Network-Free Specifications

For every model specified in a single compartment and having only mass-action kinetics, a modeler is able to create a new rule-based BioModel. Every rule-based enabled element of a model (molecules, observables, species with molecular details, reaction rules) are transferred to a new model without changes. Regular elements of a model (species without molecular detail and reactions) are converted into rule-based physiology by generating of molecule per species, and having reactions written as fully-defined reaction rules.

For user convenience, the Network-Free tab provides statistics of rule-enabled and regular elements of current model physiology, and the same stgatistics for the rule-based model to be created.

Create New Rule-Based VCell BioModel generates a new BioModel and opens it in a new window.

Note that the same reaction expression treated as a reaction and as a reaction rule will have different rates:

• VCell will take care of reactions of the form A + A -> product(s), and the rate of generated reaction rules will be multiplied by 2 to account for symmetry factors.
• VCell does not take care of reactions where reactants have symmetric sites and reaction rule will have a statistical factor. If this is not properly treated by a modeler, the resultant rule-based model may show different simulation results than its network precursor.