ABI CellML meeting minutes 2009-09-02

Present: Dougal Cowan, James Lawson, Julian Eden, David "Andre" Nickerson, Mike Cooling, Tommy Yu, Andrew Miller, Justin Marsh, Jonna Terkildsen, Poul Nielsen.

Apologies: Randall Britten, Peter Hunter, Catherine Lloyd.

Last week's action items:

1) Justin to contact Morgan Taschuk about libannotateSBML

  • Not yet done.

2) Justin to send specs for a new Mac to Randall

  • Done.

3) Tommy to organise a further meeting to discuss the structure of PMR2.

  • Done.

4) James to follow up on [redirecting http://cellml.org] with Andrew Cantell

  • Done.

5) Justin to contact Alan about merging within Hg.

  • Done.

6) Randall will ensure that ABI IT grant Justin root access to bioeng46

  • Done.

This week's agenda:

1) Removal of the team-cellml@list.bioeng.auckland.ac.nz mailing list

  • The list has been removed.

2) Enquiry from Ben Curran about CellML curation work

  • James has been communicating with Ben Curran about possible curation work, including coding up new models.

3) Update on CellML group's publications (James)

  • Andrew reported that most of the API paper is now written, and only requires a small amount of work to complete. A breakaway meeting was called immediately following the CellML meeting to discuss the paper.
  • Mike asked if we are including external papers that mention or use CellML in the listing; it was agreed that we are.
  • Mike started a discussion on Ely Matos' paper, and said that we should keep in touch with him in the future. This paper will be put up in the publications section.

Action item 1) James to put Ely's paper on the publications section of the website.

  • Mike has a paper on synthetic biology being revised, currently with additional input from James Lawson
  • Mike as a book chapter submitted to Springer; a basic tutorial on CellML.
  • James received some papers from Jonathon Cooper for the publication list.
  • Poul reported that Sarala's paper should be published soon.

4) CellML Specs - update

  • Nothing to report on the specs.

5) Metadata specifications

  • James wondered if it is worth using the current proposed spec before formalizing it. There was a brief discussion about this.

6) OpenCell development update

  • Justin has fixed a problem with the variable selector. He has also fixed a problem causing non-editable text boxes in the tree view.
  • Justin has been working on the Windows build.
  • Justin reported that Alan has finished some COR-text related things.
  • Alan has fixed tracker item 1986.
  • Alan has worked towards a fix for tracker item 1861.
  • Alan has also merged the trunk into his COR-text branch.

7) CellML API - update

  • No commits have been made.
  • Poul reported that Sarala is still working on the Java.

8) cellml.org update

  • James reported the work that has been done on logos and branding of the site. The layout is finalized and ready to deploy.
  • James mentioned work that the group have been doing on integrating PMR2 and cellml.org.
  • Julian mentioned that the meeting minutes navigation portlet should have its order reversed, so that newer items appear at the top.
  • James started a discussion about how the meeting minutes are edited and checked. There was general support for the old system where a single editor writes the minutes and makes all the suggested changes. This system will be retained for the time being until Randall returns and can discuss it.
  • There was a brief discussion about the text accompanying the Physiome logo; whether to remove it.

9) Repository contributions update

  • James uploaded a new Sheffield cardiac model, a large complex CellML 1.1 model, by Yubing Shi et al.
  • James has also been making changes to the capitalization of exposure titles, at Peter's request.
  • Jonna asked about the inability to clone private workspaces; Tommy says is a known bug to be fixed in 0.2.
  • Jonna has uploaded several kidney models into workspaces, no exposures have yet been made.

10) PMR2 development - update

  • James would like PMR2 0.2 to be ready before summer students start using the repository - especially important is some kind of metadata editing. This does not have to be part of PMR2.
  • Mike has had feedback about his document which shows that people do have visions of what PMR2 should be, although these are different for different people. He will try to get some high level functional requirements from a variety of PMR2 users.
  • There was a discussion about planning for PMR2 features, and Mike's document.

Action item 2) Mike to start eliciting feedback from users of PMR2. This is a post-modern self-applied action item.