ABI CellML meeting minutes 2009-09-30

Present: Dougal Cowan, Randall Britten, Andrew Miller, David "Andre" Nickerson, Peter Hunter, Poul Nielsen, Tommy Yu, Catherine Lloyd, Justin Marsh

Apologies: Mike Cooling, James Lawson

Last week's action items:

1) Dougal to get the IUPS notes with photos up on the website.

  • Content is created and up as private on the website; almost complete pending a few bits and pieces.

2) Tommy will look into how a rapid exposure rollover can be done.

  • Tommy thinks that the rollover can be done fairly quickly. There was a discussion about workflows to deprecate exposures; currently this is done by setting an expiry date for the page.

3) Catherine to create a tracker item about the authors (curators and paper authors) for exposure pages.

  • Done, tracker item 2002. Catherine has discovered that there is a lot of metadata not being used to create exposures.

This week's agenda:

1) (Randall) Editing policy on www.cellml.org site:
Should be restored to something more similar to previous site's policy:broaden who can edit, but have changes reviewed.  Other possible policies?

  • Randall raised the issue of it being impossible for CellML team members to edit pages at the moment.
  • Catherine explained the approach we will be using with the Plone roles and workflows, to enable everyone to be able to do what they need to to on the site.
  • Tommy said that this will require the creation of new custom roles and workflows.

2) (Randall) The way we do revisions to meeting minutes: directly editing minutes and using RSS feeds vs sending e-mails.

  • Randall strongly supports the ability to edit in place, which is working well for OpenCMISS minutes.
  • There was a discussion about how to utilize RSS feeds and on-site editing to accomplish the minute editing. It seems that at the moment, Plone does not support the facilities we need to make on-site editing of the minutes by meeting attendees practical and useful.

3) CellML Specs - update

  • No update.

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

  • No update.

5) OpenCell development update

  • Justin has written a graphical setup for the build environment in Windows, which sets up the Physiome build environment on any machine. This is almost finished.
  • Randall reported that Alan Garny has made improvements to the COR text parsing, and is making progress towards parsing COR text into CellML; this is blocked by tracker item 1331.
  • Catherine asked if the units checking issue has been fixed.
  • There was a long discussion about errors and warnings issued by the validate CellML service.
  • Peter Hunter is strongly in favour of keeping all warnings, and having a range of warning severities.
  • There was a discussion about what should cause a warning to be issued - it is clear that errors should be reported when CellML is not valid, but there are a range of style or best practice issues that could potentially cause warnings of various severities to be shown.

Action item 1) Andrew to create a a tracker item about showing warnings for unit definitions problems.

Action item 2) Andrew to create a tracker item about warning severity levels.

6) CellML API - update

  • Andrew continues to work on the paper, and is working on including comments and changes by co-authors.
  • Andrew is working on code for top-level split piecewise equations and reset rules.
  • Randall reported that Sarala is now waiting for Justin to make progress on the Windows build problems.
  • Peter asked about progress on DAE support. Randall said that this is a big job, which could be a good project for Justin.
  • Randall said that we need to go for another release and then we can start another round of planning.

7) cellml.org update

  • Catherine reported on the discussions within the website group about roles and privileges.
  • Peter requested documentation on a few details of PMR2 to be put up on the site.
  • Randall said that Dougal can re-work his old documentation from the prototype and put it up on models.cellml.org. A documentation section will be created on the site.
  • Catherine said that we need best practice docs for a lot of things in PMR2.
  • There was a discussion about how to get people to use Mercurial instead of emailing files and requesting that curators put models into the repository.
  • Randall said that we will always have to provide these email-based services for the people for whom CellML is a very small part of their work.

8) Repository contributions update

  • James has been overwhelmed with curation requests and has just gone on leave. Consequently, Catherine curated twelve models yesterday; Catherine has therefore now learned how to use PMR2.
  • Catherine reported that two fourth-year honours students have just finished, both submitting excellent reports.

9) PMR2 development - update

  • Tommy has been distracted from PMR2 by multiple website issues.
  • Tommy has been working on a metadata viewing tool for Catherine, and has taught her to use the repository for her curation work.