Meeting Minutes 11th September 2006
Meeting Minutes 11th September 2006
Present: Tommy Yu, Shane Blackett, Andrew Miller, Poul Nielsen
Tommy: Has two weeks left on his current contract.
Erik Butterworth from the University of Washington has about 30-50 models which now run in JSim. The models are modified versions of repository models, There was some discussion about how these should be put in to the repository, and the consensus was that if they differ from the published paper, they should be new variants of the repository models.
Tommy has been having trouble with the current 4Suite RDF library in Python, because it seems to produce the wrong RDF graph when inputs containing empty attributes are encountered. He is keen for there to be RDF support in the CellML API. Shane is less keen to have a generalised RDF API, and would prefer to only allow access to a more specialised API. Andrew noted that in order to provide support for a more specific API, implementations are already burdened with having to parse RDF, so they might as well allow more generic access (for RDF metadata which was never contemplated). The consensus was that Matt needed to be present for this discussion. Poul will ask Matt to discuss this with Andrew and Tommy later today.
Shane noted that he has now put ITK into cmgui.
Poul noted that there has been a single applicant for the model curator position. The applicant apparently does not have much formal training in biology, although has a software engineering background. Poul will interview him later today.
Andrew noted that he had been working on trying to get the RDF/XML parser patch for Mozilla checked in, as he is concerned that the codebase will diverge if it is not in the Mozilla CVS. There has been some difficulty getting anyone to review it, partly due to fear by the RDF module owner that something in Mozilla which depends on RDF will break. Andrew has written code to test against the W3C testsuite, and has also done some work to test Firefox and Thunderbird still works with the patch (and especially the RDF dependent parts).
Andrew has also made some progress towards getting a release of PCEnv.
Poul hasn't heard back from the synthetic biology group yet, but will post the URL to the website by a group involved to people at the institute who are interested.
Tommy: Has two weeks left on his current contract.
Erik Butterworth from the University of Washington has about 30-50 models which now run in JSim. The models are modified versions of repository models, There was some discussion about how these should be put in to the repository, and the consensus was that if they differ from the published paper, they should be new variants of the repository models.
Tommy has been having trouble with the current 4Suite RDF library in Python, because it seems to produce the wrong RDF graph when inputs containing empty attributes are encountered. He is keen for there to be RDF support in the CellML API. Shane is less keen to have a generalised RDF API, and would prefer to only allow access to a more specialised API. Andrew noted that in order to provide support for a more specific API, implementations are already burdened with having to parse RDF, so they might as well allow more generic access (for RDF metadata which was never contemplated). The consensus was that Matt needed to be present for this discussion. Poul will ask Matt to discuss this with Andrew and Tommy later today.
Shane noted that he has now put ITK into cmgui.
Poul noted that there has been a single applicant for the model curator position. The applicant apparently does not have much formal training in biology, although has a software engineering background. Poul will interview him later today.
Andrew noted that he had been working on trying to get the RDF/XML parser patch for Mozilla checked in, as he is concerned that the codebase will diverge if it is not in the Mozilla CVS. There has been some difficulty getting anyone to review it, partly due to fear by the RDF module owner that something in Mozilla which depends on RDF will break. Andrew has written code to test against the W3C testsuite, and has also done some work to test Firefox and Thunderbird still works with the patch (and especially the RDF dependent parts).
Andrew has also made some progress towards getting a release of PCEnv.
Poul hasn't heard back from the synthetic biology group yet, but will post the URL to the website by a group involved to people at the institute who are interested.