ABI Meeting Minutes 2008-09-03

Present: Dougal Cowan, Randall Britten, Justin Marsh, Poul Nielsen, Tommy Yu, Andrew Miller, Jonna Terkildsen, Michael Backhaus, James Lawson

Apologies: Peter Hunter, Mike Cooling, Catherine Lloyd

Last week's action items

1.)  Randall will create a tracker item to discuss a possible 'multiple equation math input' feature

2.)  Randall will create a tracker item to discuss possible drag and drop functionality within the model tree view in PCEnv
  • Justin will do this.
Action item 1.)  Justin will create a tracker item to discuss possible drag and drop functionality within the model tree view in PCEnv

3.)  Justin will create a tracker item to discuss a possible 'merge compatible elements' feature

4.)  Mike will add a tracker item to suggest a feature that displays the y-axis variable and the co-ordinates of the point when a graph trace is moused-over or clicked.

5.)  This issue warrants further discussion [whitebox grouping / virtual containment]. Randall will make it a standing item on the meeting agenda
  • done

6.)  Tommy will post to the tracker a summary of the most salient feedback he received on the PMR2 prototype
Action item 2.)  Tommy to post this summary to CellML-discussion mailing list

This week's agenda

James - proposal that: Ely Edison Matos's work on the CellO ontology for CellML be added as a related effort
  • Ely has done his masters thesis at Universidade Federal de Juiz de Fora, Brazil on CellO, an OWL description of CellML and supporting cyberinfrastructure (website for this work is here)
  • He has posted to cellml-discussion several times about his work but the group appeared to be unaware of it
  • James would like this project to be linked on the 'Related efforts' page of cellml.org
  • Poul agrees is keen for any respectable related project to be linked on this page
Action item 3.)  James will put up the link the CellO ontology

Catherine Lloyd and Mike Hucka are suggesting holding a combined CellML, BioModels Database, SBGN, SBO, BioPAX week-long super-hackathon in Auckland next year
  • Catherine has been talking to Mike Hucka at the SBML meeting in Goteborg, and they have proposed a week-long super-hackathon in Auckland.
  • The bottom of the South Pacific is obviously a long way for Europeans and North Americans to come (especially considering that the 2008 hackathon was in South Africa.) Combining a number of meetings into a week-long event may serve as enough incentive for people to come to Auckland
  • Poul noted that this would be good for the visibility of CellML within the systems biology community; CellML was highly involved with the SBML community during the early years of SBML development, but involvement has dropped off over the last four years or so
  • The meeting would probably consist of a number of half-day workshops, and could provide a much needed opportunity for cross-pollination of ideas between the proposed groups
  • Randall thinks this meeting would be great for the Auckland bioscience modelling community as well
  • The meeting would not necessarily have to be in Auckland if people are not willing / able to come down to New Zealand
  • Poul suggested that the time is really right for this kind of initiative: we will have completed a number of development milestones, such as PMR2, PCEnv is now at a fairly decent level of development and will be even better by then, Sarala will have finished her PhD and will hopefully have started working on integrating her ontology into the models etc. etc.
  • Such a meeting would constitute a very large amount of organisational work - Poul assumes that Catherine would take the lead in organising it, given her experience with organising the 2008 CellML workshop and the Waiheke Multiscale Modelling of the Heart conferences
  • The group thinks this is a fantastic idea in principle. So we should get to work on guaging interest and looking into its feasibility

Activating syndication (RSS) on cellml.org/news
  • Marco Viceconte is requesting that we activate syndication on www.cellml.org/news so Biomed Town can subscribe to the RSS feed
  • James mentioned that we don't actually produce much news on this page. Maybe more things should be newsworthy - e.g. release of spec proposals such as Andrew's lambda calculus typing system etc.
  • Tommy should be able to do this very easily
Action item 4.)  Tommy to activate RSS on cellml.org/news

ICBME2008: have letters of acceptance come through?
  • James and Tommy have received letters notifying them of their acceptance for a talk and a poster, respectively
  • Other members of the group had not received a letter yet
  • Writing a short (max 6 pages) paper has been confirmed as a mandatory requirement
  • James noted that because his subject is essentially a mashup which discusses what we intend to do with the projects currently under development, he should be able to compile a paper fairly easily
  • Poul and Randall are keen for Tommy to write a paper as well
  • Poul believes it is important to document the development process, particularly since this is some fairly novel work
  • We have less than a month to put together these papers. We also need to decide what the details of our plans are.
  • We did plan for Alan, Sarala or Andre to be able to present the work we have submitted - this may be more difficult for oral presentations than posters, however

Update on repository contributions
  • James has been curating the circadian rhythm models. He has curated a number and also added several SVG sessions
  • He has also been going through the tracker and resolving old items

Progress on PCEnv
  • Justin has been looking into drag and drop functionality for PCEnv and a putative connection editor UI
  • He has also made some minor bug fixes

  • Jonna mentioned that she has been trying to use the validator in the latest snapshot for validating a fairly large model with DAEs in it, and that it crashes.
Action item 5.)  Jonna will put up a tracker item re: her problems with using the validator for large models containing DAEs

  • When PCEnv is started, it automatically opens the last model or session that the user was working on.
  • At the moment there is no way to 'close' the session - this presents a problem if a XUL file is loaded into one of the graph panes because there is no way to get rid of it
  • Jonna would like some way to close the session
  • It was suggested that initially, a workaround is to save a blank session and load it when required
  • This issue requires a valid, hardcoded solution, however
  • User preferences are probably the answer to this: the user could tell PCEnv whether to load up the last session they were working on, or simply to start with a blank session
  • James noted that he would prefer a 'recent files' listing such as in MSWord to PCEnv reloading the last session a user was working on. Randall said that these two features need not be mutually exclusive

Progress on CellML API
  • Andrew has been working on API-side RDF parsing
  • Jonna asked if there had been any progress on her problem with models running fine in PCEnv 0.4 but not in the recent releases. There was a tracker item for this [minutes note: cannot find item]
  • Andrew has been looking into this. He thinks it is because of the DAE solver - even though the models themselves do not contain any DAEs
  • Randall has been looking at the DAE solver. It has not been performing well so he has been considering other options - including the Sundials 'IDA' solver
  • Andrew noted that this is quite different from the current approach; Randall suggested the API could use both
  • Andrew believes that the time spent implementing the a new solver would be better spent debugging the current implementation
  • Randall thinks it should be investigated. hHe has found very little information exists on our current approach; the little information he has found essentially says "don't do this"
  • We did get confirmation from John Butcher (the University of Auckland DAE specialist) that the current approach should be viable, however
  • Jonna noted that in the cases that she has been able to validate her models sufficiently and get the DAE solver to solve them, she has gotten good results

  • Tommy needs the API to be patched so he can leverage the CORBA server to talk to the CCGS from Python
  • There was some discussion about whether a 1.4.1 release of the API should be made
  • This discussion was moved to a breakaway meeting

PMR2 progress report
  • Tommy has been working on the backend integration with Hg. Specifically, how to integrate more existing code from the Hg web module into PMR2