Meeting Minutes 21 November 2007

Present: Randall Britten, James Lawson, Catherine Lloyd, Justin Marsh, Poul Nielsen, Andrew Miller, Tommy Yu

Review of last week's action items

  • Poul will organize meeting with James and Sarala on the materials and diagrams.

    • Poul didn't do it yet, but noted Sarala needs more time on building the diagrams as she already has a lot on her plate

      • It is quite a daunting task, such as the need to specify the metadata tags required to properly represent what reaction elements currently describes.

      • Action item: Catherine will take a look at writing the documentation to remove reaction elements and to provide examples/best practices.

  • James will also look at/notify other repositories about deprecation of reaction elements.

    • James has identified sites using CellML and notified them about the discussion lists, encouraging them to join it.

  • James will put SVG demo up on the CellML site.

    • The demo is completed and put up on the site, with a session that is properly working. Just needs a link.


Update on CellML 1.2

  • Since CellML 1.1.1 has not been formally proposed as a standard, we will jump straight to CellML 1.2.

  • It was decided that reaction elements are going to be removed, but there needs to be examples that converts those elements to let it be represented by metadata for people who have used it. There needs to be a set of metadata, and Sarala has been working on it. Catherine will be looking at the issue and James has expressed interest to help out. Also, it will be nice to have Matt give any guidance he can give regarding this.

  • Andrew wanted to clear whether it was OK for him to spend more of his time on CellML specification work, and hence less on PCEnv development.  It was agreed that this was a good idea, and that he should do this.  He will still ensure that he allows sufficient time for helping Justin, as needed.
  • Randall mentioned that there was a response to the "Git/Docbook proof of concept", and that he will look into Mercurial, in case it might be suitable.  Mercurial has the disadvantage that hosting is not as easily available.

CellML workshop/meeting 2008

  • There will be a Multiscale model meeting next year at Waiheke. Since there will be many people there, including those who have used CellML, it may be possible to tack on a one day CellML meeting onto that one, and host it in-house to make it cost effective.

    • Still needs decision on this

    • James would like comfy chairs for this workshop

  • Catherine will arrange the meeting.  Thanks Catherine.

Update on PMR2

  • Randall has created tracker items for PMR2.

    • Action item: Randall to email Matt, asking him on the readiness of deployment of Plone 3

  • Tommy has been familiarising himself further with Plone. He also is now checking in work on the prototype (via git-svn).

Updates on PCEnv 0.3

  • Justin noted that functional tests have passed on both the Linux and Windows builds

  • Mac OS X build has some major issues.

  • Decision was made to not let the release of 0.3 stall because of issues in OS X, but do put more focus on getting OS X support for 0.4.

  • Release candidate could be made for PCEnv 0.3.

  • James will suggest an implementation of PMR2 for the proposed Standard Registry of Biological Parts (an in silico adjunct to the in vitro Standard Registry of Biological Parts) to Barry Canton from MIT and Vincent Rouilly from Imperial College London.
  • Catherine asked how a query regarding mapping variables had been addressed.  James had forwarded it to CellML discussion.  Poul noted that meta-data will one-day help address this.