ABI Meeting minutes 2009-04-22

Present: Dougal Cowan, James Lawson, Andrew Miller, Poul Nielsen, Mike Cooling, Alan Garny, Randall Britten, Catherine Lloyd, Tommy Yu

Last week's action items:

1) Catherine to get in touch with Allyson Lister to ask very nicely about CellML support in Saint.
  • Catherine is in email contact with Allyson, and pending sorting out the Java API, she is happy to extend Saint to support CellML.
2) Tommy to check if the script supports both cases of e(E).
  • This was not done, as it was decided not to fix the e-notation during the migration to PMR2 (see agenda item 1 below for an elaboration of this).
3) Catherine to email workshop participants for permission to publish audio/video recordings of them.
  • Catherine has sent the emails, still waiting on 6 or 7 responses.

This week's agenda:

1) E-notation script for automatically fixing models
  • Catherine, Alan and Randall had an impromptu meeting about this during the week. Alan said that as JSim (and, most likely, other CellML tools) does not support the correct MathML e-notation, batch fixing all the repository models would break them all in JSim.
  • Randall said that even if the e-notation is fixed, the models will still need to be re-validated and fixed by hand anyway.
  • Poul favours an automatic expansion of e-notation (1E10 to 10000000000) to make the repository models valid while maintaining compatibility.
  • Alan said that we will have to contact all tool developers and tell them about the correct MathML e-notation.
  • It was agreed that the bulk fix should be performed using a script, after having contacted tool developers.  Developers will be given a date at which the bulk fix will be applied, by which time their tools should be compliant.

2) IUPS flights etc.
  • James said that Nirosha had found some cheap flights which had to be decided upon by the end of the day. This was to be discussed with the appropriate parties after the meeting.

3) PMR2 update
  • Tommy had made bug fixes, and given Mike  and Alan a demo.
  • Mike has tried PMR2, and it all seems to be working fine.  Mike is keen to start using it, and wants to use PMR2 for a paper rather than PMR1; he asked when PMR2 is going to be deployed?
  • Tommy said that he can probably stage it within 2 weeks.
  • Randall said that a decision is required on how to handle citation metadata editing before PMR2 is deployed.
  • Andrew suggested that metadata editing is probably best handled by OpenCell.
  • There was an extensive discussion about how to implement citation metadata editing.
  • James asked if he could have a version of the PMR1 metadata editor running until there is another option.
  • Tommy would prefer to implement a standalone tool version of the PMR1 editor.
  • Tommy would like to strip out the BQS and have Dublin Core only.
  • It was agreed that we not make metadata editing a blocker of PMR2, and agree to edit metadata on people's behalf [as part of the curation process].  James is happy to edit people's metadata.

4) Website redesign - update
  • Tommy reported that Gareth is still working on the templates.
  • Randall asked about decoupling the website redesign and PMR2 - Tommy said this would be too much extra work.
Action item 1) Randall and Poul to talk to Gareth, then talk to Mike to tell him when PMR2 v0.1 is likely to be deployed as per Mikes question under agenda item 3.

5) CellML Specs - update
  • James will be spending more time on curation, reducing his time spent working on specs.
  • Poul said that at the workshop a commitment was made to making the new metadata spec in line with MIRIAM.
  • Andrew has sent an email about a functional programming language as an approach to the future of CellML.
Action item 2) Andrew to create a tracker item about functional programming proposal for CellML.

6) CellML API - update
  • Randall talked about trying removing fixnans from the CCGS Levmar solver.

7) OpenCell development - update
  • Randall said that we might want to organize a fixed frequency of building snapshots while Justin is away.
  • Andrew said that he would build snapshots on request, for example if someone wants to test/use new features.
  • Andrew has been working on changes that make it easier to change the tree view; eg. adding new nodes, or provide view filtering.
  • Randall asked about a way to serialize simulation metadata to SED-ML.
  • Poul said that we need to ensure that SED-ML meets our simulation metadata requirements.
  • Randall commented that we will still need our simulation metadata for non-time-based models.
  • Randall suggested that we target OpenCell 0.8 for the earliest implementation of SED-ML.
  • Alan suggested that Andrew and Andre might be the best people to stay in touch with the SED-ML development process.
  • Randall said that we should use their tracker and mailing lists to keep up to date with SED-ML development.

8) Repository contributions - update
  • Catherine has been working on updating the conference website and writing other documents. Will aim to commit 50% of her time in the future to curation, as will James.
  • James wants to talk about the curation tasks best done during the PMR to PMR2 migration process. This might be at the next meeting.

  • Randall mentioned the euHeart report that he has drafted and circulated among interested parties. Peter is currently reviewing it.


9) Additional items
  • Andrew asked if anyone had an objection to clearing David Cumin's moderation flag on the mailing list.  No one had any objection.
Action item 3) Andrew to create a tracker item about mailing list purposes and number of lists.