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2012-05-20 During HARMONY

SBML Editors' meeting minutes

Editors present: Sarah Keating, Nicolas Le Novere, Chris Myers, Michael Hucka, Lucian Smith
Editors absent: Jim Schaff
Visitors present: Frank Bergmann
Location: Maastricht University, Maastricht, Netherlands
Scribe: Michael Hucka
Recording(s): none

Note: A Summary of the decisions made at the meeting is also available.


Topics about specific issues with SBML

  • Validity question: Consider a model with a species with no rules about how the species itself changes (no reactions, no rules), with the attribute 'hasOnlySubstanceUnits=false', and which is in a compartment whose size changes. Its amount does not change, but its concentration does. Is it valid to give this species the attribute 'constant=true', or must it be flagged 'constant=false'?
  • SBOTerm attribute: Sarah assured Nick Juty she would raise this issue. Since allows annotations to be resolvable from the model, could we consider having a syntax for the sboTerm attribute that would take the whole resolvable string instead of just the number.

Nicolas's proposals



Candidate changes:

  • All L2v5 fixes (agreed) All L3v1 errata
  • Look through old tracker items
  • Move the required attribute of the packages from the sbml core element: change to the 'listOfPackages' structure.
  • SId's on everything (discuss with group)
  • Also, we can discuss whether a path should be created to move packages into core
  • Extend MathML (discuss with group)
    • min, max
    • prod, sum (used)
    • selector (used)
    • ci and cn type=vector
    • exists
    • forall (no?)
    • matrix (Use 2d vectors instead?)
    • selector
    • bvar
    • lowlimit, uplimit (used)
    • interval
    • condition
    • vectorproduct
    • scalarproduct
    • innerproduct
    • transpose
  • Ask the list if people have other ideas
  • Relax SIdRef rules for the 'variable' attribute of assignments and rules to allow references to SIds from packages? (discuss with group)
  • Clarify what rules are available to package writers when they declare 'id' attributes, specifically what it means when they declare that an attribute is of'type SId' vs. 'type [package]SId'.

Package Statuses

  • What is the status of the various packages?
Name Label PWG list Editor
Layout layout sbml-layout Frank
Flux Balance Constraints fbc sbml-flux Frank
Rendering render sbml-render Frank
Hierarchical Model Composition comp sbml-comp Lucian
Qualitative Models qual sbml-qual Sarah
Annotations annot sbml-annot Nicolas
Spatial Processes spatial sbml-spatial Jim
Groups groups sbml-groups Mike
Required Elements req sbml-required Lucian
Multistate multicomponent species multi sbml-multi Nicolas
Distribution & ranges distrib sbml-distrib Nicolas
Arrays & sets arrays sbml-arrays Chris
Dynamic structures dyn sbml-dynamic Chris

Package acceptance

  • What are the specific requirements for package final approval: what counts as "two implementations"?

IDs and IDRefs

  • Lucian has a short summary of issues he's discovered with comp with respect to IDs and IDRefs, and has a couple questions.

Not Comp

  • Model ownership
  • Strengthening vs. loosening requirements

Promoting/demoting elements to/from packages

Fuller discussion of Nicolas's issues and proposals

  • How best can we continue the discussion, and move forward with more ideas and refinements?

Other topics?

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