ABI CellML Meeting Minutes 2009-05-20

Present: Randall Britten, Mike Cooling, Andrew Miller, Peter Hunter, James Lawson, Tommy Yu, Andre, Julian Eden
Apologies: Dougal Cowan, Catherine Lloyd

Last week's action items:

  1. Tommy to change PCEnv instances to OpenCell in PMR2. [Done]
  2. Everyone to read Matt's email on the Saint/annotation issue.
    • Still not everyone managed to read it.
    • James and Mike have read it.
    • James has replied.
    • It was agreed that James and Mike having read and responded was sufficient.
  3. Everyone to send their various tutorials to Dougal. [Done]
  4. Andrew to write up the requirements for building Python bindings.   Andrew will do this over the coming weeks, it was decided not to follow this up as an action item.

This week's agenda:

  1. (Mike) BestGRID opportunities for CellML.
    • Mike has been contacted by people responsible for BestGRID to see if there are any possible projects that could benefit from using it.
    • Trial with some CellML models and the API or serialisation solvers.
    • Could a web service be used with BestGRID?
    • Randall mentioned the CellML simulator as a possible?
  2. (Randall) Alan Garny finds SVN hosted in Auckland frustratingly slow.
    • Is the bottleneck in the access via International links?
    • ITS should be able to provide some insight into this.
    • Hosting on external resource like Sourceforge, Berlios, Amazon EC2?
    • Retrieving appears to be the main issue.
    • Moving to a distributed repository system should alleviate some of the problems.
    • Mercurial being a distributed repository system is a good choice.
    • PMR2 is also using Mercurial.
    • Peter agrees with this direction.
    • Randall suggests to host on an external Mercurial repository.
    • Separate repositories for each project?
    • Andrew thinks this would be a good idea.
    • Randall said that we would proceed with migration to an externally hosted Mercurial repository.  We would not go through a consultation on this decision with the wider community, since that would cost time, and we need to balance consultation with time spent.  A break-away meeting was held to work through some of the details of the migration.
  3. PMR2 update.
    • Testing of PMR2 v0.1 RC1.
      • Stress testing will be today (20/05/2009).
      • Randall received quote from ITS.
      • Peter Schmiedeskamp said timeframe would be 2 days from go ahead to ready to use.
      • Mike is going to be testing PMR2.
    • General.
      • Randall queried the necessity of the sidebar portlet.
      • Sidebar portlet to be removed prior to testing by Mike.
      • Peter would like simple CellML model put in by Mike.
      • Mike already has in simple model in mind.
      • James commented that the workflow seems a bit complicated.
      • Renaming of exposure pages?  It's not a common thing.
      • James has a list of issues.
      • James to upload 1.1 file.
      • Tommy to email Mike about PMR2 will be ready for testing.
      • Mercurial Forest is not going to be part of v0.1
      • Peter asked what 'forest' is.  Extension to Mercurial to link to other repositories local and external.
      • All Mikes modules depend on other repositories currently.
      • Randall queries why separate workspaces for each model?
      • Randall thinks that the sandbox idea should be rethought.
      • The ability to create logins will be restricted once the release happens.
      • Also restricts workspace creation.
  4. Website redesign - update.
    • James is reviewing and has a list of issues.
    • Icons are required prior to release.
    • There are some dead links.
    • Logos and links to funding agencies needs to be reviewed/updated.  VPH and IUPS.
  5. Repository contributions - update.
    • James has gone through models reviewing units and has found some more difficult than others.
    • Peter suggested flagging model as working or not and why.
  6. CellML Specs - update.
    • Metadata specifications (general, citations, graphing, simulation, other).
      • Tommy still to have a look once v0.1 is out.
    • General issues.
  7. CellML API - update.
    • General issues.
      • Andrew fixed problem where model with large number of equations is slow to solve.
      • Andrew has added option to eliminate unused equations.
  8. OpenCell development - update.
    • Andrew has done work on treeview node.
    • Snapshot problem on windows.
    • Code is still slow.
    • Builds perhaps not integrating fixes.
    • Andrew Cantell is in the process of providing a couple of machines for CellML work.
  9. Time permitting: Updates or additional items from volunteering attendees.
    • Mike asked for an update on Java API for Windows work.