Formalized graphical reaction rules and conventions accounting for chemical states and binding or reaction states are provided for modeling complex biological systems such as signal transduction pathways. A system model is derived by defining typed attributed graphs which delimit molecular entities and their possible states. Graph transformation rules defining a class of potential reactions are defined and applied to the graphs and all new graphs that subsequently arise as a result of graph transformation. In one embodiment, a model is generated through the use of graph-rewriting rules which are associated with rate laws and applied iteratively to a seed set of chemical species graphs until a termination condition occurs.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
 This invention was made with Government support under Grant No. GM35556 and RR18754 awarded by The National Institute of Health as well as Department of Energy Contract No. W-7405-ENG-36. The Government has certain rights in this invention.