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Bioinformatics visualization and integration with open standards: The Bluejay genomic browser

In Silico Biology 2005年第2期5卷 187-198页

作者： Turinsky, Andrei L. Ah-Seng, Andrew C. Gordon, Paul M.K. Stromer, Julie N. Taschuk, Morgan L. Xu, Emily W. Sensen, Christoph W. University of Calgary Faculty of Medicine Sun Center of Excellence for Visual Genomics Calgary Alta. T2N 4N1 3330 Hospital Drive NW Canada

We have created a new java™-based integrated computational environment for the exploration of genomic data, called Bluejay. The system is capable of using almost any XML file related to genomic data. Non-XML data sources can be accessed via a proxy server. Bluejay has several features, which are new to Bioinformatics, including an unlimited semantic zoom capability, coupled with Scalable Vector Graphics (SVG) outputs;an implementation of the XLink standard, which features access to MAGPIE Genecards as well as any BioMOBY service accessible over the Internet;and the integration of gene chip analysis tools with the functional assignments. The system can be used as a signed web applet, Web Start, and a local stand-alone application, with or without connection to the Internet. It is available free of charge and as open source via http://***. © 2005 IOS Press and Bioinformation Systems e.V. and the authors. All rights reserved.

关键词： Bioinformatics BioMOBY web services Bluejay eXtensible Markup Language (XML) java™ Open standards Scalable Vector Graphics (SVG) Visualization

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Active objects made easy

引用

Software: Practice and Experience 1999年第1期28卷

作者： Martin Carroll Bell Laboratories Innovations for Lucent Technologies 700 Mountain Avenue Murray Hill NJ 07974-2070 U.S.A.

A widely useful technique for implementing complex programs is to use multiple threads of execution. Unfortunately, when we multithread a program we introduce the potential for bugs caused by unprotected critical sections. A widely useful technique for reducing the number of critical sections, and hence the number of bugs, is that of active objects . This paper presents a design for active objects that is easy to understand, implement and use in any sufficiently powerful object-oriented programming language. We show the implementation and use of our design in both the java TM and C++ programming languages. © 1998 John Wiley & Sons, Ltd.

关键词： multithreading active objects embedded programming java™ C++

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