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FAME, the Flux Analysis and Modeling Environment
Joost Boele1, Brett G Olivier, Bas Teusink
1Systems Bioinformatics/AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands.
BMC Systems Biology
|February 1, 2012
Summary
The Flux Analysis and Modeling Environment (FAME) is a new, open-source web tool that integrates metabolic model creation, editing, running, and analysis. This user-friendly platform simplifies stoichiometric modeling for researchers and educators.
Area of Science:
- Systems Biology
- Metabolic Engineering
- Computational Biology
Background:
- Genome-scale metabolic model creation and modification require specialized software.
- Current tools often involve disjointed code for running and visualizing models, hindering routine use by biologists.
Purpose of the Study:
- To develop an integrated, user-friendly, web-based platform for stoichiometric modeling.
- To streamline the process of creating, editing, running, and analyzing metabolic models.
Main Methods:
- Developed the Flux Analysis and Modeling Environment (FAME), a web-based application.
- Integrated model creation, editing, running, and analysis functionalities into a single program.
- Utilized PHP for the web interface and PySCeS-CBM (Python-based) for linear solving capabilities.
Main Results:
- FAME is the first web-based tool to combine all stoichiometric modeling tasks.
- Analysis results can be automatically visualized on KEGG-like maps.
- The tool is accessible online with a comprehensive manual and tutorial.
Conclusions:
- FAME provides an open-source, user-friendly, web-based solution for stoichiometric modeling.
- The application is expected to benefit both researchers and educators in the field.
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