDA or OpenCL, which can consume significant time and resources. Thus, the amount of parallelism achieved is proportional to the skills of the programmer and the time spent in code optimizations. This paper proposes a new open source compiler, Rubus, to achieve seamless parallelism. The Rubus compiler relieves the programmer from manually specifying the low-level details. It analyses and transforms a sequential program into a parallel program automatically, without any user intervention. This achieves massive speedup and better utilization of the underlying hardware without a programmer’s expertise in parallel programming. For five different benchmarks, on average a speedup of 34.54 times has been achieved by Rubus as compared to Java on a basic GPU having only 96 cores. Whereas, for a matrix multiplication benchmark the average execution speedup of 84 times has been achieved by Rubus on the same GPU. Moreover, Rubus achieves this performance without drastically increasing the memory footprint of a program. PMID:29211758

Automating Security Protocol Analysis

DTIC Science & Technology

2004-03-01

language that allows easy representation of pattern interaction. Using CSP, Lowe tests whether a protocol achieves authentication. In the case of...only to correctly code whatever protocol they intend to evaluate. The tool, OCaml 3.04 [1], translates the protocol into Horn clauses and then...model protocol transactions. One example of automated modeling software is Maude [19]. Maude was the intended language for this research, but Java

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

NASA Astrophysics Data System (ADS)

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

2012-03-01

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

A Customized Drought Decision Support Tool for Hsinchu Science Park

NASA Astrophysics Data System (ADS)

Huang, Jung; Tien, Yu-Chuan; Lin, Hsuan-Te; Liu, Tzu-Ming; Tung, Ching-Pin

2016-04-01

Climate change creates more challenges for water resources management. Due to the lack of sufficient precipitation in Taiwan in fall of 2014, many cities and counties suffered from water shortage during early 2015. Many companies in Hsinchu Science Park were significantly influenced and realized that they need a decision support tool to help them managing water resources. Therefore, a customized computer program was developed, which is capable of predicting the future status of public water supply system and water storage of factories when the water rationing is announced by the government. This program presented in this study for drought decision support (DDSS) is a customized model for a semiconductor company in the Hsinchu Science Park. The DDSS is programmed in Java which is a platform-independent language. System requirements are any PC with the operating system above Windows XP and an installed Java SE Runtime Environment 7. The DDSS serves two main functions. First function is to predict the future storage of Baoshan Reservoir and Second Baoshan Reservoir, so to determine the time point of water use restriction in Hsinchu Science Park. Second function is to use the results to help the company to make decisions to trigger their response plans. The DDSS can conduct real-time scenario simulations calculating the possible storage of water tank for each factory with pre-implementation and post-implementation of those response plans. In addition, DDSS can create reports in Excel to help decision makers to compare results between different scenarios.

Using Multimedia Metadata to Improve Network Efficiency

DTIC Science & Technology

2012-09-01

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

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

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

2003-12-01

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

An Application of Artificial Intelligence to the Implementation of Electronic Commerce

NASA Astrophysics Data System (ADS)

Srivastava, Anoop Kumar

In this paper, we present an application of Artificial Intelligence (AI) to the implementation of Electronic Commerce. We provide a multi autonomous agent based framework. Our agent based architecture leads to flexible design of a spectrum of multiagent system (MAS) by distributing computation and by providing a unified interface to data and programs. Autonomous agents are intelligent enough and provide autonomy, simplicity of communication, computation, and a well developed semantics. The steps of design and implementation are discussed in depth, structure of Electronic Marketplace, an ontology, the agent model, and interaction pattern between agents is given. We have developed mechanisms for coordination between agents using a language, which is called Virtual Enterprise Modeling Language (VEML). VEML is a integration of Java and Knowledge Query and Manipulation Language (KQML). VEML provides application programmers with potential to globally develop different kinds of MAS based on their requirements and applications. We have implemented a multi autonomous agent based system called VE System. We demonstrate efficacy of our system by discussing experimental results and its salient features.

A Network Design Architecture for Distribution of Generic Scene Graphs

DTIC Science & Technology

1999-09-01

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

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…

Factors to Consider When Implementing Automated Software Testing

DTIC Science & Technology

2016-11-10

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

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

PubMed

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

2017-10-01

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

Networked vision system using a Prolog controller

NASA Astrophysics Data System (ADS)

Batchelor, B. G.; Caton, S. J.; Chatburn, L. T.; Crowther, R. A.; Miller, J. W. V.

2005-11-01

Prolog offers a very different style of programming compared to conventional languages; it can define object properties and abstract relationships in a way that Java, C, C++, etc. find awkward. In an accompanying paper, the authors describe how a distributed web-based vision systems can be built using elements that may even be located on different continents. One particular system of this general type is described here. The top-level controller is a Prolog program, which operates one, or more, image processing engines. This type of function is natural to Prolog, since it is able to reason logically using symbolic (non-numeric) data. Although Prolog is not suitable for programming image processing functions directly, it is ideal for analysing the results derived by an image processor. This article describes the implementation of two systems, in which a Prolog program controls several image processing engines, a simple robot, a pneumatic pick-and-place arm), LED illumination modules and a various mains-powered devices.

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

NASA Astrophysics Data System (ADS)

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

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

OHD/HL - National Weather Hydrology Laboratory

Science.gov Websites

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

Context-Based Mobile Security Enclave

DTIC Science & Technology

2012-09-01

29  c.  Change IMSI .............................30  d.  Change CellID ...........................31  e.  Change Geolocation ...Assisted Global Positioning System ADB Android Debugger API Application Programming Interface APK Android Application Package BSC Base Station...Programming Interfaces ( APIs ), which use Java compatible libraries based on Apache Harmony (an open source Java implementation developed by the Apache

Visualized kinematics code for two-body nuclear reactions

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

2017-11-01

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for online validation of Monte Carlo event samples through a web interface.

Agent-based paradigm for integration of interactive cable television operations and business support systems

NASA Astrophysics Data System (ADS)

Wattawa, Scott

1995-11-01

Offering interactive services and data in a hybrid fiber/coax cable system requires the coordination of a host of operations and business support systems. New service offerings and network growth and evolution create never-ending changes in the network infrastructure. Agent-based enterprise models provide a flexible mechanism for systems integration of service and support systems. Agent models also provide a mechanism to decouple interactive services from network architecture. By using the Java programming language, agents may be made safe, portable, and intelligent. This paper investigates the application of the Object Management Group's Common Object Request Brokering Architecture to the integration of a multiple services metropolitan area network.

Representing metabolic pathway information: an object-oriented approach.

PubMed

Ellis, L B; Speedie, S M; McLeish, R

1998-01-01

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.

An Object-Oriented Network-Centric Software Architecture for Physical Computing

NASA Astrophysics Data System (ADS)

Palmer, Richard

1997-08-01

Recent developments in object-oriented computer languages and infrastructure such as the Internet, Web browsers, and the like provide an opportunity to define a more productive computational environment for scientific programming that is based more closely on the underlying mathematics describing physics than traditional programming languages such as FORTRAN or C++. In this talk I describe an object-oriented software architecture for representing physical problems that includes classes for such common mathematical objects as geometry, boundary conditions, partial differential and integral equations, discretization and numerical solution methods, etc. In practice, a scientific program written using this architecture looks remarkably like the mathematics used to understand the problem, is typically an order of magnitude smaller than traditional FORTRAN or C++ codes, and hence easier to understand, debug, describe, etc. All objects in this architecture are ``network-enabled,'' which means that components of a software solution to a physical problem can be transparently loaded from anywhere on the Internet or other global network. The architecture is expressed as an ``API,'' or application programmers interface specification, with reference embeddings in Java, Python, and C++. A C++ class library for an early version of this API has been implemented for machines ranging from PC's to the IBM SP2, meaning that phidentical codes run on all architectures.

EUMIS - an open portal framework for interoperable marine environmental services

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

Southeast Asia Report

DTIC Science & Technology

1987-05-05

With NASA 13 New Gas Find 14 Transmigration From Central Java 14 Transmigration From West Java 14 Bali’s Rice Fields Decreasing 14 Trade Surplus...Mar 87 p A2] /9274 RESEARCH PROGRAM WITH NASA —Indonesia is still hoping for the continuation of the outer space research program by Dr Pratiwi...Sudharmono under NASA program, Tourist. Post, and Telecommunications Minister Akhmad Tahir said in Jakarta yesterday. The minister said he was still

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

PubMed

Lindenbaum, Pierre; Redon, Richard

2018-04-01

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

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.

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

NASA Technical Reports Server (NTRS)

Deen, Robert G.; Levoe, Steven R.

2011-01-01

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

A Sociolinguistics Study on the Use of the Javanese Language in the Learning Process in Primary Schools in Surakarta, Central Java, Indonesia

ERIC Educational Resources Information Center

Saddhono, Kundharu; Rohmadi, Muhammad

2014-01-01

This study aims at describing the use of language at primary schools grade 1, 2, and 3 in Surakarta. The study belongs to descriptive qualitative research. It emphasizes in a note which depict real situation to support data presentation. Content analysis is used as research methodology. It analyzes the research result of the observed speech event.…

Visualization Development of the Ballistic Threat Geospatial Optimization

DTIC Science & Technology

2015-07-01

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

Simulating Operations at a Spaceport

NASA Technical Reports Server (NTRS)

Nevins, Michael R.

2007-01-01

SPACESIM is a computer program for detailed simulation of operations at a spaceport. SPACESIM is being developed to greatly improve existing spaceports and to aid in designing, building, and operating future spaceports, given that there is a worldwide trend in spaceport operations from very expensive, research- oriented launches to more frequent commercial launches. From an operational perspective, future spaceports are expected to resemble current airports and seaports, for which it is necessary to resolve issues of safety, security, efficient movement of machinery and people, cost effectiveness, timeliness, and maximizing effectiveness in utilization of resources. Simulations can be performed, for example, to (1) simultaneously analyze launches of reusable and expendable rockets and identify bottlenecks arising from competition for limited resources or (2) perform what-if scenario analyses to identify optimal scenarios prior to making large capital investments. SPACESIM includes an object-oriented discrete-event-simulation engine. (Discrete- event simulation has been used to assess processes at modern seaports.) The simulation engine is built upon the Java programming language for maximum portability. Extensible Markup Language (XML) is used for storage of data to enable industry-standard interchange of data with other software. A graphical user interface facilitates creation of scenarios and analysis of data.

Cache and energy efficient algorithms for Nussinov's RNA Folding.

PubMed

Zhao, Chunchun; Sahni, Sartaj

2017-12-06

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.

[The therapeutic drug monitoring network server of tacrolimus for Chinese renal transplant patients].

PubMed

Deng, Chen-Hui; Zhang, Guan-Min; Bi, Shan-Shan; Zhou, Tian-Yan; Lu, Wei

2011-07-01

This study is to develop a therapeutic drug monitoring (TDM) network server of tacrolimus for Chinese renal transplant patients, which can facilitate doctor to manage patients' information and provide three levels of predictions. Database management system MySQL was employed to build and manage the database of patients and doctors' information, and hypertext mark-up language (HTML) and Java server pages (JSP) technology were employed to construct network server for database management. Based on the population pharmacokinetic model of tacrolimus for Chinese renal transplant patients, above program languages were used to construct the population prediction and subpopulation prediction modules. Based on Bayesian principle and maximization of the posterior probability function, an objective function was established, and minimized by an optimization algorithm to estimate patient's individual pharmacokinetic parameters. It is proved that the network server has the basic functions for database management and three levels of prediction to aid doctor to optimize the regimen of tacrolimus for Chinese renal transplant patients.

TOMML: A Rule Language for Structured Data

NASA Astrophysics Data System (ADS)

Cirstea, Horatiu; Moreau, Pierre-Etienne; Reilles, Antoine

We present the TOM language that extends JAVA with the purpose of providing high level constructs inspired by the rewriting community. TOM bridges thus the gap between a general purpose language and high level specifications based on rewriting. This approach was motivated by the promotion of rule based techniques and their integration in large scale applications. Powerful matching capabilities along with a rich strategy language are among TOM's strong features that make it easy to use and competitive with respect to other rule based languages. TOM is thus a natural choice for querying and transforming structured data and in particular XML documents [1]. We present here its main XML oriented features and illustrate its use on several examples.

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

NASA Astrophysics Data System (ADS)

Oxburgh, Stephen; Tyc, Tomáš; Courtial, Johannes

2014-03-01

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

The Resource, Spring 2002

DTIC Science & Technology

2002-01-01

wrappers to other widely used languages, namely TCL/TK, Java, and Python . VTK is very powerful and covers polygonal models and image processing classes and...follows: � Large Data Visualization and Rendering � Information Visualization for Beginners � Rendering and Visualization in Parallel Environments

Designing for the Next Web.

ERIC Educational Resources Information Center

Bremser, Wayne

1998-01-01

Discusses how to choose from the available interactive graphic-design possibilities for the World Wide Web. Compatibility and appropriateness are discussed; and DHTML (Dynamic Hypertext Markup Language), Java, CSS (Cascading Style Sheets), plug-ins, ActiveX, and Push and channel technologies are described. (LRW)

Multidisciplinary High-Fidelity Analysis and Optimization of Aerospace Vehicles. Part 1; Formulation

NASA Technical Reports Server (NTRS)

Walsh, J. L.; Townsend, J. C.; Salas, A. O.; Samareh, J. A.; Mukhopadhyay, V.; Barthelemy, J.-F.

2000-01-01

An objective of the High Performance Computing and Communication Program at the NASA Langley Research Center is to demonstrate multidisciplinary shape and sizing optimization of a complete aerospace vehicle configuration by using high-fidelity, finite element structural analysis and computational fluid dynamics aerodynamic analysis in a distributed, heterogeneous computing environment that includes high performance parallel computing. A software system has been designed and implemented to integrate a set of existing discipline analysis codes, some of them computationally intensive, into a distributed computational environment for the design of a highspeed civil transport configuration. The paper describes the engineering aspects of formulating the optimization by integrating these analysis codes and associated interface codes into the system. The discipline codes are integrated by using the Java programming language and a Common Object Request Broker Architecture (CORBA) compliant software product. A companion paper presents currently available results.

Multidisciplinary High-Fidelity Analysis and Optimization of Aerospace Vehicles. Part 2; Preliminary Results

NASA Technical Reports Server (NTRS)

Walsh, J. L.; Weston, R. P.; Samareh, J. A.; Mason, B. H.; Green, L. L.; Biedron, R. T.

2000-01-01

An objective of the High Performance Computing and Communication Program at the NASA Langley Research Center is to demonstrate multidisciplinary shape and sizing optimization of a complete aerospace vehicle configuration by using high-fidelity finite-element structural analysis and computational fluid dynamics aerodynamic analysis in a distributed, heterogeneous computing environment that includes high performance parallel computing. A software system has been designed and implemented to integrate a set of existing discipline analysis codes, some of them computationally intensive, into a distributed computational environment for the design of a high-speed civil transport configuration. The paper describes both the preliminary results from implementing and validating the multidisciplinary analysis and the results from an aerodynamic optimization. The discipline codes are integrated by using the Java programming language and a Common Object Request Broker Architecture compliant software product. A companion paper describes the formulation of the multidisciplinary analysis and optimization system.

Using XML and Java Technologies for Astronomical Instrument Control

NASA Technical Reports Server (NTRS)

Ames, Troy; Case, Lynne; Powers, Edward I. (Technical Monitor)

2001-01-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center, under the Instrument Remote Control (IRC) project, is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is that the software is driven by an instrument description, written using the Instrument Markup Language (IML), a dialect of XML. IML is used to describe the command sets and command formats of the instrument, communication mechanisms, format of the data coming from the instrument, and characteristics of the graphical user interface to control and monitor the instrument. The IRC framework allows the users to define a data analysis pipeline which converts data coming out of the instrument. The data can be used in visualizations in order for the user to assess the data in real-time, if necessary. The data analysis pipeline algorithms can be supplied by the user in a variety of forms or programming languages. Although the current integration effort is targeted for the High-resolution Airborne Wideband Camera (HAWC) and the Submillimeter and Far Infrared Experiment (SAFIRE), first-light instruments of the Stratospheric Observatory for Infrared Astronomy (SOFIA), the framework is designed to be generic and extensible so that it can be applied to any instrument. Plans are underway to test the framework with other types of instruments, such as remote sensing earth science instruments.

Enhanced Data Authentication System v. 2.0

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

Thomas, Maikael A.; Tolsch, Brandon Jeffrey; Schwartz, Steven Robert

EDAS is a system, comprised on hardware and software, that plugs in to an existing data stream, and branches all data for transmission to a secondary observer computer. The EDAS Junction box, which inserts into the data stream, has Java software that forms these data into packets, digitally signs, encrypts, and sends these packets to a safeguards inspector computer. Further, there is a second Java program running on the secondary observer computer that receives data from the EDAS Junction Box to decrypt, authenticate, and store incoming packets. Also, there is a stand-alone Java program that is used to configure themore » EDAS Junction Box.« less

Program Instrumentation and Trace Analysis

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Conversion of the Aeronautics Interactive Workstation

NASA Technical Reports Server (NTRS)

Riveras, Nykkita L.

2004-01-01

This summer I am working in the Educational Programs Office. My task is to convert the Aeronautics Interactive Workstation from a Macintosh (Mac) platform to a Personal Computer (PC) platform. The Aeronautics Interactive Workstation is a workstation in the Aerospace Educational Laboratory (AEL), which is one of the three components of the Science, Engineering, Mathematics, and Aerospace Academy (SEMAA). The AEL is a state-of-the-art, electronically enhanced, computerized classroom that puts cutting-edge technology at the fingertips of participating students. It provides a unique learning experience regarding aerospace technology that features activities equipped with aerospace hardware and software that model real-world challenges. The Aeronautics Interactive Workstation, in particular, offers a variety of activities pertaining to the history of aeronautics. When the Aeronautics Interactive Workstation was first implemented into the AEL it was designed with Macromedia Director 4 for a Mac. Today it is being converted to Macromedia DirectorMX2004 for a PC. Macromedia Director is the proven multimedia tool for building rich content and applications for CDs, DVDs, kiosks, and the Internet. It handles the widest variety of media and offers powerful features for building rich content that delivers red results, integrating interactive audio, video, bitmaps, vectors, text, fonts, and more. Macromedia Director currently offers two programmingkripting languages: Lingo, which is Director's own programmingkripting language and JavaScript. In the workstation, Lingo is used in the programming/scripting since it was the only language in use when the workstation was created. Since the workstation was created with an older version of Macromedia Director it hosted significantly different programming/scripting protocols. In order to successfully accomplish my task, the final product required correction of Xtra and programming/scripting errors. I also had to convert the Mac platform file extensions into compatible file extensions for a PC.

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.

Using Runtime Analysis to Guide Model Checking of Java Programs

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Norvig, Peter (Technical Monitor)

2001-01-01

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

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

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

Using XML and Java for Astronomical Instrument Control

NASA Astrophysics Data System (ADS)

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

1999-12-01

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

Cross-platform validation and analysis environment for particle physics

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

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for onlinemore » validation of Monte Carlo event samples through a web interface.« less

Optimizing Aspect-Oriented Mechanisms for Embedded Applications

NASA Astrophysics Data System (ADS)

Hundt, Christine; Stöhr, Daniel; Glesner, Sabine

As applications for small embedded mobile devices are getting larger and more complex, it becomes inevitable to adopt more advanced software engineering methods from the field of desktop application development. Aspect-oriented programming (AOP) is a promising approach due to its advanced modularization capabilities. However, existing AOP languages tend to add a substantial overhead in both execution time and code size which restricts their practicality for small devices with limited resources. In this paper, we present optimizations for aspect-oriented mechanisms at the level of the virtual machine. Our experiments show that these optimizations yield a considerable performance gain along with a reduction of the code size. Thus, our optimizations establish the base for using advanced aspect-oriented modularization techniques for developing Java applications on small embedded devices.

Protyping machine vision software on the World Wide Web

NASA Astrophysics Data System (ADS)

Karantalis, George; Batchelor, Bruce G.

1998-10-01

Interactive image processing is a proven technique for analyzing industrial vision applications and building prototype systems. Several of the previous implementations have used dedicated hardware to perform the image processing, with a top layer of software providing a convenient user interface. More recently, self-contained software packages have been devised and these run on a standard computer. The advent of the Java programming language has made it possible to write platform-independent software, operating over the Internet, or a company-wide Intranet. Thus, there arises the possibility of designing at least some shop-floor inspection/control systems, without the vision engineer ever entering the factories where they will be used. It successful, this project will have a major impact on the productivity of vision systems designers.

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

NASA Astrophysics Data System (ADS)

Choi, Hyungjeen; Ryu, Jeha; Lee, Chansu

2004-03-01

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

JavaScript Access to DICOM Network and Objects in Web Browser.

PubMed

Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

2017-10-01

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

Wildfires - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Bosnian (bosanski) Modern Standard Arabic (Arabic dialect) (العربية الفصحى, عربي فصيح) Somali (Af- ...

Tornadoes - Multiple Languages

MedlinePlus

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Mixed-Initiative COA Critic Advisors (MICCA)

DTIC Science & Technology

2013-02-01

This java method can modify these strings to provide additional transformations that can’t be expressed in the property language.  Datatype ...vertical bar separator into one string. Instead, setting datatype to “nodeset” for a variable will cause multiple predicates to be generated for

User Evaluation of Biospice

DTIC Science & Technology

2006-10-01

pipe facilities). The Dashboard is based on the NetBeans application platform, a Java-based tool kit. Tools may be written in any language...manner loosely analogous to UNIX shells (especially with respect to UNIX pipe facilities). The Dashboard is based on the NetBeans application

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

PubMed

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

2011-01-01

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

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

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

Java PathExplorer: A Runtime Verification Tool

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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.

Obsessive-Compulsive Disorder - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Russian (Русский) Somali (Af-Soomaali ) Spanish (español) HealthReach resources will open in a new window. Russian (Русский) Expand Section Obsessive Compulsive Disorder (OCD) (An ...

Winter Weather Emergencies - Multiple Languages

MedlinePlus

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SpecPad: device-independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology.

PubMed

Guigas, Bruno

2017-09-01

SpecPad is a new device-independent software program for the visualization and processing of one-dimensional and two-dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device-independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off-line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR-related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Incorporating Speech Recognition into a Natural User Interface

NASA Technical Reports Server (NTRS)

Chapa, Nicholas

2017-01-01

The Augmented/ Virtual Reality (AVR) Lab has been working to study the applicability of recent virtual and augmented reality hardware and software to KSC operations. This includes the Oculus Rift, HTC Vive, Microsoft HoloLens, and Unity game engine. My project in this lab is to integrate voice recognition and voice commands into an easy to modify system that can be added to an existing portion of a Natural User Interface (NUI). A NUI is an intuitive and simple to use interface incorporating visual, touch, and speech recognition. The inclusion of speech recognition capability will allow users to perform actions or make inquiries using only their voice. The simplicity of needing only to speak to control an on-screen object or enact some digital action means that any user can quickly become accustomed to using this system. Multiple programs were tested for use in a speech command and recognition system. Sphinx4 translates speech to text using a Hidden Markov Model (HMM) based Language Model, an Acoustic Model, and a word Dictionary running on Java. PocketSphinx had similar functionality to Sphinx4 but instead ran on C. However, neither of these programs were ideal as building a Java or C wrapper slowed performance. The most ideal speech recognition system tested was the Unity Engine Grammar Recognizer. A Context Free Grammar (CFG) structure is written in an XML file to specify the structure of phrases and words that will be recognized by Unity Grammar Recognizer. Using Speech Recognition Grammar Specification (SRGS) 1.0 makes modifying the recognized combinations of words and phrases very simple and quick to do. With SRGS 1.0, semantic information can also be added to the XML file, which allows for even more control over how spoken words and phrases are interpreted by Unity. Additionally, using a CFG with SRGS 1.0 produces a Finite State Machine (FSM) functionality limiting the potential for incorrectly heard words or phrases. The purpose of my project was to investigate options for a Speech Recognition System. To that end I attempted to integrate Sphinx4 into a user interface. Sphinx4 had great accuracy and is the only free program able to perform offline speech dictation. However it had a limited dictionary of words that could be recognized, single syllable words were almost impossible for it to hear, and since it ran on Java it could not be integrated into the Unity based NUI. PocketSphinx ran much faster than Sphinx4 which would've made it ideal as a plugin to the Unity NUI, unfortunately creating a C# wrapper for the C code made the program unusable with Unity due to the wrapper slowing code execution and class files becoming unreachable. Unity Grammar Recognizer is the ideal speech recognition interface, it is flexible in recognizing multiple variations of the same command. It is also the most accurate program in recognizing speech due to using an XML grammar to specify speech structure instead of relying solely on a Dictionary and Language model. The Unity Grammar Recognizer will be used with the NUI for these reasons as well as being written in C# which further simplifies the incorporation.

RDF-GL: A SPARQL-Based Graphical Query Language for RDF

NASA Astrophysics Data System (ADS)

Hogenboom, Frederik; Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

This chapter presents RDF-GL, a graphical query language (GQL) for RDF. The GQL is based on the textual query language SPARQL and mainly focuses on SPARQL SELECT queries. The advantage of a GQL over textual query languages is that complexity is hidden through the use of graphical symbols. RDF-GL is supported by a Java-based editor, SPARQLinG, which is presented as well. The editor does not only allow for RDF-GL query creation, but also converts RDF-GL queries to SPARQL queries and is able to subsequently execute these. Experiments show that using the GQL in combination with the editor makes RDF querying more accessible for end users.

Computing Programs for Determining Traffic Flows from Roundabouts

NASA Astrophysics Data System (ADS)

Boroiu, A. A.; Tabacu, I.; Ene, A.; Neagu, E.; Boroiu, A.

2017-10-01

For modelling road traffic at the level of a road network it is necessary to specify the flows of all traffic currents at each intersection. These data can be obtained by direct measurements at the traffic light intersections, but in the case of a roundabout this is not possible directly and the literature as well as the traffic modelling software doesn’t offer ways to solve this issue. Two sets of formulas are proposed by which all traffic flows from the roundabouts with 3 or 4 arms are calculated based on the streams that can be measured. The objective of this paper is to develop computational programs to operate with these formulas. For each of the two sets of analytical relations, a computational program was developed in the Java operating language. The obtained results fully confirm the applicability of the calculation programs. The final stage for capitalizing these programs will be to make them web pages in HTML format, so that they can be accessed and used on the Internet. The achievements presented in this paper are an important step to provide a necessary tool for traffic modelling because these computational programs can be easily integrated into specialized software.

A Software Engineering Paradigm for Quick-turnaround Earth Science Data Projects

NASA Astrophysics Data System (ADS)

Moore, K.

2016-12-01

As is generally the case with applied sciences professional and educational programs, the participants of such programs can come from a variety of technical backgrounds. In the NASA DEVELOP National Program, the participants constitute an interdisciplinary set of backgrounds, with varying levels of experience with computer programming. DEVELOP makes use of geographically explicit data sets, and it is necessary to use geographic information systems and geospatial image processing environments. As data sets cover longer time spans and include more complex sets of parameters, automation is becoming an increasingly prevalent feature. Though platforms such as ArcGIS, ERDAS Imagine, and ENVI facilitate the batch-processing of geospatial imagery, these environments are naturally constricting to the user in that they limit him or her to the tools that are available. Users must then turn to "homemade" scripting in more traditional programming languages such as Python, JavaScript, or R, to automate workflows. However, in the context of quick-turnaround projects like those in DEVELOP, the programming learning curve may be prohibitively steep. In this work, we consider how to best design a software development paradigm that addresses two major constants: an arbitrarily experienced programmer and quick-turnaround project timelines.

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.

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

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

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.

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

PubMed

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

2014-03-07

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

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

PubMed Central

2014-01-01

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

Computer Literacy and Non-IS Majors

ERIC Educational Resources Information Center

Thomas, Jennifer D. E.; Blackwood, Martina

2010-01-01

This paper presents an investigation of non-Information Systems (IS) major's perceptions and performance when enrolled in a required introductory Computer Information Systems course. Students of various academic backgrounds were taught Excel, Hypertext Markup Language (HTML), JavaScript and computer literacy in a 14-week introductory course, in…

Heat Illness - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Bosnian (bosanski) Haitian Creole (Kreyol ayisyen) Modern Standard Arabic (Arabic dialect) (العربية الفصحى, عربي فصيح) Somali (Af- ...

Quitting Smoking - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Bengali (Bangla / বাংলা) Bosnian (bosanski) Chinese, ... HealthReach resources will open in a new window. Arabic (العربية) Expand Section Avoiding Weight Gain When Quitting ...

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

Support for User Interfaces for Distributed Systems

NASA Technical Reports Server (NTRS)

Eychaner, Glenn; Niessner, Albert

2005-01-01

An extensible Java(TradeMark) software framework supports the construction and operation of graphical user interfaces (GUIs) for distributed computing systems typified by ground control systems that send commands to, and receive telemetric data from, spacecraft. Heretofore, such GUIs have been custom built for each new system at considerable expense. In contrast, the present framework affords generic capabilities that can be shared by different distributed systems. Dynamic class loading, reflection, and other run-time capabilities of the Java language and JavaBeans component architecture enable the creation of a GUI for each new distributed computing system with a minimum of custom effort. By use of this framework, GUI components in control panels and menus can send commands to a particular distributed system with a minimum of system-specific code. The framework receives, decodes, processes, and displays telemetry data; custom telemetry data handling can be added for a particular system. The framework supports saving and later restoration of users configurations of control panels and telemetry displays with a minimum of effort in writing system-specific code. GUIs constructed within this framework can be deployed in any operating system with a Java run-time environment, without recompilation or code changes.

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

PubMed Central

Pernstich, K. P.

2012-01-01

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

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

PubMed

Pernstich, K P

2012-01-01

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

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.

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.

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

PubMed

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

2013-03-01

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

Building a High Performance Metadata Broker using Clojure, NoSQL and Message Queues

NASA Astrophysics Data System (ADS)

Truslove, I.; Reed, S.

2013-12-01

In practice, Earth and Space Science Informatics often relies on getting more done with less: fewer hardware resources, less IT staff, fewer lines of code. As a capacity-building exercise focused on rapid development of high-performance geoinformatics software, the National Snow and Ice Data Center (NSIDC) built a prototype metadata brokering system using a new JVM language, modern database engines and virtualized or cloud computing resources. The metadata brokering system was developed with the overarching goals of (i) demonstrating a technically viable product with as little development effort as possible, (ii) using very new yet very popular tools and technologies in order to get the most value from the least legacy-encumbered code bases, and (iii) being a high-performance system by using scalable subcomponents, and implementation patterns typically used in web architectures. We implemented the system using the Clojure programming language (an interactive, dynamic, Lisp-like JVM language), Redis (a fast in-memory key-value store) as both the data store for original XML metadata content and as the provider for the message queueing service, and ElasticSearch for its search and indexing capabilities to generate search results. On evaluating the results of the prototyping process, we believe that the technical choices did in fact allow us to do more for less, due to the expressive nature of the Clojure programming language and its easy interoperability with Java libraries, and the successful reuse or re-application of high performance products or designs. This presentation will describe the architecture of the metadata brokering system, cover the tools and techniques used, and describe lessons learned, conclusions, and potential next steps.

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.

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.

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 Domain Description Language for Data Processing

NASA Technical Reports Server (NTRS)

Golden, Keith

2003-01-01

We discuss an application of planning to data processing, a planning problem which poses unique challenges for domain description languages. We discuss these challenges and why the current PDDL standard does not meet them. We discuss DPADL (Data Processing Action Description Language), a language for describing planning domains that involve data processing. DPADL is a declarative, object-oriented language that supports constraints and embedded Java code, object creation and copying, explicit inputs and outputs for actions, and metadata descriptions of existing and desired data. DPADL is supported by the IMAGEbot system, which we are using to provide automation for an ecological forecasting application. We compare DPADL to PDDL and discuss changes that could be made to PDDL to make it more suitable for representing planning domains that involve data processing actions.

Modelling and Implementation of Catalogue Cards Using FreeMarker

ERIC Educational Resources Information Center

Radjenovic, Jelen; Milosavljevic, Branko; Surla, Dusan

2009-01-01

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

Tuberculosis - Multiple Languages

MedlinePlus

... this page, please enable JavaScript. Amharic (Amarɨñña / አማርኛ ) Arabic (العربية) Bosnian (bosanski) Cape Verdean Creole (Kabuverdianu) Chinese, ... Amharic) Bilingual PDF Massachusetts Department of Public Health Arabic (العربية) Expand Section Home Respiratory Precautions for Patients ...

Immunization - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Bengali (Bangla / বাংলা) Chinese, Simplified (Mandarin ... HealthReach resources will open in a new window. Arabic (العربية) Expand Section Global TravEpiNet (GTEN) Travelers' Rapid ...

Leg Injuries and Disorders - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Chinese, Simplified (Mandarin dialect) (简体中文) Chinese, Traditional ( ... HealthReach resources will open in a new window. Arabic (العربية) Expand Section Active Leg Range of Motion - ...

"Is English Also the Place Where I Belong?": Linguistic Biographies and Expanding Communicative Repertoires in Central Java

ERIC Educational Resources Information Center

Zentz, Lauren

2015-01-01

This article employs the term "communicative repertoire" in order to highlight that when one learns any new "language", one introduces new communicative resources into a unified communicative repertoire. As repertoires represent such singular "grammars" in individuals' minds, learned communicative resources can…

A Heuristics Approach for Classroom Scheduling Using Genetic Algorithm Technique

NASA Astrophysics Data System (ADS)

Ahmad, Izah R.; Sufahani, Suliadi; Ali, Maselan; Razali, Siti N. A. M.

2018-04-01

Reshuffling and arranging classroom based on the capacity of the audience, complete facilities, lecturing time and many more may lead to a complexity of classroom scheduling. While trying to enhance the productivity in classroom planning, this paper proposes a heuristic approach for timetabling optimization. A new algorithm was produced to take care of the timetabling problem in a university. The proposed of heuristics approach will prompt a superior utilization of the accessible classroom space for a given time table of courses at the university. Genetic Algorithm through Java programming languages were used in this study and aims at reducing the conflicts and optimizes the fitness. The algorithm considered the quantity of students in each class, class time, class size, time accessibility in each class and lecturer who in charge of the classes.

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

NASA Astrophysics Data System (ADS)

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

2007-07-01

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

A web-based information system for management and analysis of patient data after refractive eye surgery.

PubMed

Zuberbuhler, Bruno; Galloway, Peter; Reddy, Aravind; Saldana, Manuel; Gale, Richard

2007-12-01

The aim was to develop a software tool for refractive surgeons using a standard user-friendly web-based interface, providing the user with a secure environment to protect large volumes of patient data. The software application was named "Internet-based refractive analysis" (IBRA), and was programmed with the computer languages PHP, HTML and JavaScript, attached to the opensource MySQL database. IBRA facilitated internationally accepted presentation methods including the stability chart, the predictability chart and the safety chart; it was able to perform vector analysis for the course of a single patient or for group data. With the integrated nomogram calculation, treatment could be customised to reduce the postoperative refractive error. Multicenter functions permitted quality-control comparisons between different surgeons and laser units.

Contraceptive use in Indonesia: a history of the programme and the characteristics of users.

PubMed

Samosir, O B

1992-12-01

In Indonesia, President Suharto instituted a population policy in the late 1960s to achieve national development goals. The government also introduced education, health, and economic-oriented development programs. Since then, it has continued to provide political, legal, moral, administrative, and financial support to the national family planning (FP) program. The program was first introduced in the most populous provinces of Java and Bali. It eventually spread to the remaining provinces. It has 3 component programs to achieve national population goals: on extension program (IEC activities and free contraceptives), program maintenance (community-based distribution), and an institutionalization program (integrated programs, population education, and recruiting community leaders). In 1987, the FP Self-Reliance and Blue Circle Campaign programs began to turn FP responsibilities over to communities and individuals. Between 1967 and 1981, the total fertility rate (TFR) fell from 5.61 to 4.06. The greatest fertility declines were in Bali (48.11%) and North Sulawesi (47.2%). An analysis of 1987 National Indonesian Contraceptive Prevalence Survey data shows that the TFR fell from 4.3 to 3.5 (23%) between 1984 and 1987. Between 1980 and 1987, the contraceptive use rate rose from 27 to 48%. Java and Bali had the highest contraceptive user rates. Large family size had a significant positive effect on contraceptive use. Educated women were more likely to use contraceptives than uneducated women, especially in Outer Java-Bali regions. In some regions, the husband's education affected contraceptive use. Muslim women were less likely to use contraceptives than other women in Bali and Outer Java-Bali I. Even though urban women had the highest use rates, the FP program was more successful in rural areas. The success of the national FP program and other development programs accounted for the fertility decline as well as the decline in mortality, resulting in a fall in the population growth rate.

A JAVA-based multimedia tool for clinical practice guidelines.

PubMed

Maojo, V; Herrero, C; Valenzuela, F; Crespo, J; Lazaro, P; Pazos, A

1997-01-01

We have developed a specific language for the representation of Clinical Practice Guidelines (CPGs) and Windows C++ and platform independent JAVA applications for multimedia presentation and edition of electronically stored CPGs. This approach facilitates translation of guidelines and protocols from paper to computer-based flowchart representations. Users can navigate through the algorithm with a friendly user interface and access related multimedia information within the context of each clinical problem. CPGs can be stored in a computer server and distributed over the World Wide Web, facilitating dissemination, local adaptation, and use as a reference element in medical care. We have chosen the Agency for Health Care and Policy Research's heart failure guideline to demonstrate the capabilities of our tool.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Small Boat and Swarm Defense: A Gap Study

DTIC Science & Technology

2008-09-01

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

Development of a software and hardware system for monitoring the air cleaning process using a cyclone-separator

NASA Astrophysics Data System (ADS)

Nicolaeva, B. K.; Borisov, A. P.; Zlochevskiy, V. L.

2017-08-01

The article is devoted to the development of a hardware-software complex for monitoring and controlling the process of air purification by means of a cyclone-separator. The hardware of this complex is the Arduino platform, to which are connected pressure sensors, air velocities, dustmeters, which allow monitoring of the main parameters of the cyclone-separator. Also, a frequency converter was developed to regulate the rotation speed of an asynchronous motor necessary to correct the flow rate, the control signals of which come with Arduino. The program part of the complex is written in the form of a web application in the programming language JavaScript and inserts into CSS and HTML for the user interface. This program allows you to receive data from sensors, build dependencies in real time and control the speed of rotation of an asynchronous electric drive. The conducted experiment shows that the cleaning efficiency is 95-99.9%, while the airflow at the cyclone inlet is 16-18 m/s, and at the exit 50-70 m/s.

Database and interactive monitoring system for the photonics and electronics of RPC Muon Trigger in CMS experiment

NASA Astrophysics Data System (ADS)

Wiacek, Daniel; Kudla, Ignacy M.; Pozniak, Krzysztof T.; Bunkowski, Karol

2005-02-01

The main task of the RPC (Resistive Plate Chamber) Muon Trigger monitoring system design for the CMS (Compact Muon Solenoid) experiment (at LHC in CERN Geneva) is the visualization of data that includes the structure of electronic trigger system (e.g. geometry and imagery), the way of its processes and to generate automatically files with VHDL source code used for programming of the FPGA matrix. In the near future, the system will enable the analysis of condition, operation and efficiency of individual Muon Trigger elements, registration of information about some Muon Trigger devices and present previously obtained results in interactive presentation layer. A broad variety of different database and programming concepts for design of Muon Trigger monitoring system was presented in this article. The structure and architecture of the system and its principle of operation were described. One of ideas for building this system is use object-oriented programming and design techniques to describe real electronics systems through abstract object models stored in database and implement these models in Java language.

Developing a Graphical User Interface for the ALSS Crop Planning Tool

NASA Technical Reports Server (NTRS)

Koehlert, Erik

1997-01-01

The goal of my project was to create a graphical user interface for a prototype crop scheduler. The crop scheduler was developed by Dr. Jorge Leon and Laura Whitaker for the ALSS (Advanced Life Support System) program. The addition of a system-independent graphical user interface to the crop planning tool will make the application more accessible to a wider range of users and enhance its value as an analysis, design, and planning tool. My presentation will demonstrate the form and functionality of this interface. This graphical user interface allows users to edit system parameters stored in the file system. Data on the interaction of the crew, crops, and waste processing system with the available system resources is organized and labeled. Program output, which is stored in the file system, is also presented to the user in performance-time plots and organized charts. The menu system is designed to guide the user through analysis and decision making tasks, providing some help if necessary. The Java programming language was used to develop this interface in hopes of providing portability and remote operation.

Extension of Alvis compiler front-end

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

Wypych, Michał; Szpyrka, Marcin; Matyasik, Piotr, E-mail: mwypych@agh.edu.pl, E-mail: mszpyrka@agh.edu.pl, E-mail: ptm@agh.edu.pl

2015-12-31

Alvis is a formal modelling language that enables possibility of verification of distributed concurrent systems. An Alvis model semantics finds expression in an LTS graph (labelled transition system). Execution of any language statement is expressed as a transition between formally defined states of such a model. An LTS graph is generated using a middle-stage Haskell representation of an Alvis model. Moreover, Haskell is used as a part of the Alvis language and is used to define parameters’ types and operations on them. Thanks to the compiler’s modular construction many aspects of compilation of an Alvis model may be modified. Providingmore » new plugins for Alvis Compiler that support languages like Java or C makes possible using these languages as a part of Alvis instead of Haskell. The paper presents the compiler internal model and describes how the default specification language can be altered by new plugins.« less

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

PubMed

Swertz, Morris A; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K; Kanterakis, Alexandros; Roos, Erik T; Lops, Joris; Thorisson, Gudmundur A; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J; de Brock, Engbert O; Jansen, Ritsert C; Parkinson, Helen

2010-12-21

There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

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.

NDEx - The Network Data Exchange | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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

NASA Astrophysics Data System (ADS)

Gerlich, Ralf; Gerlich, Rainer; Dietrich, Carsten

2014-08-01

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

Data-driven decision support for radiologists: re-using the National Lung Screening Trial dataset for pulmonary nodule management.

PubMed

Morrison, James J; Hostetter, Jason; Wang, Kenneth; Siegel, Eliot L

2015-02-01

Real-time mining of large research trial datasets enables development of case-based clinical decision support tools. Several applicable research datasets exist including the National Lung Screening Trial (NLST), a dataset unparalleled in size and scope for studying population-based lung cancer screening. Using these data, a clinical decision support tool was developed which matches patient demographics and lung nodule characteristics to a cohort of similar patients. The NLST dataset was converted into Structured Query Language (SQL) tables hosted on a web server, and a web-based JavaScript application was developed which performs real-time queries. JavaScript is used for both the server-side and client-side language, allowing for rapid development of a robust client interface and server-side data layer. Real-time data mining of user-specified patient cohorts achieved a rapid return of cohort cancer statistics and lung nodule distribution information. This system demonstrates the potential of individualized real-time data mining using large high-quality clinical trial datasets to drive evidence-based clinical decision-making.

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.

Understanding the CCA Standard Through Decaf

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

Kumfert, G

2003-04-17

This document is a tutorial on the CCA Standard as realized through the Decaf implementation. Decaf does not equal the CCA standard much in the same way that Microsoft Visual C++ is not ANSI/ISO C++. This document was created because the CCA standard is evolving and still too fluid to nail down in a tutorial document. Because of its fluidity, and that it represents a hotbed of research and development, beginners can only start learning CCA by choosing one of the frameworks (warts and all). Decaf has just enough functionality to be a useful tool for beginners in the CCAmore » to get started on. Though it lacks many features of the bigger CCA frameworks (CCAFE [3], XCAT [10], and SciRUN [8]) where the heavy-duty research is still going on, it is the first CCA framework that is underpinned by Babel, which provides its language interoperability features. This document can also serve the dual-purpose of providing a reasonable-sized example of building an application using Babel. The entire source for Decaf is included in the examples/subdirectory of the Babel code distribution. This manual assumes the reader is a programmer who has a conceptual understanding of the Babel Language Interoperability Tool. They should be proficient in two or more of the following languages: Fortran77, C, C++, Java, or Python. Furthermore, this manual assumes the reader is familiar with the SPMD{sup 2} programming model that pervades the scientific computing community. Knowledge of and experience with MPI programming is helpful, but not strictly required.« less

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

PubMed

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

2005-12-01

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

XML in an Adaptive Framework for Instrument Control

NASA Technical Reports Server (NTRS)

Ames, Troy J.

2004-01-01

NASA Goddard Space Flight Center is developing an extensible framework for instrument command and control, known as Instrument Remote Control (IRC), that combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML). A key aspect of the architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). IML is an XML dialect used to describe interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms.

Ground Processing of Data From the Mars Exploration Rovers

NASA Technical Reports Server (NTRS)

Wright, Jesse; Sturdevant, Kathryn; Noble, David

2006-01-01

A computer program implements the Earth side of the protocol that governs the transfer of data files generated by the Mars Exploration Rovers. It also provides tools for viewing data in these files and integrating data-product files into automated and manual processes. It reconstitutes files from telemetry data packets. Even if only one packet is received, metadata provide enough information to enable this program to identify and use partial data products. This software can generate commands to acknowledge received files and retransmit missed parts of files, or it can feed a manual process to make decisions about retransmission. The software uses an Extensible Markup Language (XML) data dictionary to provide a generic capability for displaying files of basic types, and uses external "plug-in" application programs to provide more sophisticated displays. This program makes data products available with very low latency, and can trigger automated actions when complete or partial products are received. The software is easy to install and use. The only system requirement for installing the software is a Java J2SE 1.4 platform. Several instances of the software can be executed simultaneously on the same machine.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

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

NASA Astrophysics Data System (ADS)

Karaagac, Abdullah; Bostancı, Bulent

2016-04-01

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

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

An Ethernet Java Applet for a Course for Non-Majors.

ERIC Educational Resources Information Center

Holliday, Mark A.

1997-01-01

Details the topics of a new course that introduces computing and communication technology to students not majoring in computer science. Discusses the process of developing a Java applet (a program that can be invoked through a World Wide Web browser) that illustrates the protocol used by ethernet local area networks to determine which computer can…

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.

Classroom Interaction Strategies Employed by English Teachers at Lower Secondary Schools

ERIC Educational Resources Information Center

Suryati, Nunung

2015-01-01

This article reports a study on teachers' use of interaction strategies in English Language Teaching (ELT) in lower secondary level of education. The study involved eighteen teachers from Lower Secondary Schools in Malang, East Java. Classroom observation was selected as a method in this study by utilizing Self Evaluation Teacher Talk (SETT) as…

Dialysis - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Russian (Русский) Somali (Af-Soomaali ) Spanish (español) HealthReach resources will open in a new window. Arabic (العربية) Expand Section Dialysis - العربية (Arabic) Bilingual PDF ...

DroidSafe

DTIC Science & Technology

2016-12-01

branches of our work . 3.1 Understanding Sensitive API Call and API Information Usage Android applications are written in a type- safe language (Java...directly invoke resolved targets. Because DroidSafe works with a comprehensive model of the Android environment , it supports precise resolution of...STATEMENT. FOR THE CHIEF ENGINEER: / S / / S / MARK K. WILLIAMS WARREN H. DEBANY, JR. Work Unit Manager

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

PubMed

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

2002-01-01

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

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

Yin, Luo

2011-12-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

An Overview of the Runtime Verification Tool Java PathExplorer

NASA Technical Reports Server (NTRS)

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

2002-01-01

We present an overview of the Java PathExplorer runtime verification tool, in short referred to as JPAX. JPAX can monitor the execution of a Java program and check that it conforms with a set of user provided properties formulated in temporal logic. JPAX can in addition analyze the program for concurrency errors such as deadlocks and data races. The concurrency analysis requires no user provided specification. The tool facilitates automated instrumentation of a program's bytecode, which when executed will emit an event stream, the execution trace, to an observer. The observer dispatches the incoming event stream to a set of observer processes, each performing a specialized analysis, such as the temporal logic verification, the deadlock analysis and the data race analysis. Temporal logic specifications can be formulated by the user in the Maude rewriting logic, where Maude is a high-speed rewriting system for equational logic, but here extended with executable temporal logic. The Maude rewriting engine is then activated as an event driven monitoring process. Alternatively, temporal specifications can be translated into efficient automata, which check the event stream. 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.

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.

Nuclear data made easily accessible through the Notre Dame Nuclear Database

NASA Astrophysics Data System (ADS)

Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

Software Applications to Access Earth Science Data: Building an ECHO Client

NASA Astrophysics Data System (ADS)

Cohen, A.; Cechini, M.; Pilone, D.

2010-12-01

Historically, developing an ECHO (NASA’s Earth Observing System (EOS) ClearingHOuse) client required interaction with its SOAP API. SOAP, as a framework for web service communication has numerous advantages for Enterprise applications and Java/C# type programming languages. However, as interest has grown for quick development cycles and more intriguing “mashups,” ECHO has seen the SOAP API lose its appeal. In order to address these changing needs, ECHO has introduced two new interfaces facilitating simple access to its metadata holdings. The first interface is built upon the OpenSearch format and ESIP Federated Search framework. The second interface is built upon the Representational State Transfer (REST) architecture. Using the REST and OpenSearch APIs to access ECHO makes development with modern languages much more feasible and simpler. Client developers can leverage the simple interaction with ECHO to focus more of their time on the advanced functionality they are presenting to users. To demonstrate the simplicity of developing with the REST API, participants will be led through a hands-on experience where they will develop an ECHO client that performs the following actions: + Login + Provider discovery + Provider based dataset discovery + Dataset, Temporal, and Spatial constraint based Granule discovery + Online Data Access

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

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

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

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

Using parallel computing methods to improve log surface defect detection methods

Treesearch

R. Edward Thomas; Liya Thomas

2013-01-01

Determining the size and location of surface defects is crucial to evaluating the potential yield and value of hardwood logs. Recently a surface defect detection algorithm was developed using the Java language. This algorithm was developed around an earlier laser scanning system that had poor resolution along the length of the log (15 scan lines per foot). A newer...

Investigating Inspiring English Lecturers in a Faith-Based Educational Institution: EFL Learners' Perception

ERIC Educational Resources Information Center

Iftanti, Erna

2015-01-01

This article describes English as Foreign Language (EFL) learners' perception on an inspiring English lecturer. This study was done through a survey to 230 EFL learners of State Islamic Institute of Tulungagung, a small district in East Java-Indonesia, in order to get underlying basis of making a decision on learning policies for the sake of…

Health Problems in Pregnancy - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Chinese, Simplified (Mandarin dialect) (简体中文) French (français) Modern Standard Arabic (Arabic dialect) (العربية الفصحى, عربي فصيح) Russian (Русский) ...

Hurricanes - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Bosnian (bosanski) Chinese, Simplified (Mandarin dialect) (简体中文) ... Haitian Creole (Kreyol ayisyen) Korean (한국어) Modern Standard Arabic (Arabic dialect) (العربية الفصحى, عربي فصيح) Pashto (Pax̌tō / ...

Using XML and Java for Astronomical Instrumentation Control

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

Prototyping Tool for Web-Based Multiuser Online Role-Playing Game

NASA Astrophysics Data System (ADS)

Okamoto, Shusuke; Kamada, Masaru; Yonekura, Tatsuhiro

This letter proposes a prototyping tool for Web-based Multiuser Online Role-Playing Game (MORPG). The design goal is to make this tool simple and powerful. The tool is comprised of a GUI editor, a translator and a runtime environment. The GUI editor is used to edit state-transition diagrams, each of which defines the behavior of the fictional characters. The state-transition diagrams are translated into C program codes, which plays the role of a game engine in RPG system. The runtime environment includes PHP, JavaScript with Ajax and HTML. So the prototype system can be played on the usual Web browser, such as Fire-fox, Safari and IE. On a click or key press by a player, the Web browser sends it to the Web server to reflect its consequence on the screens which other players are looking at. Prospected users of this tool include programming novices and schoolchildren. The knowledge or skill of any specific programming languages is not required to create state-transition diagrams. Its structure is not only suitable for the definition of a character behavior but also intuitive to help novices understand. Therefore, the users can easily create Web-based MORPG system with the tool.

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

Enhanced DIII-D Data Management Through a Relational Database

NASA Astrophysics Data System (ADS)

Burruss, J. R.; Peng, Q.; Schachter, J.; Schissel, D. P.; Terpstra, T. B.

2000-10-01

A relational database is being used to serve data about DIII-D experiments. The database is optimized for queries across multiple shots, allowing for rapid data mining by SQL-literate researchers. The relational database relates different experiments and datasets, thus providing a big picture of DIII-D operations. Users are encouraged to add their own tables to the database. Summary physics quantities about DIII-D discharges are collected and stored in the database automatically. Meta-data about code runs, MDSplus usage, and visualization tool usage are collected, stored in the database, and later analyzed to improve computing. Documentation on the database may be accessed through programming languages such as C, Java, and IDL, or through ODBC compliant applications such as Excel and Access. A database-driven web page also provides a convenient means for viewing database quantities through the World Wide Web. Demonstrations will be given at the poster.

TargetCompare: A web interface to compare simultaneous miRNAs targets

PubMed Central

Moreira, Fabiano Cordeiro; Dustan, Bruno; Hamoy, Igor G; Ribeiro-dos-Santos, André M; dos Santos, Ândrea Ribeiro

2014-01-01

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. Availability http://lghm.ufpa.br/targetcompare PMID:25352731

TargetCompare: A web interface to compare simultaneous miRNAs targets.

PubMed

Moreira, Fabiano Cordeiro; Dustan, Bruno; Hamoy, Igor G; Ribeiro-Dos-Santos, André M; Dos Santos, Andrea Ribeiro

2014-01-01

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. http://lghm.ufpa.br/targetcompare.

Development of user-friendly and interactive data collection system for cerebral palsy.

PubMed

Raharjo, I; Burns, T G; Venugopalan, J; Wang, M D

2016-02-01

Cerebral palsy (CP) is a permanent motor disorder that appears in early age and it requires multiple tests to assess the physical and mental capabilities of the patients. Current medical record data collection systems, e.g., EPIC, employed for CP are very general, difficult to navigate, and prone to errors. The data cannot easily be extracted which limits data analysis on this rich source of information. To overcome these limitations, we designed and prototyped a database with a graphical user interface geared towards clinical research specifically in CP. The platform with MySQL and Java framework is reliable, secure, and can be easily integrated with other programming languages for data analysis such as MATLAB. This database with GUI design is a promising tool for data collection and can be applied in many different fields aside from CP to infer useful information out of the vast amount of data being collected.

Development of user-friendly and interactive data collection system for cerebral palsy

PubMed Central

Raharjo, I.; Burns, T. G.; Venugopalan, J.; Wang., M. D.

2016-01-01

Cerebral palsy (CP) is a permanent motor disorder that appears in early age and it requires multiple tests to assess the physical and mental capabilities of the patients. Current medical record data collection systems, e.g., EPIC, employed for CP are very general, difficult to navigate, and prone to errors. The data cannot easily be extracted which limits data analysis on this rich source of information. To overcome these limitations, we designed and prototyped a database with a graphical user interface geared towards clinical research specifically in CP. The platform with MySQL and Java framework is reliable, secure, and can be easily integrated with other programming languages for data analysis such as MATLAB. This database with GUI design is a promising tool for data collection and can be applied in many different fields aside from CP to infer useful information out of the vast amount of data being collected. PMID:28133638

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

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

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

NASA Astrophysics Data System (ADS)

Lakkaraju, Mahesh

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

Using ruby on rails to develop a web interface: a research-based exemplar with a computerized physical activity reporter.

PubMed

Blaz, Jacquelyn W; Pearce, Patricia F

2009-01-01

The world is becoming increasingly web-based. Health care institutions are utilizing the web for personal health records, surveillance, communication, and education; health care researchers are finding value in using the web for research subject recruitment, data collection, and follow-up. Programming languages, such as Java, require knowledge and experience usually found only in software engineers and consultants. The purpose of this paper is to demonstrate Ruby on Rails as a feasible alternative for programming questionnaires for use on the web. Ruby on Rails was specifically designed for the development, deployment, and maintenance of database-backed web applications. It is flexible, customizable, and easy to learn. With a relatively little initial training, a novice programmer can create a robust web application in a small amount of time, without the need of a software consultant. The translation of the Children's Computerized Physical Activity Reporter (C-CPAR) from a local installation in Microsoft Access to a web-based format utilizing Ruby on Rails is given as an example.

Web servlet-assisted, dial-in flow cytometry data analysis.

PubMed

Battye, F

2001-02-01

The obvious benefits of centralized data storage notwithstanding, the size of modern flow cytometry data files discourages their transmission over commonly used telephone modem connections. The proposed solution is to install at the central location a web servlet that can extract compact data arrays, of a form dependent on the requested display type, from the stored files and transmit them to a remote client computer program for display. A client program and a web servlet, both written in the Java programming language, were designed to communicate over standard network connections. The client program creates familiar numerical and graphical display types and allows the creation of gates from combinations of user-defined regions. Data compression techniques further reduce transmission times for data arrays that are already much smaller than the data file itself. For typical data files, network transmission times were reduced more than 700-fold for extraction of one-dimensional (1-D) histograms, between 18 and 120-fold for 2-D histograms, and 6-fold for color-coded dot plots. Numerous display formats are possible without further access to the data file. This scheme enables telephone modem access to centrally stored data without restricting flexibility of display format or preventing comparisons with locally stored files. Copyright 2001 Wiley-Liss, Inc.

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.

Session on High Speed Civil Transport Design Capability Using MDO and High Performance Computing

NASA Technical Reports Server (NTRS)

Rehder, Joe

2000-01-01

Since the inception of CAS in 1992, NASA Langley has been conducting research into applying multidisciplinary optimization (MDO) and high performance computing toward reducing aircraft design cycle time. The focus of this research has been the development of a series of computational frameworks and associated applications that increased in capability, complexity, and performance over time. The culmination of this effort is an automated high-fidelity analysis capability for a high speed civil transport (HSCT) vehicle installed on a network of heterogeneous computers with a computational framework built using Common Object Request Broker Architecture (CORBA) and Java. The main focus of the research in the early years was the development of the Framework for Interdisciplinary Design Optimization (FIDO) and associated HSCT applications. While the FIDO effort was eventually halted, work continued on HSCT applications of ever increasing complexity. The current application, HSCT4.0, employs high fidelity CFD and FEM analysis codes. For each analysis cycle, the vehicle geometry and computational grids are updated using new values for design variables. Processes for aeroelastic trim, loads convergence, displacement transfer, stress and buckling, and performance have been developed. In all, a total of 70 processes are integrated in the analysis framework. Many of the key processes include automatic differentiation capabilities to provide sensitivity information that can be used in optimization. A software engineering process was developed to manage this large project. Defining the interactions among 70 processes turned out to be an enormous, but essential, task. A formal requirements document was prepared that defined data flow among processes and subprocesses. A design document was then developed that translated the requirements into actual software design. A validation program was defined and implemented to ensure that codes integrated into the framework produced the same results as their standalone counterparts. Finally, a Commercial Off the Shelf (COTS) configuration management system was used to organize the software development. A computational environment, CJOPT, based on the Common Object Request Broker Architecture, CORBA, and the Java programming language has been developed as a framework for multidisciplinary analysis and Optimization. The environment exploits the parallelisms inherent in the application and distributes the constituent disciplines on machines best suited to their needs. In CJOpt, a discipline code is "wrapped" as an object. An interface to the object identifies the functionality (services) provided by the discipline, defined in Interface Definition Language (IDL) and implemented using Java. The results of using the HSCT4.0 capability are described. A summary of lessons learned is also presented. The use of some of the processes, codes, and techniques by industry are highlighted. The application of the methodology developed in this research to other aircraft are described. Finally, we show how the experience gained is being applied to entirely new vehicles, such as the Reusable Space Transportation System. Additional information is contained in the original.

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

PubMed

Drummond, A; Strimmer, K

2001-07-01

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

Online learning tools in an M.Ed. in Earth Sciences program

NASA Astrophysics Data System (ADS)

Richardson, E.

2011-12-01

Penn State's Master of Education in Earth Sciences program is a fully online 30-credit degree program serving mid-career secondary science teachers. Teachers in the program have a diverse background in science and math, are usually many years removed from their most recent degree, and are often deficient in the same geoscience skills as are beginning undergraduates. For example, they habitually assign incorrect causal relationships to concepts that are taught at the same time (such as sea-floor spreading and magnetic field reversals), and they have trouble with both object and spatial visualization. Program faculty also observe anecdotally that many teachers enter the program lacking the ability to describe their mental model of a given Earth science process, making it difficult to identify teachers' knowledge gaps. We have implemented many technical strategies to enhance program content delivery while trying to minimize the inherent barriers to completing quantitative assignments online and at a distance. These barriers include competence with and access to sophisticated data analysis and plotting programs commonly used by scientists. Here, I demonstrate two technical tools I use frequently to strengthen online content delivery and assessment. The first, Jing, is commercially-available, free, and platform-independent. Jing allows the user to make screencasts with narration and embed them into a web page as a flash movie or as an external link. The second is a set of simple sketching tools I have created using the programming language Processing, which is a free, open source, platform-independent language built on Java. The integration of easy-to-use drawing tools into problem sets and other assessments has enabled faculty to appraise a learner's grasp of the material without the steep technical learning curve and expense inherent in most computer graphics packages. A serendipitous benefit of teaching with these tools is that they are easy to learn and freely available and so the teachers in the program learn to use them, too. Qualitative assessment of feedback from the teachers in the program shows that they find the explanations, screencasts, animations, and discussions arising from these tools not only enhance their own learning but also inspire them to try them in their classrooms.

Unrestricted Warfare Symposium 2006: Proceedings on Strategy, Analysis, and Technology. 14 - 15 March 2006

DTIC Science & Technology

2006-03-01

hibernate underground and tend to be highly secretive for the first time exposed their dirty laundry in public and provided an authentic view...coercion and amnesty programs to remove, village by village, support for the Dar’ul Islam in West Java , eventually defeating the insurgency...issue. One of the biggest differences between the Northwest frontier province or central Java and London is Internet

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

DTIC Science & Technology

2008-03-01

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

Les Chansons de la Francophonie Web Site and Its Two Web-Usage-Tracking Systems in an Advanced Listening Comprehension Course

ERIC Educational Resources Information Center

Weinberg, Alysse

2005-01-01

The "Les Chansons de la francophonie" web site is based on French songs and was developed using HTML and JavaScript for the advanced French Comprehension Course at the Second Language Institute of the University of Ottawa. These interactive listening activities include true-false and multiple-choice questions, fill in the blanks,…

Safety - Multiple Languages

MedlinePlus

... sharing features on this page, please enable JavaScript. Arabic (العربية) Bosnian (bosanski) Burmese (myanma bhasa) Chinese, Simplified ( ... 日本語) Karen (S’gaw Karen) Korean (한국어) Modern Standard Arabic (Arabic dialect) (العربية الفصحى, عربي فصيح) Russian (Русский) ...

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

PubMed Central

2010-01-01

Background There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. Methods The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. Results In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure. Conclusions The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org. PMID:21210979

JGromacs: a Java package for analyzing protein simulations.

PubMed

Münz, Márton; Biggin, Philip C

2012-01-23

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

Multibiodose radiation emergency triage categorization software.

PubMed

Ainsbury, Elizabeth A; Barnard, Stephen; Barrios, Lleonard; Fattibene, Paola; de Gelder, Virginie; Gregoire, Eric; Lindholm, Carita; Lloyd, David; Nergaard, Inger; Rothkamm, Kai; Romm, Horst; Scherthan, Harry; Thierens, Hubert; Vandevoorde, Charlot; Woda, Clemens; Wojcik, Andrzej

2014-07-01

In this note, the authors describe the MULTIBIODOSE software, which has been created as part of the MULTIBIODOSE project. The software enables doses estimated by networks of laboratories, using up to five retrospective (biological and physical) assays, to be combined to give a single estimate of triage category for each individual potentially exposed to ionizing radiation in a large scale radiation accident or incident. The MULTIBIODOSE software has been created in Java. The usage of the software is based on the MULTIBIODOSE Guidance: the program creates a link to a single SQLite database for each incident, and the database is administered by the lead laboratory. The software has been tested with Java runtime environment 6 and 7 on a number of different Windows, Mac, and Linux systems, using data from a recent intercomparison exercise. The Java program MULTIBIODOSE_1.0.jar is freely available to download from http://www.multibiodose.eu/software or by contacting the software administrator: MULTIBIODOSE-software@gmx.com.

JGromacs: A Java Package for Analyzing Protein Simulations

PubMed Central

2011-01-01

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

Integrating medical imaging analyses through a high-throughput bundled resource imaging system

NASA Astrophysics Data System (ADS)

Covington, Kelsie; Welch, E. Brian; Jeong, Ha-Kyu; Landman, Bennett A.

2011-03-01

Exploitation of advanced, PACS-centric image analysis and interpretation pipelines provides well-developed storage, retrieval, and archival capabilities along with state-of-the-art data providence, visualization, and clinical collaboration technologies. However, pursuit of integrated medical imaging analysis through a PACS environment can be limiting in terms of the overhead required to validate, evaluate and integrate emerging research technologies. Herein, we address this challenge through presentation of a high-throughput bundled resource imaging system (HUBRIS) as an extension to the Philips Research Imaging Development Environment (PRIDE). HUBRIS enables PACS-connected medical imaging equipment to invoke tools provided by the Java Imaging Science Toolkit (JIST) so that a medical imaging platform (e.g., a magnetic resonance imaging scanner) can pass images and parameters to a server, which communicates with a grid computing facility to invoke the selected algorithms. Generated images are passed back to the server and subsequently to the imaging platform from which the images can be sent to a PACS. JIST makes use of an open application program interface layer so that research technologies can be implemented in any language capable of communicating through a system shell environment (e.g., Matlab, Java, C/C++, Perl, LISP, etc.). As demonstrated in this proof-of-concept approach, HUBRIS enables evaluation and analysis of emerging technologies within well-developed PACS systems with minimal adaptation of research software, which simplifies evaluation of new technologies in clinical research and provides a more convenient use of PACS technology by imaging scientists.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

A Java-based tool for creating KML files from GPS waypoints

NASA Astrophysics Data System (ADS)

Kinnicutt, P. G.; Rivard, C.; Rimer, S.

2008-12-01

Google Earth provides a free tool with powerful capabilities for visualizing geoscience images and data. Commercial software tools exist for doing sophisticated digitizing and spatial modeling , but for the purposes of presentation, visualization and overlaying aerial images with data Google Earth provides much of the functionality. Likewise, with current technologies in GPS (Global Positioning System) systems and with Google Earth Plus, it is possible to upload GPS waypoints, tracks and routes directly into Google Earth for visualization. However, older technology GPS units and even low-cost GPS units found today may lack the necessary communications interface to a computer (e.g. no Bluetooth, no WiFi, no USB, no Serial, etc.) or may have an incompatible interface, such as a Serial port but no USB adapter available. In such cases, any waypoints, tracks and routes saved in the GPS unit or recorded in a field notebook must be manually transferred to a computer for use in a GIS system or other program. This presentation describes a Java-based tool developed by the author which enables users to enter GPS coordinates in a user-friendly manner, then save these coordinates in a Keyhole MarkUp Language (KML) file format, for visualization in Google Earth. This tool either accepts user-interactive input or accepts input from a CSV (Comma Separated Value) file, which can be generated from any spreadsheet program. This tool accepts input in the form of lat/long or UTM (Universal Transverse Mercator) coordinates. This presentation describes this system's applicability through several small case studies. This free and lightweight tool simplifies the task of manually inputting GPS data into Google Earth for people working in the field without an automated mechanism for uploading the data; for instance, the user may not have internet connectivity or may not have the proper hardware or software. Since it is a Java application and not a web- based tool, it can be installed on one's field laptop and the GPS data can be manually entered without the need for internet connectivity. This tool provides a table view of the GPS data, but lacks a KML viewer to view the data overlain on top of an aerial view, as this viewer functionality is provided in Google Earth. The tool's primary contribution lies in its more convenient method for entering the GPS data manually when automated technologies are not available.

Socioeconomic and familial characteristics influence caretakers' adherence to the periodic vitamin A capsule supplementation program in Central Java, Indonesia.

PubMed

Pangaribuan, Rosnani; Scherbaum, Veronika; Erhardt, Jürgen G; Sastroamidjojo, Soemilah; Biesalski, Hans K

2004-06-01

The adherence of program participants to periodic vitamin A capsule (VAC) supplementation among children aged 1-5 years (n = 677) in Central Java, Indonesia was assessed. Fourteen villages from five sub-districts and one ward from one sub-district in Central Java were included in the study to represent rural and suburban areas. All questions about demographic factors, socioeconomic conditions, current dietary practice and healthcare-seeking attitudes for common childhood illnesses, previous breastfeeding experience, their knowledge about vitamin A and adherence to the VAC program after capsule distribution (two periods in 2000) were asked. Caretakers with limited knowledge about the health benefits of vitamin A, households with more than one preschool child, and households with older children (> 36 months) were associated with a decreased likelihood of regular participation in the program with odds ratios of 0.38, 0.55, and 0.26, respectively (p < 0.01). The percentage of caretakers who utilized community health centers, village health posts or midwives' practices in rural areas, was significantly higher (86.6 per cent, p < 0.001) than in suburban areas (62.8 per cent). Living in a rural location was associated with an increased adherence to participate in the program regularly with an odds ratio of 2.02 (p < 0.01). In conclusion, nutritional education and periodic social marketing should be re-emphasized and other potential delivery channels, such as private healthcare practices, could also contribute to an increase adherence of supplementation program.

A Verification System for Distributed Objects with Asynchronous Method Calls

NASA Astrophysics Data System (ADS)

Ahrendt, Wolfgang; Dylla, Maximilian

We present a verification system for Creol, an object-oriented modeling language for concurrent distributed applications. The system is an instance of KeY, a framework for object-oriented software verification, which has so far been applied foremost to sequential Java. Building on KeY characteristic concepts, like dynamic logic, sequent calculus, explicit substitutions, and the taclet rule language, the system presented in this paper addresses functional correctness of Creol models featuring local cooperative thread parallelism and global communication via asynchronous method calls. The calculus heavily operates on communication histories which describe the interfaces of Creol units. Two example scenarios demonstrate the usage of the system.

Simulating Candidate Missions for a Novel Glider Unmanned Underwater Vehicle

DTIC Science & Technology

2007-03-01

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

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

PubMed

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

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

PubMed

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

2011-08-05

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

Integer programming of cement distribution by train

NASA Astrophysics Data System (ADS)

Indarsih

2018-01-01

Cement industry in Central Java distributes cement by train to meet daily demand in Yogyakarta and Central Java area. There are five destination stations. For each destination station, there is a warehouse to load cements. Decision maker of cement industry have a plan to redesign the infrastructure and transportation system. The aim is to determine how many locomotives, train wagons, and containers and how to arrange train schedules with subject to the delivery time. For this purposes, we consider an integer programming to minimize the total of operational cost. Further, we will discuss a case study and the solution the problem can be calculated by LINGO software.

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.

Environmental Epidemiology Program

Science.gov Websites

accessible with JavaScript activated. Utah Department of Health Bureau of Epidemiology Environmental Epidemiology Program (EEP) The Environmental Epidemiology Program strives to improve the health of Utah residents through science-based environmental health policy and by empowering citizens with knowledge about

Scaffolding Java Programming on a Mobile Phone for Novice Learners

ERIC Educational Resources Information Center

Mbogo, Chao; Blake, Edwin; Suleman, Hussein

2015-01-01

The ubiquity of mobile phones provides an opportunity to use them as a resource for construction of programs beyond the classroom. However, limitations of mobile phones impede their use as typical programming environments. This research proposes that programming environments on mobile phones should include scaffolding techniques specifically…

A Type-Preserving Compiler Infrastructure

DTIC Science & Technology

2002-12-01

understand this code. This is, in essence , the object encoding we use to compile Java. Before embarking on the formal translation, wemust explore onemore...call. This solution works quite well. We used Jasmin , a JVML assembler (Meyer and Down- 102 CHAPTER 7. FUNCTIONAL JAVA BYTECODE ing 1997), to generate a...European Symp. on Program. 135–149. Flanagan, Cormac, Amr Sabry, Bruce F. Duba, and Matthias Felleisen. 1993, June. “The Essence of Compiling with

Indonesia's great frontier and migration policy.

PubMed

Maloney, C

1987-01-01

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

Simulation of electron spin resonance spectroscopy in diverse environments: An integrated approach

NASA Astrophysics Data System (ADS)

Zerbetto, Mirco; Polimeno, Antonino; Barone, Vincenzo

2009-12-01

We discuss in this work a new software tool, named E-SpiReS (Electron Spin Resonance Simulations), aimed at the interpretation of dynamical properties of molecules in fluids from electron spin resonance (ESR) measurements. The code implements an integrated computational approach (ICA) for the calculation of relevant molecular properties that are needed in order to obtain spectral lines. The protocol encompasses information from atomistic level (quantum mechanical) to coarse grained level (hydrodynamical), and evaluates ESR spectra for rigid or flexible single or multi-labeled paramagnetic molecules in isotropic and ordered phases, based on a numerical solution of a stochastic Liouville equation. E-SpiReS automatically interfaces all the computational methodologies scheduled in the ICA in a way completely transparent for the user, who controls the whole calculation flow via a graphical interface. Parallelized algorithms are employed in order to allow running on calculation clusters, and a web applet Java has been developed with which it is possible to work from any operating system, avoiding the problems of recompilation. E-SpiReS has been used in the study of a number of different systems and two relevant cases are reported to underline the promising applicability of the ICA to complex systems and the importance of similar software tools in handling a laborious protocol. Program summaryProgram title: E-SpiReS Catalogue identifier: AEEM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.0 No. of lines in distributed program, including test data, etc.: 311 761 No. of bytes in distributed program, including test data, etc.: 10 039 531 Distribution format: tar.gz Programming language: C (core programs) and Java (graphical interface) Computer: PC and Macintosh Operating system: Unix and Windows Has the code been vectorized or parallelized?: Yes RAM: 2 048 000 000 Classification: 7.2 External routines: Babel-1.1, CLAPACK, BLAS, CBLAS, SPARSEBLAS, CQUADPACK, LEVMAR Nature of problem:Ab initio simulation of cw-ESR spectra of radicals in solution Solution method: E-SpiReS uses an hydrodynamic approach to calculate the diffusion tensor of the molecule, DFT methodologies to evaluate magnetic tensors and linear algebra techniques to solve numerically the stochastic Liouville equation to obtain an ESR spectrum. Running time: Variable depending on the task. It takes seconds for small molecules in the fast motional regime to hours for big molecules in viscous and/or ordered media.