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Open Access Highly Accessed Software

FAME, the Flux Analysis and Modeling Environment

Joost Boele12, Brett G Olivier123 and Bas Teusink12*

Author Affiliations

1 Systems Bioinformatics/AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands

2 Netherlands Institute for Systems Biology (NISB), Amsterdam, The Netherlands

3 Life Sciences, Centrum voor Wiskunde en Informatica (CWI), Science Park 123, 1098XG, Amsterdam, The Netherlands

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BMC Systems Biology 2012, 6:8  doi:10.1186/1752-0509-6-8

Published: 30 January 2012

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/ webcite.

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.