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

F. Le Fèvre; S. Smidtas; C. Combe; M. Durot; Florence D'Alché-Buc; V. Schachter

doi:10.1093/bioinformatics/btp268

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

F. Le Fèvre
, S. Smidtas
, C. Combe
, M. Durot
, Florence D'Alché-Buc
, V. Schachter

Genoscope - Centre National de Séquençage
GENOPOLE

Research output: Contribution to journal › Article › peer-review

23 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	1987-1988
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	15
DOIs	https://doi.org/10.1093/bioinformatics/btp268
Publication status	Published - 1 Jan 2009
Externally published	Yes

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10.1093/bioinformatics/btp268

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AU - Le Fèvre, F.

AU - Smidtas, S.

AU - Combe, C.

AU - Durot, M.

AU - D'Alché-Buc, Florence

AU - Schachter, V.

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AB - 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.

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JO - Bioinformatics

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

Abstract

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