[cellml-discussion] [BioModels Database] 14th release

[Chen Li]

Hinxton, Wednesday 16th June 2009

Dear colleagues,

We are pleased to announce the fourteenth release of BioModels Database.

In this release, 5 new models have gained entry to the curated branch. 
The public version of BioModels Database now contains 216 models in the 
curated and 196 in the non-curated branch. Together these 412 models 
comprise 28901 species and 36264 reactions. Some of the existing models 
have been slightly changed for correction and to enhance reusability. 
Also the annotations of some existing models have been updated. The 
database now features around 14611 cross-references.

Out of the 196 models that are in the non-curated branch, 92 models are 
imported from the CellML repository (http://www.cellml.org/), which 
would subsequently be moved to the curated branch in future.

After the last release, the BioModels Database software has been 
enhanced to alter some new features.

Some features concerning public users are:
* Submission of models now accepts models encoded in SBML Level 2 Version 4
* On the homepage, besides "Search", there is another button "Go to the 
model". After giving the model's name or ID, user could directly go the 
model presentation page.
* Subversion is adopted for models revision control. When a model is 
submitted or replaced, a copy of the model will be go into SVN repository.
* In model's presentation page, there is a new tab called Curation, in 
which, user can find curation result and all revisions of the model. 
Authorized user also could download the past revisions or choose 
different revisions and compare them.
* On the top left of model presentation page, there are links for 
downloading models in different versions of SBML level 2. The link of 
curated version is highlighted with bold font. Other versions are 
automatically generated by using libsbml.
* BioModels Database now stores more complete information of Taxonomy 
terms to help improving the search result.
* Along with the release, there are also some bugs fixed.

For more details, please check:
http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_16June2009

BioModels Database is being developed by the Computational Neurobiology 
group (EMBL-European Bioinformatics Institute, United-Kingdom) and the 
SBML Team (California Institute of Technology, USA).  Collaborators 
include the Database Of Quantitative Cellular Signalling (National 
Center for Biological Sciences, India), the Virtual Cell (University of 
Connecticut Health Center, USA), JWS Online (Stellenbosch University, 
ZA) and the CellML team (Auckland Bioengineering Institute, NZ).

BioModels Database development is funded by the European Molecular 
Biology Laboratory (Computational Neurobiology group), the Biotechnology 
and Biological Sciences Research Council (Computational Neurobiology 
group), the National Institute of General Medical Sciences (SBML team 
and Computational Neurobiology group), and the National Center for 
Research Resources (Virtual Cell team).

BioModels Database also benefited from the help of Herbert Sauro 
(Washington University, USA) and Hiroaki Kitano (Systems Biology 
Institute, Japan), and from the funds of the DARPA (Sauro team).

A big thank you to all collaborators and submitters.

We also want to thank the SBML community for their support and the tools 
they provide and develop.

The BioModels Database Team
http://www.ebi.ac.uk/biomodels