ABI Meeting Minutes 2008-09-17

Present: Peter Hunter, Mike Cooling, Dougal Cowan, Randall Britten, Justin Marsh, Tommy Yu, Andrew Miller, James Lawson, Peter Schmiedeskamp, Catherine Lloyd, David Cumin, Poul Nielsen, Professor David Smith.

Jonna Terkildsen, Michael Backhaus.

Last weeks action items

1) James will email the conference organisers and confirm whether or not a paper is explicitly required.

  • A paper is definitely required, but is not reviewed.  At a maximum of 4 pages, it is fairly brief.
  • Co-authors may present; each attendee may present 2 items.
[Papers are not required, see below].

2) PCEnv users to obtain latest snapshot and try out the prefs service, and post feedback to tracker item 277.

  • A discussion of the preferences concluded that only the RDF warning will be in the preferences for PCEnv 0.5.
  • Another tracker item was created for session behaviour, tracker item 1358.

3) Justin to create a tracker item for relative session sizing.  However, this would not be included in PCEnv 0.5.

  • Justin created this tracker item; tracker item 1372

This weeks agenda

1) Taishin Nomura's workshop type symposium on Physiome and systems biology in San Fransisco 1 & 2 December.

  • Peter Hunter announced that Nomura would like 4-5 people from ABI to attend, with full funding provided.
Action item 1.) Randall to canvas who could/would like to go.
  • Catherine asked if it was to be attendance only, or whether presentations were required.  Peter H said it was assumed ABI attendees would be presenting.
  • Catherine asked what the deadline is; Peter said that in the next few days attendees need to be chosen, and abstracts submitted within a week or so.

2) ICBME Singapore: planning who presents, writing of papers

  • James has been accepted for an oral presentation
  • Mike, Sarala and Tommy have been accepted for posters.
  • James and Tommy would like to go.
  • There was a discussion on who could present Mike and Sarala's posters.
  • Catherine asked if Andre could present one of ours.
  • Catherine again highlighted the conference calendar;
      • Users should flag conferences they are interested in.
      • Randall thought that submission deadlines for each conference should be added to the calendar.
      • Poul said it would be useful if someone could remind the group about upcoming deadlines, at meetings.
      • Randall asked Peter S. about the options for subscribing to Google calendars - Peter said it is possible to subscribe to an RSS feed of a calendar.
  • Catherine raised the possibility of having the CellML hackathon in Auckland.
  • Poul wondered what the numbers would be at a combined CellML, SBML, Biomodels, BIOPAX meeting.

3) PMR2 update

  • Tommy is still working on the wrapper between Mercurial and Plone.
  • He has been working on his ICBME paper.

4) CellML API progress update

  • working on code to parse RDF/XML, which is now partially complete.
  • Object model finished.
  • Still writing test cases.
  • Andrew has been fixing bugs with the validation service on Windows.
  • Andrew fixed a numerical solver bug that resulted in DAEs not working.  DAEs are now working but need testing on more complex models.

5) PCEnv progress update

  • Randall mentioned a mini developers conference (Andrew, Justin, Randall, and Alan Garny via telephone).  At this meeting they decided what stays in 0.5 and what is pushed back to 0.6.  These features can be found at tracker items 1089 and 1373.
  • Catherine mentioned that she thinks a Mac version is a high priority due to the number of Mac users in the field.
  • Randall highlighted some of the 0.5 features;
      • Improved connection view
      • New maths view
      • DAEs
      • Tabulation
  • Peter Hunter enquired as to how well Alan Garny is being brought into the development process. Randall said that Alan's suggestions are already making it into PCEnv, for example, the priority given to the Validation feature, which is a feature that COR has had for a long time. Randall said that Alan said at the developers' phone conference that he will have more time to do direct development after about another week or two.

6) Update on repository contributions

  • James has been adding status reports to models.
  • James has curated several bone models.
  • Catherine has almost finished the Saucerman 2008 model through her work in airports around the world.
  • 2003 Saucerman model remains a difficult work in progress.

7) CellML Spec progress update

  • No feedback on either the spec or virtual containment.

8) Additional items

  • Catherine mentioned John Olav Vik's request for a function that exports math renderings for publications from PCEnv.
  • Randall said this could be a 0.6 feature.
  • There was a discussion on variable name formatting - greek letter names being automatically parsed into greek characters.  Andrew does not believe it would be good practice to parse information out of variable in this way, given that we are working with an XML format, and presentation MathML provides a better alternative.
  • There was a discussion around methods for specifying variable name formatting;
      • Embedding presentation MathML in the content MathML
      • A quick hack method, eg parse "alpha" to alpha character - this has many problems.
      • Metadata for presentation
      • Possibly unicode support
  • Catherine said that conversion tools between SBML and CellML have been much requested.
  • Catherine suggested it would be good to add export options to PCEnv, such as SBML, Matlab, C++ etc.

Post minute comment (Mike Cooling): Note a paper for the ICBME is NOT required. See enclosed email:
Dear Sir/Mdm,

Regardless of the mode of presentation, you need to submit your final paper by 30 Sept 08, as per stated in the acceptance email to you.

However, if you wish to attend the conference to just present it as a poster without submitting the full paper, and you are able to complete the registration payment by 30 Sept 08, the committee will still include it in the programme but with no publication of the paper.  Only the abstracts will be published.

Kindly update us (with your paper ID, title) so that we can follow up accordingly.

Thank you.

ICBME 2008 Conference Manager