ABI Meeting minutes 2008-10-01

ABI Meeting minutes 2008-10-01

Present: Dougal Cowan, Sarala Dissanayake, Peter Hunter, James Lawson, Catherine Lloyd, Justin Marsh, Andrew Miller, Poul Nielsen, Tommy Yu

Apologies: Randall Britten, Peter Schmiedeskamp, Jonna Terkildsen, Mike Cooling

Last week's action items

1) James to send several paragraphs to Peter detailing CellML support for the MIRIAM standard as a contribution to the Royal Society metadata paper:
  • Done.
2) Justin to create new tests for PCEnv in Litmus, run these tests.
  • Done.
3) Andrew to make a tracker item about Jonathan Cooper's suggestions for the API.
4) James to email Andre about visiting him during the Singapore trip.
  • Done.

This week's agenda

CellML spec progress update
  • Tracker item 1277 seems to have become much less active, Mike Cooling absent.
  • James would like to gather a few topics to talk with Andre about during the Singapore trip; metadata spec.
  • Poul would like to assign people to tasks to get the spec finalized.
Action item 1) James to write up a plan/roadmap for the spec, including ideas of who to assign to particular tasks or areas.
Action item 2) Andrew to create a tracker item and send an email to the discussion list, proposing to finalize the spec.
  • Poul suggested that Andre and Andrew work on the graphing metadata.
  • Andrew said that PCEnv needs to be updated to use Andre's new graphic spec .
  • James asked whether this is part of the plan for PCEnv 0.6; Andrew said that it does not yet have a tracker item.

PCEnv progress update
  • Andrew is ready for 0.5 release.
  • Dougal said that he has completed updates to the manual for 0.5, and is now working on updating the tutorial.
Action item 3) Dougal to complete the tutorial ready for 0.5 release.
  • Litmus test runs have been performed for the Linux and Mac snapshots; all but one test passes.  The failed test is a relatively obscure list sorting bug that is not explicitly tested by the Litmus test regime.
  • Poul suggested that priorities for 0.6 are reviewed after the PCEnv 0.5 release.
  • Andrew mentioned that a meeting with Alan Garny has been held, and another is planned to discuss the 0.6 features.

Update on repository contributions
  • Catherine has added another 3 circadian rhythm models, a pacemaker model (currently private) and an astrocyte model for the Norwegian group.
  • James has made a session file for the astrocyte model.
  • Catherine mentioned that a student is coming today to discuss curating models over the summer.
  • James asked how summer students are chosen.
  • Poul said that the attributes of a summer student include grades, stage, and plans for postgraduate study.

PMR2 update
  • Tommy has written the paper on PMR2.
Action item 4) Tommy to email Poul a copy of the paper.
  • Tommy has also almost finished the mercurial wrapper, and is soon to start working on the Plone side of PMR2.

Additional items

    • The accommodation and flights have been booked for everyone attending the meeting in San Francisco.
    • The combined CellML SBGN SBO BioPAX MIASE Workshop for April 2009 has been announced and the registration process has begun.
    • Catherine raised the possibility of seeking corporate sponsorship, possibly for the conference dinner.

    • Poul mentioned several approaches from Peter Lister and Grace Peng encouraging us to submit an NIH grant.  Poul thinks that a focus on integrating CellML, SBML, ontologies and Biomodels would be a good idea; proposals for common tools and standards etc. CellML <=> SBML translation via OWL was raised as an example of what this grant might cover.
    Action item 5) Everyone to think of ideas for proposals for this grant.