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28th BioModels Database Release

Hinxton, Tuesday 16th September 2014

We are proud to announce the 28th release of BioModels Database, which introduces new models as well as additional features and an easier access thanks to an updated homepage.


Models and annotation

BioModels Database now publicly provides access to 144,282 models. This corresponds to 1,212 models published in the literature and 143,070 models automatically generated from pathway resources.

Within this complete set, 548 models have been manually curated. Those models are fully MIRIAM compliant. This means that they have been thoroughly checked and annotated, and when instantiated in a simulation, they reproduce the results described in their reference paper.

With this release, model level annotations were added to all non-curated models, and those are displayed on each model page. Please note that although models in the non-curated branch do contain a wealth of annotation, they were previously not annotated by the BioModels curator team.

The non-curated branch hosts different types of models, some of them being non-kinetic (such as metabolic network models, FBA models, etc.) are in this branch due to the inherent limitations of these models with regards to the possibility to check their accuracy via simulation. These models are now highlighted with a network diagram Network icon for non-kinetic models (both in the browse and model display pages) to easily distinguish them from kinetic models in this branch.

Model categorisation

The content classification relying on Gene Ontology terms usually provided in the release notes has been developed into a new browsing tool for models from the literature. This new dynamic chart allows you to find models based on the type of processes which have been modelled.

New homepage

BioModels' homepage has been updated to provide an easier access to its various features and a clear overview its content. The various sets of models (curated, non-curated and automatically generated from pathway resources) which make the content of the repository are now provided graphically with their several access options.

Secure access via HTTPS

BioModels Database now supports the secured provision of its content via HTTPs: https://www.ebi.ac.uk/biomodels/.

Download

All the models of this release are provided in the following archives from our FTP server:

Statistics

Models published in the literature

ReleasesModelsSpeciesRelationsCross-references
16 September 201412125635365572911729513
11 April 201411835609025550241724801
04 November 201310854013523410111117506
18 June 2013963156665174986171432
12 December 2012923145746165473134852
11 August 2012867133559154456108345
Expand/collapse statistics for all releases.

Path2Models

Path2Models is a branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG, BioCarta, MetaCyc, PID and SABIO-RK.

 MetabolicNon-metabolicWhole genome metabolismTotal
Models 112,898 27,531 2,641 143,070
Species 16,306,840 872,501 8,937,630 26,087,614
Relations 2,795,659 208,146 6,495,608 9,484,348
Annotations 168,908,203 6,665,757 21,444,254 196,869,504

Acknowledgements

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.


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