ABI Meeting Minutes 2008-09-24

Present:  Randall Britten, Peter Hunter, James Lawson, Catherine Lloyd, Poul Nielsen, Tommy Yu, Andrew Miller, Justin Marsh, David Cumin

Last week's action items

1.) Sort out attendees for San Francisco Physiome meeting in December
  • Poul is finalising the details

2.)  Add submission deadlines and investigate possibility of RSS feed for conference calendar

  • Catherine has done this

This week's agenda

Upcoming conferences, meetings & workshops

Joint workshop in Auckland
  • Catherine has proposed that the previously mentioned joint workshop amalgamating meetings of BioPAX, SBGN, SBO and MIASE be held on Waiheke in early May, the week of Easter
  • Registrants will be provided complimentary accommodation and food, and the registration will be free
  • Catherine anticipates that 60-80 people will attend

Physiome workshop in San Francisco
  • Poul, Justin, Catherine and Sarala will be attending
  • There are two slots for talks available to the CellML group: a 40 minute overview, which will be presented by Poul, and a 30 minute talk on tools and software which will probably be presented by Justin
  • Catherine and Sarala will be presenting posters

ICBME2008, Singapore
  • Randall suggested that if Tommy were to attend ICBME2008,  he could present Sarala's poster, while James could present Mike's
  • The alternative is that James could present Tommy's poster and Mike could present Sarala's

James - Using Dublin Core to annotate CellML elements with MIRIAM URNS
  • James presented a snippet of RDF he mocked up to simplify annotation of CellML elements with MIRIAM URNS
  • He also discussed the relevance of MIRIAM Resources to annotation of CellML models
Action item 1.) James to send Peter several paragraphs describing the CellML project's relationship with MIRIAM

Progress update on PMR2

  • Tommy has almost finished the Mercurial backend of PMR2
  • He has been primarily working on his paper for ICBME

PCEnv 0.5
  • PCEnv 0.5 is due to be released as soon as possible
  • Some bugs are still to be fixed, and a review of the documentation and updates which Dougal has made is in order
Action item 2.)  James to read through the documentation and check it for consistency
  • Testing for the release needs to be done. New tests need to be written for new features and functionality and recorded in Litmus
Action item 3.) Justin to write new tests, do Linux testing, Dougal to do Windows testing
  • James asked whether Vista testing might be needed. Justin suggested that it is probably worth checking the Vista version for any inconsistencies at a shallow level, but the core functionality probably does not need to extensively checked

Update on repository contributions
  • James has been busy working on his and Mike's poster for Synthetic Biology 4.0 and his paper for ICBME2008
  • Catherine has added a Saucerman 2008 model and several circadian rhythmns models
  • She is collaborating with Steven Niederer on getting the Saucerman 2003/2004 models to work; she has done all she can

CellML Specifications discussion
  • A paper is being penned for Philosophical Transactions of the Royal Society B about the present and future state and use of CellML metadata
  • Peter is keen to push the development of the CellML Metadata specifications
  • James suggested that we should really be finalising the current draft CellML Metadata 1.0 Specification before we make any alterations or additions, because it has been widely cited and used. This would ideally take a minimal amount of effort.
  • It was noted that the main CellML Metadata specification should remain separate from the Graphing and Simulation specifications
  • On a related note, we need to update the API and PCEnv to catch up with recent additions to the Graphing and Metadata specifications
  • The process for making decisions on the metadata specifications will be the same as the process for the main CellML specifications: community consultation, then ultimate decisions made by an appointed CellML project team panel

API documentation
  • Jonathan Cooper sent through some suggestions for updates to the API documentation
  • Some of these have been taken on board already
Action item 4.) Andrew to put those suggestions that have not yet been implemented into the tracker

PCEnv development goals
  • Peter would like the next phase of PCEnv development to be much more user focused. Users need to asked what they like / don't like and why, and what they would like to see
  • There is concern that many new users do not want to use PCEnv for model building, and prefer COR - we need to find out why this is
  • David Cumin prefers COR because of COR's text language model building interface. PCEnv is better for simulation, however
  • We have specific funding objectives that we must meet with PCEnv. Andrew would like to see a document which flags these objectives so that development can be planned according to them