FAME, the Flux Analysis and Modeling EnvironmentMethods, software and technology

• Published in: BMC systems biology Vol. 6
• Main Authors: Boele, Joost, Olivier, Brett G, Teusink, Bas
• Format: Journal Article
• Language: English
• Published: London BioMed Central 01.01.2012
• ISSN: 1752-0509
• DOI: 10.1186/1752-0509-6-8

Doc number: 8 Abstract Background: The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists. Results: The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/ . Conclusions: With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike.