Overview of Rule-Based Features

The Virtual Cell Software version 6.0 for the first time provides an integrated environment to introduce rule-based features in the VCell interface alongside familiar species and reaction concepts. The new parts of Physiology specifications include Molecules and Observables, as well as reaction rules that are specified alongside reactions in a Reactions Table.

Rule-based features and compartments

Defining Molecules allow the user to create species that have molecular details. Currently, rules can operate in a single compartment only (this is a temporary restrictions that will be lifted in the next release). Once a reaction rule is created, any new species by default will be placed in c0 compartment, and this can not be changed. Vice versa, if multiple compartments are created, no rules can be added.

Mixing Rule-based features and reaction networks

As with a regular BioModel, a rule-based BioModel consists of a model description (Physiology), and one or more Applications. Except for a limitation of a single compartment, any operations with ordinary species and reactions are supported in VCell 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 numerical simulation. A Rule-Based BioModel may have numerous Applications, including deterministic, stochastic and network-free. 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 needs to generate the complete network of species and reactions.
This network is obtained by applying the set of reaction rules to the set of seed species with initial amounts specified in Species specification tab. Network specification parameters are used to control the size of the network, which otherwise can become infinite. The generated species and reactions can be seen in Network tab, but they are not added to the Reaction Diagram view.
After the user is satified with the network that is generated using the set of species and reaction rules, he/she can run any determiministic or stochastic simulation.

Rule-Based MathModel

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