List of systems biology software

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It seemed like this was a topic some of us are up in the air about. There are dozens of programs to sift through, and they all do different things. I thought maybe some people might be interested in listing some information about software that they've found particularly helpful or promising. Feel free to record any helpful hints/tips (ie, follow the MatLab internal link and make a note of how to get some useful MatLab function working). Let's assume everything here is SBML-compatible unless otherwise noted.

Mathematical modeling

  • MatLab, of course. We use the COBRA toolbox. Mathworks also has their SimBiology Toolbox, which merits investigation.
  • GNU Octave
  • SloppyCell - A Python-based dynamic simulation tool - particularly nice for kinetic parameter estimation and stochastic simulation. Be sure to check the discussion of "Sloppy Models" at James Sethna's website. SloppyCell is by James Sethna and Chris Myers, here at Cornell.
  • Systems Biology Research Tool - an open-source "integrated software platform", which includes most of the functionality of the COBRA toolbox. See the BMC Systems biology article for more, but there doesn't seem to be much user-oriented documentation yet. Our group hasn't used this to date.

Draw networks graphically

Build networks

  • Cytoscape may be the tool of choice for constructing networks from metabolic pathways (ie, the KEGG database), from genetic/genomic information (ie, the SGD), from microarray data, or from literature reviews (which are built in!). We're also developing in-house code for grabbing information from the KEGG API to automate metabolic network reconstruction.
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