ABI Meeting Minutes 2008-03-19

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

Review of last week's action items:

1.) Poul will do this following the meeting.

  • Referring to emailing Herbert Sauro regarding the University of Washington synthetic biology standards workshop.

  • Poul has done this.

2.) Andrew will discuss his thoughts on this matter with Justin.

  • This referring to the non-linear solver Justin is working on implementing in PCEnv.

  • Justin has talked to Andrew.

3.) Poul will send an email to the CellML discussion list detailing our intentions and soliciting feedback.

  • Poul will do this after the meeting.

Agenda for this week:

Agenda Item 1 - Catherine: CellML workshop, reminder

  • Catherine thanked everyone who helped her to organise the workshop, and the group thanked her for her hard work and dedication.

  • If anyone knows where we might be able to find the Penguin Timer to time the presentations, we would very much like to have it.

  • Catherine noted that several people were to be coming to the Institute on Tuesday 25/03/08, which is a university holiday, including David Nickerson and Jose Puglisi, but that the lifts and entry to the building would be locked. She has given them her cellphone number to call her when they get here and she will let them in.

  • Tommy will also be in on that day, and will be able to answer his phone if anyone calls.

Action Item 1.) Catherine to send out an email informing potential visitors of the university holiday and notifying them that they can call her or Tommy.

  • Catherine has arranged for the use of a PC laptop and Poul's old Mac for the conference. She has asked people to bring their talk files on flash drives rather than bringing their laptops, as we have a tight schedule on the workshop day.

Agenda Item 2 - PCEnv / CellML API progress update

  • Justin has been working on the non-linear solver for PCEnv.

  • He talked with Andrew, who pointed out areas that he should concentrate on, and is working on a straight-forward implementation of the solver before he begins work on identification by the software of sets of non-linear algebraic equations.

  • Alan has also talked to Justin, and noted that Sundials, who make CVODE, may also have software which Justin could use.

  • Alan asked whether the CellML API should be supporting both GSL and CVODE libraries. He recalls that in early versions of PCEnv, which used GSL, integration was slow.

  • Andrew made the point that the CellML API should attempt to provide options to developers in this respect and should not necessarily restrict itself to one solver library.

  • Andrew also mentioned that we might want to actually mix and match components of both GSL and CVODE for the proposed non-linear solver.

  • GSL currently provides a fully implemented quasi-Newton non-linear solver, whereas CVODE does not quite provide for our requirements.

  • Interested parties to form a breakaway session after this meeting to discuss these issues.

  • Alan has been discussing with the Oxford group what they would like to see in terms of future tools

  • He mentioned that the Oxford group would like a tool that is able to convert CellML 1.0 models to a 1.1 form.

    • Peter noted that what they are probably referring to is related to our plans to decompose models in the repository into modules which can be used to construct or modify models.

    • James discussed some of his ideas about how such a library of components might look, and Catherine noted that the curation requirements for single components would be very different from whole models as components could not be tested in the same manner.

    • Poul suggested that we would need to develop some kind of platform to test components individually.

    • Peter made the analogy to a patch clamp experiment for experimentation on membrane channels.

    • Poul suggested that such a platform could be provided within PCEnv that could be used to put components through batteries of standardised tests.

  • The Oxford group would like to be able to add metadata comments to CellML elements within PCEnv.

    • Catherine brought up Peter's idea of being able to click on an entity in an SVG diagram within PCEnv and seeing associated metadata. This could also provide a platform for editing this information.

    • Andrew noted that plans for a metadata viewer/editor have been in the tracker for a long time.

    • It would be best to start with a freeform generic field which can be used to view and edit metadata comments and then increase specificity from there.

    • James noted that this would be useful for providing URLs to database entries.

  • Andrew is still working on implementing rules for the validator in the CellML API.

  • Alan mentioned that it would be useful to get an idea of what rules were going to be implemented in the validation service.

    • Andrew replied that he is basing his validation rules on a CellML 1.2 normative specification draft.

  • Randall noted that the SBML specification has in it a list of validation rules

    • Andrew suggested that the normative specification draft he is working from is essentially a set of rules anyway.

Agenda Item 3 - PMR2 progress update

  • Tommy said that the web interface to the Mercurial system for uploading models is about half done.

  • Tommy has updated the Plone3 buildout to include the Mercurial based PMR2 as part of its installation process.

  • He and Randall have been investigating cloning temporary Mercurial repositories for uploading and also talking further about how version conflict handling

  • Peter asked if there was a URL he could go to for a demonstration.

    • Tommy has shown a demonstration to Randall, but it requires his admin password and is probably not quite ready to show Peter.

  • Randall suggested that Tommy putting a buildout up onto a test server so that people could play around with this.

  • Tommy is not quite at this point yet and is concentrating on getting things ready for the CellML Workshop.

  • James suggested that he and Tommy get together when the prototype is of sufficient maturity and start testing it.

Agenda Item 4 - CellML Spec version 1.2 progress update

  • Andrew has written up a proposal for the typing system in CellML 1.2

  • The document is referred to in a tracker item but the item is not new, so people who may now be interested are not aware that the proposal has been written.

  • Poul and Randall suggested that perhaps an email should be sent out in these sorts of situations.

  • Alan mentioned his conversations with colleagues in the scientific community regarding CellML. It would seem that some of the CellML community do not believe that their opinions would carry much weight were they to voice them.

    • James suggested that perhaps we are engaging in false economy. We have been working hard to make proposal and decision process more fair and consultative of the community, but perhaps people are not as aware of this as they could be.

    • Peter suggested that the workshop was the time to talk about our efforts in this regard.

  • Alan also asked how we might reach people who investigated CellML several years ago but found it not yet fit to their purposes.

    • Peter suggested that there is probably not much we can do about this but keep pushing forward with the specification. The European Network of Excellence of which the ABI is now a part presents a good opportunity to keep others updated about the CellML project.

  • Andrew noted that he thought it was important to design the specification so that it is easy for others to get involved. Specifically, he thinks that splitting up the specification into a broad primary specification and more specialised secondary specifications is a way to achieve this.

  • Andrew asked whether there was any feedback on the proposal for the typing system that he has proposed.

    • Randall suggested that there is a need here for some concrete examples of what the CellML could look like using the proposed typing system.

    • He also asked if there would be a chance at the workshop to discuss these issues. Catherine said that there is time for discussion after each group of presentations.

    • Some people will be staying for the Multiscale Heart Modelling Workshop and so will be available to talk there. Others are staying for still longer to discuss CellML with us.

Further Items:

  • Peter has read James' documents discussing his survey of the attitudes and policies of journals to co-publication of CellML models and code for computational models in internet repositories.

    • He has sent it to Grace Peng, who will be attending a meeting in Montreal with the scientific publishing industry.

  • Peter has asked Catherine to create a document describing the curation process which will be linked to on the page that discusses the meaning of curation levels.

  • Catherine will base this document off her presentation at the workshop, and she will send it to James and Penny Noble for comments and additions when she has drafted it.

  • Jonna has been working on the Guyton model and has coded most of the individual models comprising this model .

  • She will probably want to talk to Catherine and Pulasthi about getting some SVG diagrams of the model created.

  • Peter is keen to put these models up in the repository as a classic demonstration of CellML's utlity in describing systems physiology.

  • Catherine noted that a new PhD student Abhishek Tiwari has started at the Institute and will be working on endocrine modelling. He also has a strong background in computation and is interested in visualisation of models.

    • She will encourage him to come to our meetings, and also suggested that we allow him to post to team@cellml.org. The group concurred. Andrew will wait until Abhishek asks him to join, however.