Proposal

The overall conclusion of the workshop was that 2 separate proposals will be developed. One will focus on the language elements required for the actual "model composition" (but brings also additional, initially unforeseen, functionality - such as encoding parameter sets and multiple related simulations). The other will focus on the mechanics of simply assembling SBML from bits and pieces (linking in multiple files and/or fragments thereof).

It is expected that the first proposal will be a bonafide L3 extension, wehereas the second will be (part of) L3 core enhancement(s). Links to the proposals are providede below, followed by the original materials/details/agenda, etc. of the workshop.

• Hierarchical Modeling (former Model Composition) - L3 extension proposal
• Module based core structure - L3 core enhancement proposal

Call for a workshop

Ion Moraru and Michael Blinov at UCHC suggested to host a small workshop before the 2007 SBML Forum - following up on the submodels/model composition interest group meeting from the 2007 Hackathon. The goal is to make further progress towards a draft SBML Level 3 extension.

Logistics

There will be a 2-day meeting, September 9 and 10. UCHC will be able to fund lodging, breaks, ground transportation, and airfare cost for participants that will attend in person.

Administrative contact:
Debbie Manchak
Email: manchak@nso.uchc.edu
Tel: 860-679-3565
Fax: 860-679-1039

Videoconferencing

Parts of the meeting will be available via live videoconference (H.323). The multipoint hosting site will be the CCAM conference room. Up to 6 video and 3 audio participants can connect at the same time. Dual stream is supported (video source + computer screen).

Confirmed video sites: - WE WILL DIAL OUT TO THESE SITES

• Hinxton (193.62.197.99)
• Magdeburg (193.175.52.100)

Dialing instructions: - in case somebody else wishes to join, or if you get disconnected...

• Video link (H.323): 5095@155.37.201.60 (or ccam@uchc.edu if your DNS/URI resolving config is set up properly)
• Audio only (ISDN): +1(860)679-6665 (regular phone call)

Lodging

   Homewood Suites by Hilton
   2 Farm Glen Blvd.
   Farmington, CT 06032
   Tel: (860) 321-0000
   Fax: (860) 321-0001

Background material

Updated 2007-09-05.

What is the goal of SBML composition?

Model composition refers to the ability to include models as submodels inside other models. This requires defining the interfaces between the models and rules for connecting parts of models together. The motivation is to enable the creation of standard, vetted models and use them as library components when creating larger models, much as is done in software development, electronics design, and other engineering fields.

What are the issues?

Ranjit Randhawa has a presentation summarizing his work on model fusion, aggregation and composition for his Ph.D. at Virginia Tech using models from the Tyson lab. Among other interesting features of this work, it helps frame the overall problem and distinguishes different ways in which we can think about "composing" models in SBML.

For the present meeting about composition in SBML, Martin Ginkel has just recently compiled a list of goals and issues: MartinGoals

After the 2007 SBML Hackathon in Newcastle, Andrew Finney sent email around summarizing some of the technical issues discussed in Newcastle: AndrewComments

Nicolas Le Novere posted a message on sbml-discuss in July calling for the inclusion of modules in SBML Level 3 core, similar to CellML^? components. These modules, that could contain any number of any other SBML construct, would have their own namespaces, and would use consistent units. A variable in a component (compartment, species, parameter etc.) could be private or public. The use of modules would greatly facilitate the building and curation of models, would improve interoperability with CellML^? and would provide the ground for model composition. Andrew's 2003 proposal on model composition would only require a minor change: The pointers would identify either the main SBML model or a module.

Complete proposals

• Andrew Finney's proposal of Oct. 2003. There is also a poster from ISMB 2004 that summarizes Andrew's composition proposal.

• Martin Ginkel's proposal of June 2002. Martin also gave a summary in a presentation at the 5th SBML Forum in 2002. Martin also has a web page for SBML composition containing this and an earlier presentation.

• CellML 1.1 includes a mechanism for composing models out of components. While not a proposal for SBML, there ares ideas there to keep in mind. At one point, we did state that a goal of SBML's composition facility was to allow interoperability with CellML via some sort of defined interfaces, though it is far from clear that the current proposals for SBML composition would make this possible.

Additional reference materials

• semanticSBML is a system for merging multiple SBML models into one (also see this poster). Any proposal for submodel composition will certainly affect semanticSBML, and likewise, its needs and capabilities may influence the SBML composition extension effort.

• Andrew Finney previously suggested that a proposal for sets could be another way to achieve model composition. Indeed, it remains an open question whether perhaps the model composition, sets and arrays could not somehow be combined into one overall framework using a single set of mechanisms.

• The Modelica 2.2 language provides for hierarchical object-oriented composition of components.

• JSim is a Java-based modeling framework that provides a way to do object-oriented composition.

Agenda

Updated 2007-09-09.

Topics to discuss (issues to settle?)

• What functionality to support? (i.e. what do we actually need...)
• Where is the line between standard and implementation? (i.e. what is the responsability of the language and what is the responsability of the tools)
• What are the dependencies? (i.e. coordination with core changes and other proposed extensions)
• What is the timeline? (i.e. when can we come up with the first real draft...)

Schedule (all times EDT):

Sunday, September 9

• 8:00 am - 8:30 am: Coffee, video links, etc.
• 8:30 am - 10:30 am: Live session 1 - Short presentations
  • Mike Hucka: intro-to-composition-meeting-2007-09-09.pdf: Introduction to composition meeting
  • Ion Moraru: Use_cases_-_VCell_strategy.ppt: Modeler's viewpoint - simple use cases...
  • Wolfram Liebermeister: Model merging with semanticSBML:
  • Michael Blinov: Leveraging BioPAX and other ontology concepts for modularity and model reuse 20070909.ppt:
• 11:50 am - 12:00 pm: Break
  • Cliff Shaffer for Ranjit Randhawa: UCHCpresentation.ppt: Composition in Modeling Macromolecular Regulatory Networks
  • Lenov: ModularityInCore.pdf: Advocacy that modularity should be in core. SBML files: Main.xml charybde.xml scylla.xml. See also the page Modularity In Core
  • Martin Ginkel: Object-Oriented Modeling in ProMoT: (and other tools)
  • Andrew Finney: model-composition-2007.ppt
  • Mike Hucka: review-of-proposals-2007-09-08.pdf: Brief comparison of Finney & Ginkel proposals
• 2:00 pm - 3:00 pm: Lunch
• 3:00 pm - 6:00 pm: Breakout session
• 6:30 pm - ? : Dinner The Grist Mill Restaurant

Documents produced the first day by UCHC side:

• IssuesToAddress
• ProposalTemplate

Documents produced the first day by EBI side:

• ModularityInCore

Monday, September 10

• 8:00 am - 8:30 am: Coffee, video links, etc.
• 8:30 am - 10:30 pm: Live session
• 10:30 am - 10:45 am: Break
• 10:45 am - 2:00 pm: Live session
• 2:00 pm - 3:00 pm: Lunch