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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 <david.nickerson at gmail.com> [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 at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-discussion

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• [cellml-discussion] Improved CellML support in latest version of JSim, David Nickerson, 12/20/2011
  • [cellml-discussion] Improved CellML support in latest version of JSim, Lucian Smith, 12/20/2011
    • [cellml-discussion] Improved CellML support in latest version of JSim, David Nickerson, 12/20/2011

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