ABI Meeting Minutes 2008-07-23

ABI Meeting Minutes 2008-07-23

Present: Tommy Yu, Catherine Lloyd, Mike Cooling, Andrew Miller, Geoff Nunns, Poul Nielsen, David Cumin, Randall Britten, Peter Hunter, Edmund Crampin, Dougal Cowan, Sarala Dissanayake

Apologies: James Lawson, Justin Marsh

Last week's action items

1) Andrew will create a tracker item to address the issue within the API's validation service so that the user is warned of dimensional inconsistency in units - need to inform user that they need to insert a scaling factor.

  • Tracker item already existed; Andrew is working on the issue.

2) Division by zero with modulus operations to be investigated.

  • Geoff is fairly certain that this problem is related to modulus, Justin is away.
  • Action item 1: Geoff to check if a tracker item exists for this issue.

3) Curatorial issues with CellML 1.1 models

  • Catherine given an action item to put these notes up on the CellML website under curation guidelines.

Agenda for this week

1) (Catherine) Dan Beard's model repository - steps we can take to support Dan Beard and facilitate the translation of his repository models into valid CellML

  • Edmund described the model repository's purpose as being to encourage very strict modeling technique, by having highly constrained requirements for model curation.  Current models are in MATLAB code.  The repository will grow very slowly due to the strictness of the curatorial process.  Ideally the solution would be a relatively automated process from the database to CellML, and from CellML to systems like Matlab.
  • Catherine discussed manual translation as an interim measure.

2) (Catherine) Singapore Abstracts

  • The contents of the tools abstract still need to be adjusted to take into account the issues raised by Alan Garny.
  • Action item 2: Randall to wrap up the abstract writing and submission process.
  • Most people submitting abstracts have finished, and Catherine has read these abstracts.
  • Catherine will send Poul the abstracts she has received to help him write up the abstract for the CellML overview talk.

3) (Catherine) Up-coming CellML-related conferences in the next 12 months

  • Catherine discussed the process of finding these conferences, and the Google calendar she has created to keep track of them.  This calendar is publicly viewable and can be edited by interested parties with a Google account.
  • Sarala and Poul were not certain that Sarala would have sufficient funding to attend two conferences.

4) (Catherine) Thank you to Geoff for all his hard work over the past few weeks.

  • Catherine thanked Geoff for all his hard work producing CellML models.
  • Geoff has produced approximately 20 models, of which approximately 12 are fully functional.
  • Geoff has also been producing PCENV session files, and the SVG diagrams to go with them.

5) (Sarala) Putting her software on cellml.org

  • Sarala discussed the state of her software.
  • Randall asked if the software could be put on the website; it was agreed that it would fit into the "tools" section of the website and should be made available.
  • Sarala's tool needs a nice acronym-centric name, possibly involving the word "visualiser".
  • James has previously mentioned that Sarala's tool does not use format/style of cellml model that is in line with the style used by most models in the repository.

  • Catherine said that it appeared to her that Sarala's output was fine, and wanted to find out what James' particular issues are.
  • Action item 3: It was agreed that there should be a meeting with Catherine, James, Poul, Mike and Sarala to discuss these format issues.

6) CellML API progress update

  • Andrew is still working on the CellML validation service.
  • After some discussion, it was decided that there should be a breakaway meeting about dimensionless units, especially exponents and log functions - Poul, Andrew and any other interested people to attend.

7) PMR2 update.

  • Tommy discussed progress on the curatorial functions of PMR2.
  • Tommy mentioned creating a tool that can dynamically graph the output of repository models within the browser.  This is currently just a conceptual prototype of a system that could provide useful dynamic output from models in the PMR2, independent of a simulation tool.
  • A discussion of the PMR2 prototype testing introduced the question of who outside of the ABI is submitting models.  It was decided that James should get in touch with Penny for more specific feedback about the PMR2 prototype. 
  • Action item 4: Randall to ask James about getting in touch with Penny.
  • Andrew suggested contacting people who have cited PMR1.

8) Update on repository contributions

  • Catherine has been working on a model that will be submitted shortly.
  • Geoff has been creating PCEnv session files and their SVG diagrams, in addition to models.  The Dan Beard models now have SVG diagrams.

9) CellML Spec progress update

  • Andrew had no update.

10) PCEnv progress update

  • Justin was absent.
  • Randall mentioned the addition by Justin of more information in the list of connections rather than just the repetition of the word 'connection'. Prior to this, the details pane in the latest snapshot already displayed the
    connected component names and variable names when a component node got focus.

From jlaw060 Thu Jul 24 09:53:40 +1200 2008
From: jlaw060
Date: Thu, 24 Jul 2008 09:53:40 +1200
Subject: Sarala's tool
Message-ID: <20080724095340+1200@www.cellml.org>

"James has previously mentioned that Sarala's tool does not output a format that can be used in the repository"

Hi all, actually what I meant to say is that the models in the repository are not quite in a format that is ideal for Sarala's tool (i.e. input is not in right format, rather than output.) I'd suggest we bring this up at the next meeting.