ABI CellML Meeting minutes 2009-07-15

Present: Catherine Lloyd, Mike Cooling, Jonna Terkildsen, Dougal Cowan, Poul Nielsen, Randall Britten, Tommy Yu, Amir Shirkhani, James Lawson, David "Andre" Nickerson, Justin Marsh
Apologies: Peter Hunter

This week's agenda:

0) Time delays
  • Catherine received an email this morning from Dom Layfield about time delays. Catherine spoke to Andrew, who says there is a draft spec of time delays.
  • Randall said that there is a newer tracker item than the one Don referenced; tracker item 1543. The current description is not in a very user friendly form.
  • Andrew suggested we encourage Dom to participate in the discussion about time delays.
  • Andre said that we need someone to implement the ideas we have so far into the API so we can test them; we don't have someone with the time to do this at present.
1) IUPS preparation
  • A breakaway was called.
2) CellML draft metadata specification - can we freeze it?
  • Catherine asked if we can freeze the draft.
  • James says yes. Alan has made a lot of comments and corrections to the 1.0 draft, and the fixes have been made. It is ready to freeze.
Action item 1) James to freeze the 1.0 metadata spec on Monday.

3) Exposures - what are they and how should they be used?
  • James explained the current PMR1 style usage of exposures, and the problems he sees with this; too many exposures that are hard to manage, and currently multiple exposures of single models in the listing.
  • James explained that at the moment, having a single exposure for each model in the listing is the only way to avoid a big mess. This is a presentational issue.
  • James is currently making a new exposure for every commit. This breaks the "software release" analogy, and is very time-consuming. James would prefer a workspace focus over an exposure focus.
  • Mike and others think the listing issue is a user interface problem; this can be dealt with by designing or allowing appropriate filters.
  • There was a discussion around workspaces, exposures and the main listing/s. Workspace centric listings are seen as problematic because workspaces can contain multiple models, for example, or may just be scratch-pad or resource type containers.
  • Catherine says we need documentation! A glossary and guides.
  • Jonna is confused by the repository listing, due to current naming inconsistencies.
  • Catherine suggests we need a best practice as soon as possible.
  • Andrew wonders if we need a curated list, e.g. of published models.
  • James suggests that people should only expose a model once they are sure it is ready for release; this is more akin to the "software release" analogy.
  • There was a discussion about multiple exposures.
  • It was decided to call a breakaway meeting to continue the exposure discussion.
4) PMR2 update
  • Tommy has implemented Peter's request, and released PMR2 0.1.1.
5) Repository contributions - update
  • James has made changes requested by Peter.
  • James is continuing to do unit checking, but is not yet making exposures.
  • James has been working with Jonna on using the repository, and is taking notes for fixes and features.
  • Catherine is working concurrently on several large models.
6) Website redesign - update
  • Catherine reported that the group has decided on a Monday deadline for putting up the new site.
  • Tommy said that ITS should have a VM cloned by tomorrow, then it will be time to migrate.
  • James reported that final quality control is underway.
  • There was a discussion about UK/US spelling. It was decided that we won't worry about it, unless there is mixed spelling on a single page.
7) OpenCell development - update
  • Justin has been doing bugfixes, fixing things highlighted by James.
  • Jonna reported a bug whereby opening from the windows explorer context menu (open with) does not work. This is a known issue to do with Administrator rights and spaces in paths on Windows.
8) CellML API - update
  • Andrew has got the build system on Windows mostly working, bar a couple of issues. (?) It is working on Linux, and broken on Mac, with a known cause.
  • The build system is almost there!
  • Justin has looked at Jonna's tracker items.
  • There was an extensive discussion about opening 1.1 models in OpenCell, to do with XML base.
  • Andrew reported that Sarala is now OK with the Java API, and Morgan has not yet got back to him about it.
  • Randall reported that Sarala has put together Java examples with DocBook documentation - there is no Doxygen hyperlinking possible for the Java. Andrew said that integrating the Doxygen linking would be possible, but a big job that would involve creating our own custom extensions to Doxygen.
  • Amir has been adding notes to current Python documentation.
  • James has left the API section of the website to Andrew and Justin.
9) CellML specs - update
  • James will send out 1.0 of the metadata spec for a final look and the freeze it on Monday.
  • James says that we are currently using metadata for things it was not designed for (such as the PMR2 exposures listing); this needs to be fixed.
10) Initial values
  • Jonna wants to know if the initial value fix she is currently using is going to be permanent, or a temporary fix; she wants to share the model that uses it.
  • Randall said that this brings us to the next step of the process; are we going to make this change permanent, and if so, how?
  • Andrew suggested that we need to look more deeply at the initial conditions problem, and perhaps try to tackle it using constraints.
  • Randall suggested that we know that we need initial values - what is the next step?
  • Andrew said that implementing constraints would be the next step, but that we need to standardize the initial condition hinting system. We could possibly publish a technical note on the current implementation for Jonna to refer to.
  • Poul said that we might need a technical notes section on the new website for things like this.
  • Andre asked if we have tried other DAE solvers yet - we have not.
  • Randall has tried other solvers by hand-coding.