# Model Specification

Several steps are required to specify a BioNetGen model. These include identifying the molecules to be modeled, identifying the molecular domains involved, the states and bonding of the domains and finally, the rules of all possible interactions. Next the initial conditions such as concentrations of specific states of components and reaction kinetic rate constants are specified, along with desired observables. An unlimited number of reaction rules may be incorporated.

BioNetGen provides a central chalkboard to work out these relationships. Several palette windows are used to register finalized descriptions for molecules, species and reaction rules. All descriptive specification is done graphically, thus relieving the user of adhering to any particular modeling text-based syntax. Molecules and reactions are literally drawn to suit, BioNetGen implicitly converts the graphical depiction to an internal input file that is used for mathematical modeling and prediction.