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Bioinformatics Advance Access published online on August 19, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth478
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 9, 2004
Accepted July 27, 2004

Applications note

Simulating genetic networks made easy: network construction with simple building blocks

Steven Vercruysse 1* Martin Kuiper 1

1 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052, Gent, Belgium

* To whom correspondence should be addressed. E-mail: stcru{at}psb.ugent.be.


  Abstract

Summary: We present SIM-plex, a genetic network simulator with a very intuitive interface in which a user can easily specify interactions as simple "if-then" statements. The simulator is based on the mathematical model of Piecewise Linear Differential Equations. With PLDEs, genetic interactions are approximated as acting in a switch-like manner.

Availability: The Java program, examples and a tutorial are available at http://www.psb.ugent.be/cbd/.


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