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New Release

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:

  1. Models that are perfectly fine, except we did not find time to curate them yet
  2. Models that are curatable, but not MIRIAM-compliant
  3. Models that are not curatable at the moment, because not kinetics (e.g. Flux Balance Analysis)
  4. Models for which SBML supports only part of the description, most of it being in annotation (e.g. spatial models)

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]

New Models

BioModels ID Name Publication Id
BIOMD0000000051 Chassagnole2002_Carbon_Metabolism 10.1002/bit.10288
BIOMD0000000057 Sneyd2002_IP3_Receptor 11842185
BIOMD0000000058 Bindschadler2001_coupled_Ca_oscillators 12779457
BIOMD0000000059 Fridlyand2003_Calcium_flux 12644446
BIOMD0000000060 Keizer1996_Rynodine_receptor_adaptation 8968617
BIOMD0000000061 Hynne2001 Glycolysis 11744196
BIOMD0000000062 bhartiya2003 tryptophan operon 12787031
BIOMD0000000063 Galazzo1990_pathway_kinetics 10.1016/0141-0229(90)90033-M
BIOMD0000000064 Teusink2000_Glycolysis 10951190
BIOMD0000000065 Yildirim2003_Lac_Operon 12719218
BIOMD0000000066 Chassagnole2001_ThreonineSynthesis 11368770
BIOMD0000000067 Fung2005_Metabolic_Oscillator 15875027
BIOMD0000000068 Curien2003_MetThr_synthesis 14622248
BIOMD0000000069 Fuss2006_MitoticActivation 16873466
BIOMD0000000070 Holzhutter2004_Erythrocyte_Metabolism 15233787
BIOMD0000000071 Bakker2001_Glycolysis 11415442

BioModels ID Name Publication Id
MODEL0995500644 Rodriguez2005_denovo_pyrimidine_biosynthesis 15784266
MODEL5974712823 FangeElf2006_MinSystem_MesoRD 16846247
MODEL6623597435 Fuentes2005_ZymogenActivation 15634334
MODEL6623610941 Hornberg2005_ERKcascade 15634347
MODEL6623617994 Lambeth2002_Glycogenolysis 12220081
MODEL6623628741 Kolomeisky2003_myosin 12609867
MODEL6624091635 Hoefnagel2002_Glycolysis 12241048
MODEL6624139162 Cronwright2003_GlycerolSynthesis 12200299
MODEL6624199343 Martins2001_glyoxalase 11453985
MODEL6762427183 plant_1981_version01 7252375
MODEL7944007619 Maeda2006_MyosinPhosphorylation 16923126
MODEL8293171637 Yeast_glycolysis_model_of_Pritchard_and_Kell 12180966
MODEL8568434338 Raman2006_MycolicAcid 16261191
MODEL8583955822 Singh_Ghosh2006_TCA_eco_glucose 10.1186/1742-4682-3-27
MODEL8584137422 Singh_Ghosh2006_TCA_eco_acetate 10.1186/1742-4682-3-27
MODEL8584292730 Singh_Ghosh2006_TCA_eco_model1 10.1186/1742-4682-3-27
MODEL8584468482 Singh_Ghosh2006_TCA_eco_model2 10.1186/1742-4682-3-27
MODEL8938094216 dAlcantara2003_SynapticPlasticity 12823459
MODEL9200487367 LeBeau1999_IP3R_Phosphorylation 10352035
MODEL9468910329 Yi2003_GproteinCycle 12960402

Acknowledgements

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.

Statistics

ReleaseModelsSpeciesReactionsAnnotations
03/October/2006 96 4125 48903074
05/June/2006 54 837 13073542
31/January/2006 50 761 1163 3126
28/July/2005 44 596 943 2373
01/June/2005 30 425 736 1609
11/April/2005 20 322 631 1084



Gene Ontology IDTopic# models

GO:0007154 Cell communication 27
GO:0007049 Cell cycle 8
GO:0008152 Metabolism 16
GO:0007623 Circadian rhythm 8
Other 11


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