Call for a workshop

June 13th meeting at Santa Fe was successful in some ways (getting people together and getting them to agree that an SBML extension is a good idea) but not as successful in other ways (actually settling an SBML representation).

Nicolas LeNovere^? at EBI suggest hosting a 2nd meeting, with the goal of following up on the rule-based modeling/multicomponent/multistate species meeting and making further progress on the actual SBML aspects

Travel and lodging

Available dates

In case you are not available for actual travel (attending in person), but may have time to participate during some of those days, all sessions (including computer presentations) would be available for remote attendance through live videoconferecing. This should not deter you, however, to make the trip, if at all possible

Topics to discuss at rule-based modeling/multicomponent/multistate species meeting

• List all possible features that are desirable to support
  • List features are desired for each tool.
  • Which features are critically needed to each tool.
• Describe objects
  • Have multiple states
  • Consist of other objects that may have multiple states
  • May be connected with each other via different bonds
  • Located in multiple compartments, with two objects within the third can be in three different compartments)
• Describe operations (Rules):
  • Select sets of objects with common properties
  • Transform sets of objects into another sets of objects

• Other issues
  • Terminology (compatible with BioPAX)
  • MathML^?: logic and range for states
  • Representational issues (compatible with SBGN)
    • Superset of rules for contact map and MIM
    • Notations for Inhibition/stimulation reactions
  • Simulation:
    • Rules priority, score, confidence
    • Restrictions on the number of applications (length of chain?)
    • Assigning of kinetics laws within the rule
    • Tracking mass and number of molecules
    • Tracking shape

-- MichaelBlinov - 20 Jul 2007