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Bioinformatics Advance Access originally published online on August 19, 2004
Bioinformatics 2005 21(2):269-271; doi:10.1093/bioinformatics/bth478
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.

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

Steven Vercruysse and Martin Kuiper *

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.

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 (PLDEs). 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/

Contact: {stcru,makui}{at}psb.ugent.be


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