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. On this page, we host the latest updated / tested version of the code, which may differ from versions accessible elsewhere.
  • 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
  • ModelExplorer – software for visual inspection and testing of GEMs
    • Executable for the software, written in C++:
    • Publication: TBA
  • Automated generation of genome-scale metabolic draft reconstructions based on KEGG
    • Function for the Matlab COBRA Toolbox v3.0, written in Matlab and tested on Matlab 2017b
    • Publication: TBA