ABI CellML meeting minutes 2009-09-16

Present: Dougal Cowan, Poul Nielsen, Randall Britten, Andrew Miller, Justin Marsh, James Lawson, Tommy Yu, David "Andre" Nickerson, Catherine Lloyd, Sarala Dissanayake

Apologies: Mike Cooling, Peter Hunter

Last week's action items:

1) James to update the tracker item or re-do the namespace page.

  • James has created pages, and is awaiting access to complete them.

This week's agenda:

1) Update on tracker item 87: curation flags

  • Catherine started a discussion about curation flags, and talked about Biomodels flags, which are hidden.
  • Catherine suggested we start curating a test cohort of models with the flags, and showed a document with some proposed flags.
  • Catherine wants to write a paper on this subject.
  • James talked about Mikes comments about the redundancy and varying applicability of flags.
  • There was a lengthy discussion about curation flags: what states they should have, overlap of purpose or meaning, ideas about a hierarchy or tree/graph of flags, etc.
  • Poul suggested a breakaway on flags.
  • Andre asked why we can't do all this automatically from metadata.
  • James said that we need a way to annotate who performed the curation.
  • There was a discussion on how to annotate the cases where domain experts or curators may disagree.
  • James raised the issue of development time and feature priorities for PMR2 and demands on Tommy's time.

2) CellML Specs - update

  • Andrew has been working on top-level piecewise and reset rules.

3) Metadata specifications (general, citations, graphing, simulation, other)

  • Catherine asked if the 1.0 draft has been frozen.
  • James said that the 1.0 spec has been frozen and is now the official spec. 1.1 is being discussed in the tracker.
  • Tommy is waiting on a decision on whether to use 1.0 or the upcoming 1.1 spec for PMR2 metadata editing - 1.1 uses Dublin Core instead of BQS, etc.
  • Andre asked why we should use a web based metadata editor when OpenCell will soon have metadata editing.
  • James mentioned non-model metadata, repository metadata etc.
  • There was a discussion about metadata editing tools.

4) OpenCell development update

  • Randall reported that the latest Linux snapshots are largely working, with a few bugs. James is testing these snapshots and reporting issues - they are usable but not yet releasable.
  • Justin has been working on the Windows build on a non-build machine (trying to recreate the old build machine"magic" from scratch). Not quite there yet.
  • Alan is 90% done on the COR-text parser, and the next step is to parse COR-text into CellML. Alan says that the current OpenCell text editor is buggy and unusable, therefore making any implementation of the COR-text view unusable.
  • Version 0.7 may not have a COR-text view.

5) CellML API - update

  • Andrew is still working on the paper - Alan Garny does not want to be an author any more.
  • Justin asked if it is possible to have paper supplements.
  • Randall called a breakaway to discuss the paper.
  • Andrew reported that top-level piecewise support is almost complete, and needs testing. Andrew has also been working on infintessimal delays and reset rules.

6) cellml.org update

  • James reported back on the group's decisions around access/permissions, where there will be a contributors and reviewers system.
  • There was a discussion about the order of items in the meeting navigation portlet. An action item was created for Tommy to fix this, but using newfangled "wireless" techniques he was able to achieve a fix before the meeting was complete.
  • Catherine reported that we will need to discuss who can edit which parts of the website, and why.
  • Poul outlined reasons for using these Plone workflows, having many editors and few reviewers etc.
  • Andre would like to see changes to documents - Tommy fixed the settings so that all members can see changes.

7) Repository contributions update

  • James continues to go through alphabetically performing standard curation tasks.
  • Randall reported that having Yubing Shi's model in the repository has been very positive; comments recieved at the EU Heart meeting.
  • James said that he will have three summer students and needs to decide what they're doing - these decisions may depend on the state of PMR2.
  • Catherine reported that Geoff Nunns will be starting in October, and will be able to work on Dan Beard models.

8) PMR2 development - update

  • Tommy has implemented embedded workspaces, and has fixed the access bug for private workspaces. This fix will be in PMR2 0.2.
  • Tommy will be working on bugfixes, a better UI for file access, and implementing a link to download an archive.
  • Tommy will add support for HTML documentation.
  • Andre started a discussion on the use of HTML for documentation, vs using Dublin Core metadata to create exposure documentation. There was an extensive discussion of metadata and documentation.
  • It was agreed that we need a good metadata editor soon, whether in PMR2, OpenCell, or stand-alone.
  • There was a long discussion on how to organize and present exposures.

9) Time permitting: Updates or additional items from volunteering attendees

  • Catherine has booked a room for the CellML 2010 meeting on the 25th and 26th of February. There was also discussion of a possible hackathon on either the Wednesday or Saturday.