PMR2 meeting 3/2/2012

Present: Dougal Cowan, Gareth de Walters, Mike Cooling, Duane Malcolm, Randall Britten, Tommy Yu, David "Andre" Nickerson, Hugh Sorby, Alan Wu, Edmund Crampin, Peter Hunter

PMR2 update

  • Tommy: staging of PMR2 0.5 has been up for a while now. New features include use of the latest CellML API and improved search.
  • Randall: the staged instance has been tested and so 0.5 can be deployed.
  • Tommy: working on decoupling citations from the models, using webservices to retrieve citations from PubMed etc.

Discussion on PMR2

  • Andre: could we have some way to get work done on the staged instances moved to the live repository? Not keen on testing if it means time and effort is wasted.
  • There was a discussion about the separation of the Mercurial & PMR2 hosting so that different PMR2 instances could access the same workspaces. Additionally, PMR2 objects that do not exist in the Hg repos would need to be able to be exported/imported, eg. exposures.
  • There was a discussion about hosting of large files.
  • Randall: large files would need the stable and file-version specific URL that current workspace files provide.
  • Andre: large files would need faster hosting than PMR2 is on currently, especially for international users.
  • Mike: PMR2 web interface has a range of usability problems. It would be good to have an easy exposure creation interface.
  • There was a discussion about usability and UI improvements.
  • Andre: We need to promote the collaborative model development advantages of PMR2 rather than as a publishing tool.
  • Randall: Can we add SED-ML support to enable display of results?
  • Peter: we need to work seriously towards the goal of having a library of components for model building.
  • There was a discussion about metadata and annotation issues.
  • Peter: we want to move towards being able to show parameter dependence and modification of parameters.
  • There was a discussion about modelling tool vs. PMR2 features, specifically with reference to the features of OpenCOR for: creating and working with workspaces, retrieving and uploading models, annotation, and parameter analysis and modification.

PMR2 0.6 planning points

  • Clone and synchronize workspaces across different repo hosts (eg Bitbucket, Google Code, etc).
  • Exposure export for moving exposures between PMR2 instances.
  • Sort out large file issues - test Mercurial solution, then investigate git or other solutions.
  • Improvements to advanced search.