From lpsmith at spod-central.org  Fri Feb  3 07:17:14 2012
From: lpsmith at spod-central.org (Lucian Smith)
Date: Thu, 2 Feb 2012 18:17:14 +0000
Subject: [cellml-discussion] (forw) JSim 2.06 released
Message-ID: <20120202181714.GJ34284@strackenz.spod-central.org>

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 at bioeng.washington.edu> -----

From: Erik Butterworth <butterw at bioeng.washington.edu>
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 at mit.edu>, "Huhns, Michael" <huhns at engr.sc.edu>,
        Melissa Krueger <krueger at u.washington.edu>,
        Max Neal <mneal at u.washington.edu>,
        David Nickerson <d.nickerson at auckland.ac.nz>,
        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 at gmail.com>, "Dash, Ranjan" <rdash at mcw.edu>,
        Richard Ward <wardrc1 at ornl.gov>, Herb Sauro <hsauro at u.washington.edu>,
        Andreas Schwab <andreas.schwab at staff.mcgill.ca>,
        Shiva Ayyadurai <vashiva at MIT.EDU>,
        Gary Ynvge <gyngve at cs.washington.edu>,
        Adam Alessio <aalessio at u.washington.edu>
Subject: JSim 2.06 released
Date: Thu, 2 Feb 2012 10:01:48 -0800 (PST)
Message-ID: <Pine.LNX.4.64.1202020955210.4336 at frodo.bioeng.washington.edu>

  Highlights:

  o  new Monte-Carlo analysis module;

  o  CellML output is now available;

  o  various bug fixes,  including one in SBML import which previously
mishandled time-varying compartment volumes.

  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?"

  Note to QPP users:  JSim 2.06 should not be used with the previous
QPP release (0.913).  A new QPP release, 0.914, will be made later today
that is compatible with JSim 2.06.

Erik Butterworth    butterw at uw.edu    206-685-2007
Software Engineer, University of Washington Bioengineering
http://physiome.org/~butterw/

----- End forwarded message -----

From camille.laibe at ebi.ac.uk  Thu Feb  9 08:14:51 2012
From: camille.laibe at ebi.ac.uk (Camille Laibe)
Date: Wed, 08 Feb 2012 19:14:51 +0000
Subject: [cellml-discussion] 21st release of BioModels Database
Message-ID: <4F32C9AB.6000002@ebi.ac.uk>

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.


Moreover, after consultation with BioModels Database's Scientific 
Advisory Board and to be more in agreement with the EBI terms of use, it 
was decided that from the next release, the BioModels.net Team will 
abandon its copyright on the encoded form of the models and release them 
in the public domain.


Finally various improvements were made to the underlying software 
infrastructure. The main publicly visible change is the fact that a bug, 
dealing with the handling of annotations in the non-curated branch, has 
been discovered and subsequently fixed. This results in an major 
increase in the number of annotations from models in the non-curated 
branch. However, we would like to emphasise that those annotations were 
provided during submission and are not checked by our curators.

For more information about this release, please refer to the release notes:
http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20120208


We would like to thank all our collaborators, founders and submitters. 
We also want to thank the SBML community for their support and the tools 
they develop and provide.

BioModels Database is the result of numerous current and past 
collaborations and has received funding from multiple sources. Please 
refer to our acknowledgements page for up-to-date details: 
http://www.ebi.ac.uk/biomodels-main/acknowledgements

Camille Laibe
on behalf of the BioModels.net team.

-- 
Camille Laibe
BioModels.net Coordinator
European Bioinformatics Institute, Cambridge (UK)

From tommy.yu at auckland.ac.nz  Wed Feb 15 11:10:16 2012
From: tommy.yu at auckland.ac.nz (Tommy Yu)
Date: Wed, 15 Feb 2012 11:10:16 +1300
Subject: [cellml-discussion] CellML Model Repository upgraded to PMR2 v0.5
Message-ID: <4F3ADBC8.6020106@auckland.ac.nz>

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.

From tommy.yu at auckland.ac.nz  Thu Feb 16 12:05:27 2012
From: tommy.yu at auckland.ac.nz (Tommy Yu)
Date: Thu, 16 Feb 2012 12:05:27 +1300
Subject: [cellml-discussion] CellML Model Repository upgraded to PMR2
 v0.5
In-Reply-To: <4F3ADBC8.6020106@auckland.ac.nz>
References: <4F3ADBC8.6020106@auckland.ac.nz>
Message-ID: <4F3C3A37.1050807@auckland.ac.nz>

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 at cellml.org
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