Abstract: 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.

Abstract: A method for the automatic generation of mathematical/computational models that account comprehensively and precisely for the full spectrum of chemical species implied by user-specified activities, potential modifications and interactions of the molecular components of biomolecules is described. A computer-implemented system that includes software was used to generate models. The software has a user interface that allows a user to generate new models and modify existing models.