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Lucian Smith | 2 Feb 19:17

(forw) JSim 2.06 released

Some of you might be interested in this--JSim now has CellML output as 
well as CellML input.  Since JSim models themselves are not modular, 
everything gets put into a single component; there is hope that in the 
future when JSim itself is modular, it will be able to produce modular 
CellML output.  A few more details at 

http://physiome.org/jsim/docs/MML_CellML.html#exporting

-Lucian

----- Forwarded message from Erik Butterworth
<butterw@...> -----

From: Erik Butterworth <butterw@...>
Reply-To: Erik B <butterw <at> u.washington.edu>
To: JSim Development -- Adam Alessio <aalessio <at> u.washington.edu>,
        "Dr. James Caldwell" <jcald <at> u.washington.edu>,
        Forbes Dewey <cfdewey@...>, "Huhns, Michael" <huhns@...>,
        Melissa Krueger <krueger <at> u.washington.edu>,
        Max Neal <mneal <at> u.washington.edu>,
        David Nickerson <d.nickerson@...>,
        Bart Jardine <barthj <at> u.washington.edu>,
        Gary Raymond <garyr <at> u.washington.edu>,
        "Dr. James Bassingthwaighte" <jbb2 <at> u.washington.edu>,
        Lucian Smith <lpsmith <at> u.washington.edu>,
        Rebecca Rowe <rebikah17@...>, "Dash, Ranjan" <rdash@...>,
        Richard Ward <wardrc1@...>, Herb Sauro <hsauro <at> u.washington.edu>,
        Andreas Schwab <andreas.schwab@...>,
        Shiva Ayyadurai <vashiva@...>,
        Gary Ynvge <gyngve@...>,
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Camille Laibe | 8 Feb 20:14
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21st release of BioModels Database

Dear colleagues,

We are pleased to announce the twenty-first release of BioModels 
Database (http://www.ebi.ac.uk/biomodels/).

Important changes are happening or announced in this message, so please 
read further.

In this release, 68 new models have been published and numerous existing 
models have been updated. The public version of BioModels Database now 
contains 409 models in the curated and 420 in the non-curated branch. 
Together, these 829 models comprise 130800 species, 151274 relationships 
(which include reactions, rate rules, events and assignment rules), and 
106210 cross-references.

Along with the data release, we would like to announce several important 
changes.

First of all, in addition to the SBML version of each model with 
annotations encoded with MIRIAM URNs, BioModels Database now provides a 
second SBML file with annotations encoded using Identifiers.org URLs. 
Those files can be accessed from the "Download SBML" menu displayed on 
the top left of any model page and from the models archives (now 
provided from the EBI FTP server).

BioModels Database will serve the URN form as the default until the next 
release of the database. Then the URL form will be provided as the 
default. The files with the URN annotations will still be available for 
a while. We encourage software developers to consider the 
Identifiers.org version of MIRIAM URIs for any new development.
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Tommy Yu | 14 Feb 23:10
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CellML Model Repository upgraded to PMR2 v0.5

Hi,

The CellML model repository underwent a software upgrade and is now running PMR2 v0.5.  If you encountered
any issues with this update please file a tracker item that blocks the following tracker item:

https://tracker.physiomeproject.org/show_bug.cgi?id=3211

New features that were added for this release includes more CellML specific searching (for
models.cellml.org) and updated the CellML API to version 1.11.  Some internal code changes were made also
to support some future features.

Regards,
Tommy.
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Tommy Yu | 16 Feb 00:05
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Re: CellML Model Repository upgraded to PMR2 v0.5

Hi,

There is a minor correction needed to my previous announcement.  The CellML API version I used was a specific
snapshot of the CellML API some time after 1.10 was released and not the 1.11, and that one fixed one of the
MATLAB code generation issue.

Regards,
Tommy.

Tommy Yu wrote:
> Hi,
> 
> The CellML model repository underwent a software upgrade and is now 
> running PMR2 v0.5.  If you encountered any issues with this update 
> please file a tracker item that blocks the following tracker item:
> 
> https://tracker.physiomeproject.org/show_bug.cgi?id=3211
> 
> New features that were added for this release includes more CellML 
> specific searching (for models.cellml.org) and updated the CellML API to 
> version 1.11.  Some internal code changes were made also to support some 
> future features.
> z
> Regards,
> Tommy.
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion@...
> http://lists.cellml.org/mailman/listinfo/cellml-discussion
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