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)
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