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SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets

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JOURNAL OF CHEMICAL INFORMATION AND MODELING 2010年第1期50卷 68-78页

作者： Lounkine, Eugen Wawer, Mathias Wassermann, Anne Mai Bajorath, Juergen Rhein Freidrich Wilhelms Univ Bonn Dept Life Sci Informat B IT LIMES Program Unit Chem Biol & Med Chem D-53113 Bonn Germany

We introduce SARANEA, ail open-source java application for interactive exploration Of Structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information ill Compound sets of any source. SARANEA integrates various SAR and SSR analysis functions, and utilizes a network-like similarity graph data structure for visualization. The program enables the systematic detection of activity and selectivity cliffs and corresponding key compounds across multiple targets. Advanced SAR analysis functions implemented in SARANEA include, among others, layered chemical neighborhood graphs, cliff indices, selectivity trees, editing functions for molecular networks and pathways, bioactivity summaries of key compounds, and markers for bioactive compounds having potential side effects. We report the application of SARANEA to identify SAR and SSR determinants ill different sets of serine protease inhibitors. It is found that key compounds can influence SARs and SSRs in rather different ways. Such compounds and their SAR/SSR characteristics can be systematically identified and explored using SARANEA. The program and source code are made freely available under the GNU General Public License.

关键词： CHEMICAL SPACE CYTOSCAPE NETWORKS java application semiconductor relays Serine Proteinase Inhibitors structure activity relation compounds cliffs graph data edit function Bioinformatics Software Network Rescue Specific absorption rate

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Towards software product-lines - a refinement-oriented generation language

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BT TECHNOLOGY JOURNAL 2003年第4期21卷 162-172页

作者： Lesaint, D Papamargaritis, G BT Exact Intelligent Syst Res Grp Ipswich Suffolk England BT Exact Intelligent Syst Res Grp Ipswich Suffolk England

With the advent of eBusiness and mobile computing, the need for software systems that can be automatically configured, assembled, and adapted on the fly has never been so critical. In this context, various proposals have been put forward to realise the vision of software product-lines, among them, GenVoca-a powerful model for component-based product-lines advocating large-scale step-wise refinement as a composition principle. In this paper, we introduce a refinement-oriented generation language - ReGaL - to program GenVoca product-lines. While components are programmed in java, refinements are programmed in ReGaL by the means of generic refinement aspects. Orders for applications, themselves expressed in ReGaL, are compiled by instantiating and weaving refinement aspects with components to generate the requested java applications. We illustrate ReGaL on a product-line of graph algorithms and present experiments showing the benefits of application configurability.

关键词： Product lines Flies java application electronic commerce Graph algorithms PRODUCTION LINE Software systems Language

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Seahawk: moving beyond HTML in Web-based bioinformatics analysis

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BMC BIOINFORMATICS 2007年第1期8卷 1-13页

作者： Gordon, Paul M. K. Sensen, Christoph W. Univ Calgary Fac Med Sun Ctr Excellence Visual Genom Calgary AB T2N 4N1 Canada

Background: Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY- S hold out the promise of seamlessly integrating multi- step analysis. Results: We have developed a program (Seahawk) that allows biologists to intuitively and seamlessly chain together Web Services using a data-centric, rather than the customary service-centric approach. The approach is illustrated with a ferredoxin mutation analysis. Seahawk concentrates on lowering entry barriers for biologists: no prior knowledge of the data ontology, or relevant services is required. In stark contrast to other MOBY-S clients, in Seahawk users simply load Web pages and text files they already work with. Underlying the familiar Web-browser interaction is an XML data engine based on extensible XSLT style sheets, regular expressions, and XPath statements which import existing user data into the MOBY-S format. Conclusion: As an easily accessible applet, Seahawk moves beyond standard Web browser interaction, providing mechanisms for the biologist to concentrate on the analytical task rather than on the technical details of data formats and Web forms. As the MOBY-S protocol nears a 1.0 specification, we expect more biologists to adopt these new semantic-oriented ways of doing Web-based analysis, which empower them to do more complicated, ad hoc analysis workflow creation without the assistance of a programmer.

关键词： Regular Expression Service Selection Glyph java application Service Execution

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A graphic editor for analyzing signal-transduction pathways

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GENE 2000年第1-2期259卷 235-244页

作者： Koike, T Rzhetsky, A Columbia Univ Columbia Genome Ctr New York NY 10027 USA Hitachi Software Engn Co Ltd Yokohama Kanagawa Japan Columbia Univ Dept Med Informat New York NY 10027 USA

We describe a graphical editor designed specifically to facilitate analysis and visualization of complex signal-transduction pathways. The editor provides automatic layout of complex regulatory graphs and enables users easily to maintain, edit, and exchange publication-quality images of regulatory networks. (C) 2000 Elsevier Science B.V. All rights reserved.

关键词： bioinformatics java application public-domain software regulatory pathway visualization

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Adjava ― Automatic Distribution of java applications 02

AdJava ― Automatic Distribution of Java Applications

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Australasian Computer Science Conference

作者： Mohammad M. Fuad Michael J. Oudshoorn Department of Computer Science University of Adelaide Adelaide 5005 South Australia

ISBN: (纸本)0909925828

The majority of the world's computing resources remains idle most of the time. By using this resource pool, an individual computation may be completed in a fraction of time required to run the same computation on a single machine. However, distributing a program over a number of machines proves to be a tedious and difficult job. This paper introduces a system, called Adjava, which harnesses the computing power of these under-utilized heterogeneous computers by automatically distributing the user application across the available resources. In addition to providing transparent automatic distribution, Adjava provides load balancing and migration of distributed objects through the use of intelligent software agents. The system provides all this support without any programmer involvement and without modifying the java Virtual Machine (JVM). Adjava's range of features, combined with its ease of use, makes it a powerful system for distributed computing.

关键词： distributed programming software agents Intelligent agents Distributed software user application java application Distribute machine computational power Distributed computing Load balancing

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IBM's Enterprise Server for java

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IBM SYSTEMS JOURNAL 1998年第3期37卷 323-335页

作者： Brackenbury, IF Ferguson, DF Gottschalk, KD Storey, RA IBM United Kindgom Labs Ltd Hursley Dev Lab Winchester SO21 2JN Hants England IBM United Kindgom Labs Ltd Ctr Java Technol Winchester SO21 2JN Hants England IBM Corp Thomas J Watson Res Ctr Software Grp Hawthorne NY 10532 USA IBM Corp Network Comp Software Div Res Triangle Pk NC 27709 USA

IBM is exploiting Enterprise javaBeans(TM) in a family of compatible java(TM) application servers conforming to IBM's Enterprise Server for java (ESJ) specification. The ESJ provides a common set of dynamic, adaptive system services to meet today's (and tomorrow's) middleware requirements. ESJ will provide a standard programming model and set of services across major server platforms so that implementations of ESJ are differentiated not by function but by qualify of service. Finally, ESJ increases productivity by enabling programmers to focus on business logic rather than on infrastructure details. This paper introduces the design of ESJ, including the attributes of the common execution environment, its interaction with other middleware, and its cleientserver capabilities. It provides an appreciation of the value of ESJ to application developers as a means of achieving cross-platform consistency, lower costs, and faster time to market. It also outlines the features that make ESJ the server technology base for wide-scale reuse through the "write once, run anywhere" promise of java.

关键词： .extensions APIs enterprise server business logic java application Enterprise javaBeans javaSoft EJB ESJ servers

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An interactive end-user software application for a deep-sea photographic database

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COMPUTERS & GEOSCIENCES 2005年第6期31卷 718-734页

作者： Jaisankar, S Sharma, R Natl Inst Oceanog Geol Oceanog Div Panaji 403004 Goa India

A photographic database is created for cataloguing data from underwater deep-tow photographic surveys conducted in the Central Indian Ocean Basin. This includes digitizing, encoding and merging different types of data and information obtained from different sources of the system. Date and time is used as the key reference for merging the data from different sources. Techniques that are developed to encode information from photographs and area calculations are discussed. Interactive java application software is developed to play video clippings (dynamic images), displaying photographs (static images), plotting simple graphs, searching and retrieving information from the database and finally saving the searched information into separate files. The software is the first of its kind in deep-sea applications and it also attempts to educate the user about deep-sea photography. The application software is developed by modifying established routines and by creating new routines to save the retrieved information. The information retrieval from the database with newly developed routines to create graphs and to display images are some of the outputs of the application. Finally, further modifications needed for the application are briefed in this paper. (c) 2005 Elsevier Ltd. All rights reserved.

关键词： deep-sea photography database data retrieval java application

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A web-based, collaborative, computer-aided sequential control design tool.

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IEEE CONTROL SYSTEMS MAGAZINE 2003年第2期23卷 14-19页

作者： Yen, CM Li, WJ Lin, JC Natl Hu Wei Inst Technol Dept Mech Design Engn Yun Lin 63208 Taiwan

A Web-based, collaborative, computer-aided design software tool has been developed for sequential control system design. The software includes functions for specifying a sequential control system using icons for elect... 详细信息

关键词： computer software java application lava control systems Computers Internets Consumers computer programs Electric devices ICON emulation function CIRCUIT DESIGN java Virtual Machine (JVM)

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SDAR: a practical tool for graphical analysis of two-dimensional data

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BMC BIOINFORMATICS 2012年第1期13卷 1-5页

作者： Weeratunga, Saroja Hu, Nien-Jen Simon, Anne Hofmann, Andreas Griffith Univ Eskitis Inst Cell & Mol Therapies Struct Chem Program Brisbane Qld 4111 Australia Univ Melbourne Fac Vet Sci Parkville Vic 3010 Australia Univ London Imperial Coll Sci Technol & Med Div Mol Biosci London SW7 2AZ England Univ Lyon 1 ICBMS 5246 CNRS Inst Chim & Biochim Molires & SupramolairesLab G F-69622 Villeurbanne France Queensland Trop Hlth Alliance Townsville Qld 4811 Australia

Background: Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionally, more complex software packages typically require more time by the individual user to understand and operate. Practical and convenient graphical data analysis software in java with a user-friendly interface are rare. Results: We have developed SDAR, a java application to analyse two-dimensional data with an intuitive graphical user interface. A smart ASCII parser allows import of data into SDAR without particular format requirements. The centre piece of SDAR is the java class GraphPanel which provides methods for generic tasks of data visualisation. Data can be manipulated and analysed with respect to the most common operations experienced in an experimental biochemical laboratory. Images of the data plots can be generated in SVG-, TIFF- or PNG-format. Data exported by SDAR is annotated with commands compatible with the Grace software. Conclusion: Since SDAR is implemented in java, it is truly cross-platform compatible. The software is easy to install, and very convenient to use judging by experience in our own laboratories. It is freely available to academic users at http://***/pcsb/. To download SDAR, users will be asked for their name, institution and email address. A manual, as well as the source code of the GraphPanel class can also be downloaded from this site.

关键词： java application java Classis Scalable Vector Graphic Biophysical Chemistry Left Mouse Button

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The distributed java platform

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INFORMATION SYSTEMS MANAGEMENT 1998年第1期15卷 16-20页

作者： Morgenthal, JP Java computing analyst at nc.focus an IT management consultancy focusing on distributed computing. He can be reached at jeffrey@*** or http://www.***.

java's utility in developing distributed applications extends beyond the creation of more intuitive user interfaces and expansion of access. In its greater role in the world of distributed computing, java represents a body of programming interfaces that enable java applications to communicate which each other across a process boundary, simplifying the development, deployment, and maintenance of enterprise applications.

关键词： programming interface Intuitive Access Expansion java programming language Body Distribute User Interface Device Component java platform COMMUNICATING java application creation Distributed computing

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