Hinxton, Monday 03th October 2006
We are pleased to announce the sixth release of BioModels Database.
This release, the largest in terms of number of models or reactions since the initial one, is a milestone in BioModels DB history.
With the growing success of BioModels databases, we faced two problems. First, we are now receiving many more contributed models, and those models are larger. As a consequence, we cannot curate thoroughly all the models immediately. Second, we receive many models that, although syntactically correct, cannot be curated for various reasons. We have therefore created a public branch for those models, so as not holding them up hidden for too long. Of course, this non-curated branch is meant to be only a purgatory, and it is our most dearly wish that most of the models held there join the heaven of the curated branch at some point in the future. The models held in the non-curated branch are of four types:
Note that all the models in the non-curated branch have nevertheless passed the XML check, SBML syntax check and SBML consistency checks.
To cope with the fact that many models of the non-curated branch, although syntactically correct, cannot provide the expected result without the help of the software that generate them, we added a link to the "original model". This link will point you directly toward the version of the model that was used as the basis for the encoded version we got in BioModels Database.
In order to show that, for the models the curated branch, we were able to reproduce results from the publication, we added a link to a typical simulation result. Note that all the simulation results have not been added yet. We will complete this task over the forthcoming months.
The models becoming bigger by the day, the static graphical representations are not easy to use. In order to let-you play with the models at various resolutions, we added an applet, where you can fold/unfold nodes.
This new release sees the the addition of 16 models in the curated branch, and 26 in the non-curated branch, collectively amounting to 3290 species and 3584 reactions, effectively multiplying the size of the database fourfold.
[Download All Models Under SBML L2 V1 Format]
|BioModels ID||Name||Publication Id|
|BIOMD0000000062||bhartiya2003 tryptophan operon||12787031|
|BioModels ID||Name||Publication Id|
BioModels Database is developed in collaboration by the teams of Nicolas Le Novère (EMBL-EBI, United-Kingdom), Michael Hucka (SBML Team, Caltech, USA), Herbert Sauro (Keck Graduate Institute, USA), Hiroaki Kitano (Systems Biology Institute, Japan) and Jacky Snoep (JWS Online, Stellenbosch University, ZA), as part of the BioModels.net initiative. BioModels Database development has benefitted from funds of the European Molecular Biology Laboratory (Le Novère team) and the National Institute of General Medical Sciences (SBML team).
Developers: Mélanie Courtot, Arnaud Henry, Camille Laibe, Chen Li (main developer), Lu Li, Nicolas Rodriguez (Alumni: Marco Donizelli)
Model curators and annotators: Harish Dharuri, Henuo He, Nicolas Le Novère, Lu Li, Rainer Machne, Bruce Shapiro.
External contributors: BioModels Database would not exists without the continuous support of many people, whether by their contribution of models, of software, or by their constructive comments and criticisms. It is unfortunately impossible to acknowledge all of them here, without risking to be unfair. Therefore, a big collective thank-you all.
BioModels Database is built thanks to many third-party free software such as libSBML, Jakarta Tomcat, Xindice, Xalan, Xerces, Jena and MySQL, plus all the free software coming with the GNU/Linux systems.
Main software used to curate models: CellDesigner, COPASI, Jarnac, MathSBML, XPP-Aut, SBMLdeSolver, SBMLeditor and SBMLmerge.
|Gene Ontology ID||Topic||# models|