Overview of Rule-Based Features

The Virtual Cell Software now provides an integrated environment to introduce rule-based features among species and reactions in a VCell Biomodel. Additions to the Biomodel Physiology include Molecules and Observables, as well as reaction rules that can be specified alongside reactions in the Reactions Table. Defining Molecules allows the user to create species that have molecular details.

Mixing Rule-based features and reaction networks

Similar to the traditional BioModel, a rule-based BioModel consists of a model description (Physiology) and one or more Applications. Any operations on species and reactions that are supported in VCell can be used alongside rules. Specifically, species that are used as initial seed species for rule-based models can be used as species in reaction networks.

Rule-based Applications

Each BioModel Application allows the user to define the quantitative conditions needed to define, run and visualize a numerical simulation. A Rule-Based BioModel may have mutliple Applications, solved using deterministic, stochastic or network-free approaches. Each Application, in turn, can have multiple Simulations, in which different numerical methods or conditions are used.

In order to run deterministic or stochastic ( rule-based) applications the BioNetGen network-generation algorithm first generates the complete network of species and reactions.
The network is created by applying the set of reaction rules to the set of seed species with initial amounts specified in the Species specification tab. Network specification parameters are used to control the size of the network, which otherwise can become infinitely large. The generated species and reactions can be seen in the Network tab.
After the user is satified with the network that is generated using the set of species and reaction rules, any determiministic or stochastic simulation can be run.

Rule-Based MathModel

MathModels for deterministic or stochastic applications generated by a rule-based model have a standard VCell structure with a full list of species and reactions, as well as observables defined by functions. MathModels for network-free application have a new syntax.