How to create a rule-based model

There are several ways to create a rule-based model:

Import an existing rule-based model encoded in BNGL format, using File->Import menu. The rule-based model will be created with two applications: a network-free application called NFSim, and a deterministic network application called BioNetGen. If some features in a BNGL file are not supported by VCell, a pop-up window appears with suggestions for correcting unsupported features. If features in a BNGL file (e.g. specifying a fixed concentration value) are supported by BioNetGen but not by NFSim, only a single deterministic rule-based application will be created.

Create a new rule-based model or convert an existing single-compartment reaction network model into a rule-based model by adding rule-based features using the Physiology tabs.

To create a new rule-based model, the user has to perform the following operations:

• Create one or more Molecules - structured objects with binding sites having optional attribute states
• Create one or more Species that are made of molecules (optionally) connected through binding sites. These composite species will serve as seed species for either network generation or network-free simulation.
• Create one or more reaction rules (specified in the Reactions Table) that describe transformations of species classes by specifying initial and final states of molecules participating in the reaction.
• Create one or more Observables that describe classes of species with specified features, e.g. having the same site in a phosphorylated state.