Many of the programs or data files are intended to be used together with the freely available COBRA toolbox for Matlab or COBRApy for python.
  • Yersinia genome-scale metabolic reconstructions
    • SBML-formatted genome-scale manually curated reconstructions.  Tested on the COBRA toolbox.
    • Y. pestis strain Mediaevalis 91001: [Yp_iAN840m.xml]
    • Publication: Navid, Almaas. Mol. BioSyst. (2009)
    • (To be available) :
      • Y. pestis strain Kim: Yp_iAN821.xml
      • Y. pestis strain Orientalis: Yp_iAN825o.xml
      • Y. pestis strain Antiqua: Yp_iAN873a.xml
      • Y. pseudotuberculosis: Yps_iAN859.xml
  • Robust optimization of Metabolic Pathways (RAMP)
    • Matlab scripts used to make RAMP calculations. Results produced on the following platform: Ubuntu 14.04LTS with Matlab R2015b and Gurobi versions 6.0.5 and 7.0.1 (linux64).
    • Publication: TBA