Network Specifications

The Network Tab enables the user to specify constraints for generating a reactin network from the rules in a rule-based model. Network-generation is performed by the BioNetGen engine. The network that is generated can then be used in deterministic and stoichastic applications. In addition, the user can test the size of the reaction network that would be obtained using the constraints supplied, prior to actually generating the network. The network tab is active only if at least one Molecule is specified.

• Max Iterations - how many times the rules are applied to the set of seed species to generate new species and reactions.
• Max Molecules/Species - the maximal number of molecules of any type that can be in a single species. BioNetGen will not apply any rules to species reaching this limit.
• Species - the total number of species in the reaction network generated under specified constraints, including seed species.
• Reactions - the total number of reactions in the reaction network generated under specified constraints.

Clicking the "Edit/Test Constraints" button presents a window to specify new constraints.

• Test/Run to attempt to generate a reaction network using the specified constraints.
• Apply the constraints without generating a network; a simulation will be performed sequentially after generating the network.

• Max iterations number may be insufficient suggests that the network may be not exaustively generated. In this case the Network Generation Status pane displaying the number of species will show that the number of species during the last two iterations is different. Generation of the network is generally considered complete when the last iteration does not produce new species and thus the number of species at the last two iterations is the same.
  
  
• Max Molecules/Species number may be not sufficient indicates that a species with aspecified number of molecules is a subject of a rule applied in the last interation. This indicates that the network is truncated because of the limits set for the number of molecules of that species in the network.
  
  

  Note: When the warning is displayed, the network is truncated, so a simulation using NFSim is likely to produce different results compared to deterministic or stochastic simulations that use this network.

Use the Apply button to apply the specified constraints.

• View Generated Species/View Generated Reactions after constraints are applied. The pop-up window shows the species name, depiction and searchable BNGL code. Species names are the same as seen "Generated Species" is checked in the "Simulation Results" window.
  
  
• Create New VCell BioModel from Network launches a new BioModel in a new window. This BioModel consists of all generated species and reactions, species have molecular details, while reactions carry rule name under reaction name.

  Note: reaction rates in reaction network are adjusted for symmetry factors and statistical factors.