Software for Modeling Biochemical Reactions

Cellerator is a computer program that auto- matically generates and solves differential equations for complex sets of chemical reac- tions like those in living cells. Cellerator provides a mathematical and computational infra- structure for char- acterizing reaction pathways and the interactions between complex molecules (e.g., proteins and nucleic acids) and cellular environments. The user effectively defines the pathways by specifying an input set of chemical reactions. Examples include enzymatic reactions, creation and degradation of various chemical species, binding and unbinding reactions, phosphorylation reactions, and transcription and translation of nucleic acids. More complex signals, such as a chemical cascade, can also be specified. Cellerator translates the specifications of chemical reactions into the corresponding set of differential equations, then solves these equations numerically. Cellerator provides an explicit description of output at several steps through the model-generation process; this feature affords flexibility by facilitating intervention by the user to modify the computational model “on the go,” as might be desirable, for example, to correct errors.