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.
- Done.
- Done, see Tracker item 1395
- 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 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.
- 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.
- 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.