PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of bmcsysbioBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Systems Biology
 
BMC Syst Biol. 2012; 6: 8.
Published online 2012 January 30. doi:  10.1186/1752-0509-6-8
PMCID: PMC3317868

FAME, the Flux Analysis and Modeling Environment

Reviewed by Joost Boele,1,2 Brett G Olivier,1,2,3 and Bas Teusinkcorresponding author1,2

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.


Articles from BMC Systems Biology are provided here courtesy of BioMed Central