technical report Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes


Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves. Discrete stochastic simulation of molecular kinetics potentially o ers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described by simple mass action chemistry. Moreover, modelling every individual molecular interac- tion in the cell is probably unnecessary and currently impractical. Simulation is a form of computer aided analysis, relying on human inter- pretation to derive meaning. To improve eciency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties.

Paper Details


S. Sedwards,  T. Mazza