[cellml-discussion] Summary of the inaugural CellML Editorial Board meeting
*The CellML Editorial Board (consisting of Jonathan Cooper, Edmund Crampin, Alan Garny, David “Andre” Nickerson and Poul Nielsen) had their inaugural meeting on the 8th of December 2011. All members of the board were present.* David Nickerson was unanimously elected chairman of the editorial board. At this meeting we discussed the purpose of the CellML editorial board and all agreed that while there is certainly a role in the guardianship of the CellML specifications, we are also responsible for growing the CellML community. To this end, we agreed that it is best to focus immediate efforts on identifying any barriers preventing adoption of CellML. As such, the editorial board is embarking on a review of the CellML API and the CellML model repository in order to identify any existing issues and to provide guidance for future development of these projects. Establishing the process by which the CellML specifications will develop was deferred to the next meeting of the editorial board. The CellML Editorial Board aim to meet monthly with the next meeting currently scheduled for the 12th of January 2012. Cheers, The CellML Editors. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Improved CellML support in latest version of JSim
Thanks Lucian. For CelML model developers and curators, I wrote a new section on using > JSim to help curate the model: > > http://physiome.org/jsim/docs/MML_CellML.html#curation > > that looks particularly helpful! ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Improved CellML support in latest version of JSim
Thanks for the notice, Andre! I want to note that if anyone finds some aspect of their favorite model doesn't survive the new translation, be sure to email me, and I'll see what I can do. I downloaded 1055 models from the repository as my test bed for this project, and got 884 of them working up to the point of making them simulatable. The one thing we don't do yet that prevented most of the remaining models from working in JSim is the feature that imports a component from another file. That feature is on the list of things we'd like to do at some point, but if it would be particularly helpful for your work, let us know and we'll bump it up the priority list. I found 141 models of this sort, leaving only 30 that failed for some other reason; mostly due to using some MathML construct JSim doesn't support (like 'partialdiff'). For CelML model developers and curators, I wrote a new section on using JSim to help curate the model: http://physiome.org/jsim/docs/MML_CellML.html#curation It explains how to take the JSim-translated version of your model and find potential sources of error in the model itself. In particular, JSim should now be a good tool for figuring out if the model is over- or under-determined, and for getting the units correct. More details can be found on that same page: http://physiome.org/jsim/docs/MML_CellML.html >From my work for this, I now also have translated versions of all 1055 models, so I can tell you which are the 159 models we found unit errors in, which models were overdetermined, etc. If some curator is interested in the list (and/or how they could make this list themselves), let me know. -Lucian * David Nickerson [2011-12-19 19:36] writes: > Hi all, > > JSim 2.05 has just been released and now has improved support for CellML > models. See the release announcement below. > > Cheers, > Andre. > > > > Highlights: > > o JSim now uses Java 6 rather than Java 5, resulting in various minor > improvements. If you're running JSim applets in your browser, but sure to > update your Java to version 6. > > o JSim's CellML importer has been substantially improved (thanks to LS). > JSim now runs 95% of the CellML 1.0 models in the CellML archive out of box > (no editing required). > > o Parameter set functionality has been substantially improved, including > the addition of loops, sensitivity and optimization configuration to > parameter sets. > > o Various minor fixes and feature improvements. > > See the JSim home page for complete information on JSim, including > documentation, downloads, documentation and model repositories: > > http://physiome.org/jsim/ > > For complete details on the latest release, click on "What's New?" > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://lists.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Improved CellML support in latest version of JSim
Hi all, JSim 2.05 has just been released and now has improved support for CellML models. See the release announcement below. Cheers, Andre. Highlights: o JSim now uses Java 6 rather than Java 5, resulting in various minor improvements. If you're running JSim applets in your browser, but sure to update your Java to version 6. o JSim's CellML importer has been substantially improved (thanks to LS). JSim now runs 95% of the CellML 1.0 models in the CellML archive out of box (no editing required). o Parameter set functionality has been substantially improved, including the addition of loops, sensitivity and optimization configuration to parameter sets. o Various minor fixes and feature improvements. See the JSim home page for complete information on JSim, including documentation, downloads, documentation and model repositories: http://physiome.org/jsim/ For complete details on the latest release, click on "What's New?" ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Announcing the 2012 CellML Workshop
Hi all, On behalf of the Auckland Bioengineering Institute and the CellML Editorial Board, I am pleased to announce that the 2012 CellML Workshop (http://www.cellml.org/community/events/workshop/2012/) will be held March 12 & 13 2012 at Goldwater Estate, the University of Auckland vineyard on Waiheke Island. Please save the date and stay tuned for further updates. Cheers, David. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
