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2012-08-19 During COMBINE

SBML Editors' meeting minutes

Editors present: Michael Hucka, Nicolas LeNovere, Chris Myers, Jim Schaff, Lucian Smith, Sarah Keating (as robot)
Editors absent:
Visitors present: Stuart Moodie, Michael Blinov
Location: University of Toronto, Canada
Scribe: Lucian Smith

Revisiting MathML subsets defined by packages

What to do when packages interact?

  • In particular, comp and arrays interact in two ways:
    • All comp's SIdRef attributes may need to have a selector on that SIdRef.
      • This might be able to be covered by a clever rule in arrays 'elements with SIdRefs may have a child 'selector' object...' But maybe not; more research needed.
    • You may want arrays of Submodels.
      • This will need an explicit specification. Where does it go? In the arrays package, because the arrays package came out after comp? In r2 of comp only? In a separate 'Specifications For Package Interactions'? Those are all possible options; we'll have to choose when the arrays package comes out.

Let's write the arrays package at the SBML Editor's Meeting

  • Dimensions:
    • Need an ID (probably?)
    • Need a 'size' which will be a constant parameter SIdRef.
    • Need an 'order' attribute.
    • We need examples to make some more technical decisions like whether these IDs are local or global.

It was decided that Sarah and Stuart would work on a prototype implementation for libSBML and the DDMore project; which will hopefully iron out some issues.

What does 'distrib' need?

  • Worked out that Stuart and Sarah can work together on what libsbml needs and what the spec needs to get some implementation done by the end of the year.

How do we finalize comp (and future specs)

  • Lucian to come up with cover letter from authors to editors, explaining how the package adheres to the principles from the package guidelines.
  • Email to authors out now, with feedback due by Aug 31. Assuming approval:
  • Email to sbml-comp on Sept 1 saying 'here is the spec, implementations, and cover letter to editors; we will send them all to the editors on Sept 14, assuming no objections.' Assuming no objections:
  • Email to editors with cover letter, implementations, spec: this is 'release candidate'.
  • Editors email sbml-discuss saying 'hey, here's the release candidate'. They also evaluate cover letter, implementation completeness, etc. Assuming no issues:
  • Maybe Oct 14, the editors vote for final approval (with Lucian, Chris, and Mike voluntarily recusing themselves from the vote), and the spec is finalized!
  • We change the procedures page to mention what bit is the 'release candidate' stage.

Anything we need to do about the RevisedMulti proposal?

  • Michael Blinov visited and explained that they were unable to implement the current Multi spec, and had no plans to try. The new proposal from the Simmune group (RevisedMulti) actually sounds more promising, and he can imagine being able to encode their models with that, instead. So basically, everyone likes the idea of the new spec, and that's where immediate future efforts should be encouraged.


  • If we can sweep the allowable-mathml issue under the rug and let packages redefine allowable constructs, the remaining listed issues from Harmony are all uncontroversial. Mike will send an email (/emails?) to sbml-discuss for discussion.

Scientific Advisory Board

  • Nicolas's proposal is that we have 1/3 'friends of SBML', 1/3 modelers who *could* use SBML but don't, and 1/3 big names people tangentially involved in experiments, bits of which could use modeling. We came up with many names to pu on this list; we'll divvy them up, figure out exactly what we're asking them to commit to, and start inviting them.

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