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Bioinformatics Advance Access published online on May 6, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp268
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CycSim - an online tool for exploring and experimenting with genome-scale metabolic models

F Le Fèvre 1, S Smidtas 1, C Combe 1,2, M Durot 1, Florence d'Alché-Buc 2 and V Schachter 1,*

1 CEA, DSV, IG, Genoscope, UMR 8030, Evry, F-91057, France.
2 IBISC, FRE 3190 CNRS, Université d'Evry, Evry, France.

*To whom correspondence should be addressed. Dr. Vincent Schachter, E-mail: vs{at}genoscope.cns.fr


  Abstract

Summary: CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes, and direct visualization of both on metabolic maps. The web interface is designed for simplicity, putting constraint-based modelling techniques within easier reach of biologists. CycSim also functions as an online repository of genome-scale metabolic models.

Availability: http://www.genoscope.cns.fr/cycsim

Contact: cycsim{at}genoscope.cns.fr

Supplementary Information: http://www.genoscope.cns.fr/cycsim

Associate Editor: Prof. Thomas Lengauer

Received on October 7, 2008; revised on March 20, 2009; accepted on April 17, 2009

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