ABI Meeting Minutes 2008-05-14

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

Review of last week's action items:

1.) Tommy has given Alan Garny permission to edit pages on cellml.org

2.) Randall talked to Peter about the possibility of getting funding for building Java bridges to the CellML API
  • Peter said that our current funding allows some room for work on non-GUI projects.
  • Whether we would need to apply for specific funding depends on how big the project is likely to be.
  • Andrew estimates that it would take approximately 80 hours, although this would depend on familiarity with the CellML API etc.
  • It might also be worth getting bindings to Python, MATLAB and perhaps other languages, done at the same time.
  • Peter suggested the possibility of getting a computer science or software engineering student to work on this between semesters, with the possibility of an on-going part time position.
  • Randall noted that this work could possibly be done by the developer who he is planning to hire in the near future
  • Peter noted that we could be engaging more with the software engineering and computer science departments to let them know about the kind of projects that students might be able to work on for us.
    • On a related note, Poul has organised a meeting with Valeriy Vyatkin from the software engineering department to discuss possible collaboration opportunities. Meeting is at 2pm on Friday 16/05/08 in the 6th floor ABI meeting room - all welcome.

Agenda for this week:

Catherine: xCellerator

  • xCellerator is a Mathematica package that Catherine was introduced to by people she met at the conference she recently attended in Amsterdam. It allows easy generation of pathway models based on a number of different types of kinetics, and Catherine has been particularly impressed by the quality of the models it is able to generate. She has coded up two models into CellML from straight from the journal papers without any hitch at all, which is rare.
  • The xCellerator website has a model repository, which offers models in Mathematica and SBML formats, Catherine noted that this repository contains many of the same models as the CellML Model Repository.
  • xCellerator, while running in Mathematica, can read and write SBML models using MathSBML, a tool which translates between Mathematica and SBML.
  • Peter noted that Abhishek might be interested in xCellerator, as he is currently in the process of drawing up a proposal for a graphically based tool for creating and editing CellML models of biochemical pathways. It is possible that this could be a module within PCEnv/COR/YAPE in the sense that Alan Garny is creating an 'electrophysiology' module.
Action item 1.) Catherine will give Abhishek a demonstration of xCellerator

Randall: Removal of the PCNG tracker from cellml.org
  • The CellML and CMISS websites go down occasionally and Andrew Cantell from the ABI IT team has been looking into this. He has identified the PCNG tracker on the cellml.org site as troublesome.
  • Since we no longer use this tracker, Randall proposed that we should remove it from the website.
  • We would need to make sure any data within this old PCNG instance is archived or migrated to the Bugzilla tracker
  • Andrew transferred all open tracker items to the Bugzilla tracker when it was set up, but there may have been some closed tracker items that he did not migrate. These may contain valuable information and should be migrated.
Action item 2.) Andrew to check if any major data needs to be transferred before the PCNG tracker is removed.
  • www.cellml.org/tracker still points to the old PCNG tracker, rather than the Bugzilla tracker
Action item 3.) Tommy to move old PCNG tracker and make www.cellml.org/tracker point to the Bugzilla tracker

Randall / Alan Garny: User defined functions in CellML 1.2
  • Alan has proposed that CellML 1.2 include a capability for users to define functions
    • such as sum, maximum, minimum, etc.
  • The consensus was that it would be inappropriate to try to add a feature like this at the level of an input language, and so instead it should be addressed properly in CellML. It was noted that proposals already under discussion for CellML 1.2 to allow lambda calculus address this already. Catherine noted that at present she works around this issue, as well as the lack of vectors and matrices, by duplicating the mathematics in the model.

Catherine: Feedback on meeting with Martin Fink
  • Catherine posted minutes from her meeting with Martin Fink when she was in Oxford
  • Two of the main issues he was concerned about were functionalities for the CellML repository and standardised naming of variables and components in CellML models of electrophysiology
  • Many of the requests that were made for the repository are in fact being developed for PMR2
  • James has started research into ontological annotation of CellML models using Sarala's CellML-Bio ontology and references to other constrained vocabularies and ontologies from within the CellML-Bio ontology. He hopes to have some examples of annotated models ready to show the community within several weeks.
  • Peter noted that it is very important for our commitments to the European groups that we respond to these sorts of requests and feedback.
Action item 4.) James to get in touch with Martin Fink and let him know of our discussions regarding his requests.
  • Peter will see if he can find information about constrained vocabularies and ontologies from the ion channel research community, as will James.
  • James should work on some basic ion channel / electrophysiology models as his annotated examples.

  • James also mentioned a draft paper lead-authored by Nicholas le Novere that discusses the development and use of ontologies in annotating systems biology models. The three principle ontologies discussed are Systems Biology Ontology (SBO,) Kinetic Simulation Algorithm Ontology (KiSAO) and Terminology for the Description of Dynamics (TeDDY.)
    • He suggested that KiSAO might have something to teach us about equation / system identification, or about things we can do with simulation metadata in general.
Action item 5.) James to forward this draft document to the team@cellml.org list

PCEnv  / CellML API progress update
  • Justin is currently working on bugs that are tagged as blocking the release of PCEnv 0.4
  • Andrew has been working on the API's code generation service, which is requiring some refactoring to allow for the new non-linear solver functionality
  • There was some discussion about the practicalities of annotating non-linear algebraic systems of equations.
  • Andrew noted that trivial changes to models annotated in such a manner, such as adding an initial value to a variable where there was none before, could break the annotation. Consideration of these issues is ongoing.

PMR2 progress update
  • Tommy has created VMware images for both PMR1 and the PMR2 prototype for Peter to use in presentations where he does not have web access
  • He has also been working on the indexing system in ZOPE

Models downloaded from repository in Opera lack *.cellml extension
  • Alan Garny noticed this recently. Files are downloaded with a *.xml extension instead
  • This is most likely a bug in Opera
  • Since use of Opera is not particularly widespread, the team did not consider this to be a pressing issue

CellML 1.2 specification progress update
  • Andrew received correspondence from Kevin Burrage regarding representation of stochastic models in CellML
  • Kevin is keen to talk to Andrew via Skype
  • Other members of the team are keen to listen in if possible
Action item 6.) Andrew to organise a Skype or BestGRID meeting with Kevin, hopefully at a time that whoever wants to is able to join in

cellml.org committee

PCEnv / COR developers meeting
  • The PCEnv / COR developers met recently to discuss the project
  • Randall will post minutes from this meeting soon.

Osaka group
  • Peter has recently been to Osaka and the InSilicoIDE group there is keen for closer relations with the CellML team
  • James mentioned that he is keen to facilitate this kind of increased collaboration by encouraging groups such as Osaka to put content on cellml.org

Poul's visit to Monash University (Melbourne)
  • Poul recently visited Monash University and discussed a possible collaboration project
  • Researchers at Monash have been collecting large amounts of data from physiological experiments on rat trabeculae (cardiac myocyte tissue.)
  • They would like to use their large grid computing resources to reparameterise a well defined CellML model such as Jonna's Pandit-Niederer-Hinch model using this physiological data.
  • This would involve hooking the CellML API into their grid tool, and would probably require Python bindings to the CellML API