- Systems Biology Workbench: While SBW does not in and of itself deal with flux balance analysis, it does make it easy to construct networks. And makes it easy to send models between applications.
- FluxBalance; An application to add constraints and objectives to SBML models and to evaluate them using LPsolve.
- CBMPy: comprehensive python package for analyzing flux balance models. Installation instructions are here.
- OpenCOBRA: MATLAB toolbox for genome scale reconstruction. Instructions on how to use are here.
- KEGG Pathway: KEGG PATHWAY Database (used by F.A.M.E for visualization).
- BIGG Database: Database of genome scale reconstructed networks. Among them the global reconstruction of the human metabolic network.