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.
Signalling and protein-protein interaction (PPI) networks differ from metabolic processes in many aspects. One can not relay there on mass conservation constraint. At the same time, Boolean type of modelling gives an effective modelling tool limiting the states just by active (=1) or inactive (=0) states. Boolean modelling can be combined also with kinetic modelling technologies whenever a sufficient amount of details is available.
PPI networks of actin polymerisation in humans and signalling networks in plants are addressed by our group so far.
We use GinSim, CellNetAnalyzer and Cellcollective software tools.