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29th BioModels Release

Hinxton, Thursday 16th April 2015

We are proud to announce the 29th release of BioModels, which introduces new models as well as additional and updated features.


Models

BioModels now publicly provides access to 144,366 models. This corresponds to 1,296 models published in the literature and 143,070 models automatically generated from pathway resources.

Within this complete set, 575 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.

AgedBrainSYSBIO

The team behind BioModels is involved in AgedBrainSYSBIO, a collaborative research project funded by the European Commission, aiming to address the basis of brain ageing by studying the pathways involved in this process and by identifying the interactions through which the ageing phenotype develops in normal and in disease conditions.

As part of this project, we are encoding and curating models related to neurodegenerative diseases. You can get a direct access to this growing set of models.

SBML L3 packages support

BioModels now provides some initial support for models making use of SBML L3 packages. This means that one can submit them to the repository and users will be informed that a given model makes use of packages from the model display page.

For example, we recently made available the logical model Chaouiya2013 - EGF and TNFalpha mediated signalling pathway.

Donwload URLs

URLs for individual model download in any available formats are now shorter and more user friendly. They now follow the pattern: http://biomodels.caltech.edu/download?mid=[model identifier]&format=[format], where format can be 'BioPAX-L2', 'BioPAX-L3', 'm-file', 'PDF', 'Scilab', 'VCML', 'XPP', 'PNG' or 'SVG'. Not all exports are available for all models. This should facilitate the work of anybody needing to programmatically access model files.

Model categorisation

The classification of models published in the literature, relying on Gene Ontology terms, has been refined to provide a more user friendly experience.

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 April 201512968088687639272004125
16 September 201412125635365572911729513
11 April 201411835609025550241724801
04 November 201310854013523410111117506
18 June 2013963156665174986171432
12 December 2012923145746165473134852
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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