ABI Meeting minutes 2009-05-06

Present: Dougal Cowan, Andrew Miller, Mike Cooling, Randall Britten, Tommy Yu, Poul Nielsen, Matt Halstead, Catherine Lloyd
Apologies: Justin Marsh, Peter Hunter

Last week's action items:

1) Sarala will send an email to Allyson about [CellML support in Saint]
  • Not yet done, but Matt has offered to contact Allyson and Morgan on this subject.
2) Tommy will speak to Gareth about getting Apache configured to redirect the legacy repository to the root of PMR. This can happen ASAP.
  • Done.
Action item 1) Tommy to remove link to legacy repository (PMR0).

3) Andrew will add a tracker item about [refactoring tree view]
  • Done.
4) Andrew will add a tracker item about [alternative graphical platforms]
  • Andrew has done this, and there has been some discussion on the tracker about the issue, including from David Nickerson, Alan Garny, and Carey Stevens.
5) James & Randall will talk to Gareth about migrating the content to Plone 3 fairly soon.
  • The website working group have decided to decouple PMR2 from the content site. There was a discussion about migrating old content to a new Plone 3 site as an interim measure.

This week's agenda:

1) PMR2 update
  • Tommy has been tidying up various things, and has added workspace creation.
  • James started a discussion on various aspects of  the testing of PMR2.
  • Dougal reported that the PMR2 tutorial is awaiting a few features of PMR2 to be usable.
  • Mike asked whether he would be able to publish a paper next week with public and persistent PMR2 links - Randall and Tommy said that this should be possible.
  • Randall asked whether Dougal could finish the PMR2 tutorial by the end of today.  Dougal said this was possible if the workspace creation is now working.  Dougal also suggested that he go through the use of PMR2 with Catherine while she is still here.
  • James likes the command-line interface of Mercurial, and will probably continue to use it even when Mercurial access is available through the website.
  • James highlighted the need for unique sub exposure names/links - require the use of a metadata tag?
  • Andrew suggested annotating the workspace to label the separate cellml files.
  • Mike asked whether you can make multiple exposures from one workspace - Tommy said that you can.
  • There was an extensive discussion about workspace/exposure heirarchy and what workspaces are tied to (publication or other).
Action item 2) Tommy to change PCEnv instances to OpenCell in PMR2.
  • Randall said that there will be other kinds of exposure in the future - at the moment PMR2 0.1 only has PMR1 style exposures.
  • Mike asked: if you wanted to create say six exposures from a workspace that are all "equal"; is this possible? Tommy said yes.
  • Catherine would like to be able to manually rename the sub exposure titles.
  • Matt suggested that we need "title" metadata; we will need a separate model title anyway, for unpublished models which have no citation title.
Action item 3) Tommy to allow editing of sub-exposure titles
Action item 4) Dougal to take Catherine through PMR2 usage (including Mercurial).
  • There was an extensive discussion about migration, including the need for the manifest files to be finished in order that all variants will have useful names in PMR2.
Action item 5) James to complete the migration manifest files.
  • It was decided to make the staging site have the default Plone skin with the CellML logo - as seen on the current cellml.org site. This is what the initial deployment will look like.
  • Randall said that front (index) pages need to be added to guide users.
  • Mike asked how testing is handled - who organizes it, who to report to?
  • Randall suggested a meeting on Friday to discuss the testing. Randall will organize this.
  • Randall said that efforts should be made to make the staging site as close as possible in appearance to the initial deployment.
  • James asked whether PMR2 0.2 will have an interface redesign - aye, say all!
Action item 6) Randall to create a tracker item for PMR2 deployment.
  • There was a discussion about the search function, which currently lists the names of Plone objects (not a useful results list). James suggested that the function simply be removed in favour of a compete listing of exposures/workspaces that can then be text searched in the browser window.

2) Website redesign - update
  • Dougal reported that it was decided at the meeting to completely decouple PMR2 from the content site. Work continues on the skin and front-facing content for the new site.
3) Repository contributions - update
  • James has been updating curation status.
  • Catherine has completed the Moss et al. 2009 Kidney Model - the first model which "attempts" to use vectors (admitted there is no tool support for this yet).
4) CellML specs - update
  • No update
5) OpenCell development - update
  • James mentioned the model title issue again.
  • Mike talked about MIASE.
  • Andrew mentioned that he had been looking into some of the options for the graphical platform. 
  • Andrew has also continued with the work on refactoring the model tree view so that the metadata support can be implemented more easily.
6) CellML API - update
  • Randall mentioned that there has been some discussion on the tracker about Java bindings.
  • Mike suggested trying the build on a clean Linux install to try to isolate the problem/s with the build.