Wish List

From BioNetWiki

Documentation

• Installation Guide

Feature Requests

• Ability to select a patten of observables (e.g. ability to select substrates that have 6/10 sites phosphorylated from a 10-site substrate).
• Ability to suppress .cdat output. This is useful when only .gdat are of interest and .cdat files become extremely large.
• Zeroth order reactions.
  • This is simple to do on a reaction by reaction basis, but it's tricky if a class of reaction can undergo a zeroth order reaction.
• Math expressions for parameters and observables.
  • These will be preserved as assignment rules in the SBML output.
• Better handling of species/molecule creation.
• Parameter scanning.
• Parameter fitting.
• Link to NuSMV output.
• Allow bonds between Molecules, bypassing components.

Items

1. Allow whitespace to appear within molecules, patterns, and species.
2. Check that allowed component state labels are compatible when mapping component states through the Label mechanism.
3. Require that bonds are uniquely labelled across all patterns on one side of a reaction rule {UPDATE: now implemented).