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Thursday, April 18, 2013

Flux Balance Tools

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

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

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