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|
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 identifiers.org 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.
- Are there aspects of any of the proposals which would be reasonable to add to SBML Level 3 version 2?
- We need to discuss what changes for this and establish a timeline ...
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
- forall (no?)
- matrix (Use 2d vectors instead?)
- lowlimit, uplimit (used)
- 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'.
- What is the status of the various packages?
|Flux Balance Constraints|| ||sbml-flux||Frank|
|Hierarchical Model Composition|| ||sbml-comp||Lucian|
|Qualitative Models|| ||sbml-qual||Sarah|
|Spatial Processes|| ||sbml-spatial||Jim|
|Required Elements|| ||sbml-required||Lucian|
|Multistate multicomponent species|| ||sbml-multi||Nicolas|
|Distribution & ranges|| ||sbml-distrib||Nicolas|
|Arrays & sets|| ||sbml-arrays||Chris|
|Dynamic structures|| ||sbml-dynamic||Chris|
- 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.
- 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?