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Bioinformatics Advance Access originally published online on July 23, 2004
Bioinformatics 2004 20(18):3680-3681; doi:10.1093/bioinformatics/bth422
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

The JigCell Model Builder and Run Manager

Marc Vass 1, Nicholas Allen 1, Clifford A. Shaffer 1,*, Naren Ramakrishnan 1, Layne T. Watson 1 and John J. Tyson 2

1 Department of Computer Science and 2 Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0106, USA

Received on May 20, 2004; revised on July 7, 2004; accepted on July 10, 2004
Advance Access Publication July 23, 2004

Summary: We describe the JigCell Model Builder (JCMB), a tool for creating biochemical reaction network models. JCMB is designed for ease of use and its interface uses the standard spreadsheet metaphor. The JigCell Run Manager (JCRM) is a tool for organizing the large collections of simulation runs typically required by reaction network modeling activities.

Availability: JCMB and JCRM are part of the JigCell suite available at http://jigcell.biol.vt.edu

Contact: shaffer{at}cs.vt.edu

* To whom correspondence should be addressed.


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