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Bioinformatics Advance Access originally published online on May 6, 2009
Bioinformatics 2009 25(15):1987-1988; doi:10.1093/bioinformatics/btp268
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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 and 2 IBISC, FRE 3190 CNRS, Université d'Evry, Evry, France

* To whom correspondence should be addressed.


  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

Associate Editor: Thomas Lengauer

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

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