Simulations
can be used to test the physico-chemical limitations and feasibility of
certain proposed reactions. In addition, simulating increasingly
complex networks will help to understand the impact of various factors
(e.g. drugs) on metabolic systems. Part of this project is the
development of tools for the simulation of biochemical networks.
Together with the group of Pedro Mendes (Virginia Bioinformatics Institute),
we are developing a software package which allows the simulation and
detailed analysis of biochemical pathways. The package is based on
software which was developed by Pedro Mendes (Gepasi) and on the
software STODE developed by us and is called Copasi (Complex Pathway
Simulator).
Copasi incorporates a model generator, different
simulation techniques (e.g. determistic and stochastic), optimization
routines, sensitivity analysis and userfriendly visualisation
techniques. To name only the most important parts.
