How to create a rule-based model
There are several ways to create a
rule-based model:
- Import existing rule-based model encoded in BNGL format, using File->Import menu.
The rule-based model will be created with two applications:
network-free
called NFSim, and
deterministic
network application called BioNetGen.
If some features in BNGL file are not supported by VCell, a pop-up window is launched
with a suggestion to correct unsupported features.
In some cases, when some features in BNGL file (such as fixed value of concentration) are supported by
BioNetGen but not
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
rule-based by adding rule-based features using 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 state
- 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 Reactions Table) that describe transformations
of species classes by specifying of the initial and final states of participating in reaction molecules.
- Create one or more Observables that describe classes of species with specified features,
e.g. having the same site being phosphorylated.