Systems medicine is a very complicated and rewarding research area where signaling, transport and metabolism modeling skills can be applied.
We are developing and optimising kinetic models of metabolism, pharmacokinetics and signalling. Other types of processes can be addressed depending on the amount of the available information.
Usually, we work with systems of ordinary differential equations, while other approaches can be exploited on demand. Our particular strength is the experience in the use of global stochastic optimisation methods in parameter estimation and optimisation tasks. In both cases, we are implementing different types of constraints to improve the credibility of results.
Our main modelling tool is software COPASI. We have used COPASI alone and in combination with COPASI wrapper SpaceScanner to manage parallel optimisation runs of global stochastic optimisation methods.