ABI Meeting Minutes 2008-03-05

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

Review of last week's action items:

1.) Justin will add this issue to the tracker and continue his work on this

  • This item is regarding Justin's work on adding the capability to use the percentage normalisation feature in PCEnv sessions.

  • Item complete.

2.) Andrew will update the posting permissions for team@cellml.org

  • Item complete - John Davidson and Penny Noble now have permission to post to team@cellml.org

3.) Catherine will change the name [of the "What's New?" in CellML 1.1/1.2 page] to something more appropriate

  • This issue became more complicated after last week's meeting, so the item was not appropriate.

  • David Nickerson would like the specifications page to contain only the specifications; discussions of the specifications or related information should be in the main wiki or somewhere else.

    • Poul voiced his disagreement, so did James.

  • The group decided that it would be best to split the "What's New?" page into two: essentially, one page describing the differences between CellML 1.0 and 1.1 and another describing the proposed modifications to the CellML specification in version 1.2

Action Item 1.) Catherine will carry out these modifications.

  • David also suggested that we use the wiki rather than Plone pages for such articles.

    • Randall noted that the Plone wiki software can be fairly buggy.

    • Catherine noted that she finds wiki pages complex to use.

    • Justin suggested that wikis are useful for works continually in progress

    • Peter suggested that we may want to use wikis for discussion and collaboration on articles, but use Plone pages for formally 'finished' pages.

4.) Peter asked Tommy to write him an email explaining how we are currently dealing with this issue [3-tiered databasing], which Peter will forward to Shankar to see whether he thinks we are in fact taking an appropriate approach, and what further suggestions he has.

  • Tommy has done this. Peter to read.

5.) Justin will announce the release of PCEnv 0.3.1 on the CellML discussion mailing list.

  • Justin has done this.

6.) Poul to email Herbert Sauro regarding this matter [Andrew attending University of Washington Synthetic Biology conference instead of Jonna]

  • Poul wasn't at the meeting and wasn't made aware of this.

  • In future, we should assign action items to people present at meetings to request non-present individuals to perform tasks.

Action item 2.)  Poul will email Herbert Sauro

7.) James will investigate which journals hold this policy and create a comprehensive list of such.

  • This concerning journals which hold a policy of encouraging modellers to submit their models in CellML when they submit papers for publication.

  • James has not yet done this.

  • Peter noted that there is a conference organised by the NIH at which this issue will be discussed, and that he has told Grace Peng he will send her this list when James has completed it.

Action Item 3.)  Carrying over action item from last week.

Agenda for this week:

Agenda Item 1 - Peter: Ten Tusscher et al. [2004] model issues

  • Peter was emailed by Brian Carlson of the Medical University of Wisconsin regarding his experience running and using the Ten Tusscher 2004 model in JSim.

  • Brian noted that while the latest version of this model on the repository reproduced the published results, the model was mathematically different from the model described in the publication, and it took him a week to figure out what had been done to the model to get it to reproduce the results in the publication.

  • There has been discussion by email among the curation team regarding this.

  • If Brian had been able to access a comprehensive modification history for this model, it would have made his work much easier.

  • James noted that the central issue here is that Penny Noble sent him the curated model, but that he did not know the specifics of what had actually been changed, and therefore did not fill in the modification history metadata appropriately.

  • Catherine noted that even if the modification history had been filled in fully, it is not immediately obvious how to access it from the repository.

    • The group considered this and it was noted that we should look into making this information more accessible.

  • Andrew noted that the current DOCBOOK technology used for model documentation was originally intended to be temporary and that we really need to be moving towards generating the documentation from RDF metadata.

  • Catherine said that she will be visiting the UK and will be able to meet with Penny and teach her how to upload models to the repository herself. Hopefully then she will be able to teach the rest of the Oxford team, or upload their models for them.

Agenda Item 2 - Randall: Proposal handling

  • Following the discussion of this issue at last week's meeting, there has been further discussion on the tracker and mailing lists.

  • Randall wanted to make a decision on how proposals would be handled, specifically, proposals for the CellML 1.2 specification.

  • Poul urged that when an important proposal has been discussed and a decision is imminent, the community should be notified so that are aware of this via the CellML Discussion mailing list, and can make comment.

  • Andrew was concerned that while decisions should be able to be revisited if necessary, we should have formal processes for this.

  • Regarding the issue of voting, Justin noted that the use of voting to make a binding decision and to conduct a poll to consider community opinion are very different matters.

  • We made the decision to use the process discussed this week and last. Simply put:

    • We attempt to reach decisions by general consensus.

    • If consensus is not obvious, the decision will be put to a panel of senior CellML community members consisting of: Poul Nielsen, Alan Garny, David Nickerson, Andrew Miller and Randall Britten.

    • In the event that the above process still does not address the issue, Poul Nielsen, as the leader of the CellML project, will make a judgement.

Agenda Item 3 - PCEnv / CellML API progress update

  • Justin has started coding the non-linear solver, but has not yet made any commits.

  • Peter asked how he has addressed the issue of how the sets of these equations will be identified and how they will be processes.

    • Justin said that if a system can be isolated, it will be shunted off into a 'slow path' to the non-linear solver. The user will be able to set a limit on the number of such equations.

  • Peter asked what kind of solver is being used, whether it is a Newton-Raphson solver.

    • Justin replied that it is a hybrid solver built into GLSL.

  • Poul asked if the solver being used handles constraints. It does not, but if constraints are required, an additional constraint handling solver could be added.
  • James asked if Justin was tailoring requirements for this solver to the models that we would like to be able to solve, and would Justin like some examples of such models?

    • Randall said yes, and noted that there was a tracker item discussing this. There are a few example models referred to in the tracker item, and they will be used for determining completion of the task. Additional examples are welcome, to allow for testing, but won't necessarily be part of the validation test set.

Action Item 4.)  James will CC himself to the tracker item and add example models to this item.

  • Andrew has added some validation rules to the CellML API, which has resulted in the identification of a model with redundant unit definitions.

Agenda Item 4 - PMR2 Update

  • Tommy has been working on 'exposing' models and the manner in which models can be listed and views.

  • The next thing to work on is a system for uploading models using a browser instead of the Mercurial client.

  • Randall noted that uploading is one of the key issues regarding the proof-of-concept of the use of Mercurial with PMR2.

  • Tommy has created and shown Randall a demonstration of a CellML 1.1 model within his software that uses relative URLs. This is an important milestone in the development of PMR2, and Tommy is confident that he will be able to give a good presentation and demonstration of the PMR2 prototype at the CellML Workshop later this month.

  • Peter mentioned that Mike Cooling is considering a post-doctoral position at the ABI, and if he takes this up, he will be dealing with creating a library of modular components from models in the repository. Interaction between Tommy and Mike would thus be beneficial to both parties.

  • Peter also mentioned that we would have to work on metadata frameworks for this modularisation process.

    • James said that there has been much discussion on the Biobricks Standards mailing list dealing with essentially the same issues: how and with what information Biobricks should be described such that it is possible to query a database to find specific items for specific functions.

      • Mike also subscribes to this list.

Agenda Item 5 - CellML Spec version 1.2 progress

  • Andrew talked with our Japanese visitors last week about what they would like to see in the CellML 1.2 specification.

    • They would like the ability to describe PDEs and further integration with FieldML.

  • Peter would like the group to look at InSilicoIDE's markup language in some more detail, he is interested in how they deal with agent based models, amongst other things.

  • James asked if agent based models are necessarily spatial, or whether we could currently deal with them using CellML 1.1

    • Peter replied no, they are not inherently spatial, and that we could probably deal with them using CellML currently, although we would have to work on the metadata frameworks for describing how agents communicate with eachother.

  • Randall suggested that if InSilicoIDE's markup language goes open, we might even be able to incorporate its infoset within CellML.

Further items:

Requirement for someone to operate the video camera at upcoming CellML and MSMH conferences:

  • Catherine said that she received no replies to her request for someone to act as the cameraman for the upcoming CellML workshop and MSMH events.

  • James said he'd be quite happy to do it, with the caveat that he has little experience in working the camera. He noted that when David Nickerson recorded the CellML conference, it seemed to mainly require changing tapes.

  • Gareth is in charge of the camera and can probably provide James with some training
Action Item 5.)  James to get in touch with Gareth and learn to use the camera
  • Catherine said that Gareth would do the editing of the video, as he has done in the past.