Stoichiometric modeling approach can be used for analysis of feasible steady states (metabolite concentrations are not changing in time) and minimally need information just about reaction stoichiometry. Additional constraints like lower and upper bounds of fluxes, reaction directionality and others can make the model predictions more accurate. Small amount necessary of information per reaction enable development of large models. At the same time the disadvantage is that stoichiometric models can not be used to simulate any changes in time and can not calculate metabolite concentrations.

We have been stoichiometrically modeling metabolism of very different organisms:

  • bacteria Zymomonas mobilis and Escherichia coli,
  • unconventional yeast Kluyveromyces marxianus,
  • plant Arabidopsis thaliana,
  • human metabolism.

We see high potential of genome scale modeling application in Personalised Mecicine

We have used several software platforms COBRA, ScrumPy and COBRApy.

We have developed some software for stoichiometric modeling like Paint4Net for COBRA, AltFluxes for COBRA.