Flux Balance Tools

For the Friday morning here a collection of links to software applications and databases all around flux balance analysis.

Tools

• 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.
  Download 
• FluxBalance; An application to add constraints and objectives to SBML models and to evaluate them using LPsolve.
  Download
• 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.

WEB

• F.A.M.E: Web based environment for Flux Analysis. With a tutorial here. 

Databases

• 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.