Optimization of cellular metabolism
Cellular metabolism is one of the most measured phenomena and can be modeled by many formalisms, approaches and their combinations. We use just some of them.
The stoichiometric modelling approach can be used for the 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. The small amount necessary of information per reaction enables the 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 modelling metabolism of very different organisms:
bacteria Zymomonas mobilis and Escherichia coli,
unconventional yeast Kluyveromyces marxianus,
plant Arabidopsis thaliana,
We see a high potential of genome scale modelling application in Personalised Medicine.
We have used several software platforms COBRA, ScrumPy and COBRApy. We have developed some software for stoichiometric modelling like Paint4Net for COBRA, AltFluxes for COBRA.