ABI CellML Meeting Minutes, 30th June 2010

Present: Dougal Cowan, Randall Britten, Tommy Yu, David "Andre" Nickerson, Justin Marsh, Catherine Lloyd (first half), Andrew Miller

Apologies: Mike Cooling, Peter Hunter

 

Last week's action items:

 

1) Dougal: Find out what was in the EMBC workshop proposal.

  • Still in progress.

This week's Agenda:

 

1) (Randall) Plan for PMR2 v0.4.

Discussion:

  • Andre: There are various aspects of the exposure system that don't work. What is required is to be able to create an exposure by picking a file(s) from a workspace at a particular revision, and the exposure is created depending on the content chosen. The simulation results should be displayed, these are essential to compare with curation claims. Users should also be able to link to model maths from results and vice versa. Andre's exposure ideas can be found in Nickerson & Buist 2009, and demonstrated at http://www.bioeng.nus.edu.sg/compbiolab/p3/hh.html (referred to in the aforementioned paper).
  • Randall: Andre's "workflow" for exposure creation is quite different. Any user should be able to make exposures (who is in this any user group needs discussion), but these would not enter the main listing until curated. Alternative versions of the "main list of exposures" could be compiled, possibly independent of the main curators.  This would allow for competition between listings, which could be beneficial.
  • Catherine: Supports the display of results on exposures. Does not object to curation flags being postponed in favour of new exposure development.
  • Andrew: New curation flags do not depend upon new exposure system being in place, as long as their meaning is agreed and remains consistent. Metadata should be created recording who set the flags and when.
  • Tommy: Andre's exposure styles can be built on existing PMR2. The system specification may need to be upgraded, due to the extra burden of computing models, and other aspects of these types of exposures.  New exposure types can probably be developed within the next iteration, and make it into PMR2 0.4.
  • Randall: Exposures system currently allows multiple exposures per commit - this should be maintained. Ideally, in the future any user can see an exposure for any commit in any workspace, created on the fly and then cached.

Planning:

  • Randall: Current attendees support proposal to work on new exposure styles for v0.4 of PMR2. This needs to be discussed with Peter & Poul, since the FieldML side of PMR2 is quite new and also likely to require work.
  • Action Item 1: Randall to e-mail Poul and Peter for input on this.

2) (Andre) Discussion of Andrew's provenance manuscript.

Discussion:

  • Andre: Inclusive authorship should work both ways - rather than dropping authors who disagree with the paper, discussion of possible changes should be had with them. The paper does not show anything about provenance, but rather number of commits.
  • Randall: A closer look at the overlap in content between the PMR2 papers needs to be undertaken.
  • Further discussion took place at a break-away meeting.

Planning:

  • Action item 2: Andrew will send out a new draft incorporating Andre's comments.

3) Repository contributions - update

Progress:

  • Catherine: Hanne has created a large number of SVG sessions. She has completed the electrophysiology category, and has created a number in metabolism and endocrine. Catherine is working on a couple of big bone cell models for Marco. 

New issues:

  • Catherine: A bug has been found in OpenCell or the API to do with units checking.
  • Action item 3: Catherine to send more info to Justin.

Current activity:

  • Catherine: Working with Hanne on SVG session files. Soon to begin work on a large virtual liver project with Adriano Henney.

Planning:

  • Action item 4: Catherine to contact Geoff Nunns about helping with the Saucerman model again.

4) PMR2 development - update

Progress:

  • Tommy: Fixed issue with fresh installations of PMR2. Sorted out the domain name and theming issues.

5) CellML API - update

Progress:

  • Andrew: Closed off old tracker items.

New issues:

  • Randall: Justin found that the Saucerman model is not working in RunCellML - we think this is a recent change since Geoff tried it.

Current activity:

  • Andrew: Spending a lot of time on the Windows build environment, which is still disconnecting from the build master.

Planning:

  • Randall: Hugh Sorby will be contacting Andrew about Windows build slave - there is a shared build resource being obtained from ITS. CellML-API/OpenCell Windows build environment will be moved to shared virtual resource from ITS.

6) OpenCell development

Progress:

  • Justin: Failure to converge when integrating is now communicated back to OpenCell, which gets rid of silent failures.
  • Randall: There was a Scala/JVM vs Qt/C++ meeting on Friday involving most of the members of the ABI "bioengineering software development group" (BSDG) as well as some others.  There were not strong objections to the Scala/JVM approach, and those in favour of using Scala/JVM included participants outside of the OpenCell ABI team.

Planning:

  • Randall: Further discussions will be held about the platform choice issue. Busy collaboratively writing/compiling a recommendation document summarising the decision factors.

7) CellML core specs - update

  • No updates.

8) Metadata specifications (general, citations, graphing, simulation, other) - update

  • No updates.