30th release of BioModels

10th May 2016

We are extremely happy to announce the 30th release of BioModels!

The resource now provides 1483 literature-based models and 143,070 models automatically generated from pathway resources, and introduces additional and updated features.

For more information about this release, please refer to the the following release notes.

[Download models archives]

Release notes

30th BioModels Release

Hinxton, Tuesday 10th May 2016

We are extremely pleased to announce the 30th release of BioModels

Models

BioModels now provides access to 1,483 literature-based models and 143,070 models automatically generated from pathway resources (path2models).

About 41% (611 models) of the literature-based models have been manually curated, and are fully MIRIAM compliant. This means that they have been thoroughly checked for accuracy, and when instantiated in a simulation, they reproduce the results published in the reference publication. These models are cross-linked (annotated) to external database resources and ontological terms.

The remaining 59% (872) models are in the non-curated branch, of which 358 models (24% of the whole list of literature-based models) are non-kinetic models (FBA models and Genome-scale metabolic models), and are indicated by a network symbol network flag for non-kinetic models. There are 514 kinetic models in the non-curated branch (34% of the whole literature-based models). Efforts are ongoing to curate these models, though several models will remain in this branch for the foreseeable future due to the lack of quantitative information in the original publication, and/or the inability to contact appropriate authors for clarification

Curation Contributions

We gratefully acknowledge contributions towards this release from the following individuals and groups:

Ryan Gutenkunst and his students: External curation collaboration that resulted in extensive curation and annotation of models from the uncurated branch. Model curation tasks were assigned as mini-projects to the students of the Quantitative Biology course. Ryan and his students curated 10 models (BIOMD0000000599-607,610), during this collaborative trial.

Alastair Hume: For the curation and annotation of a series of models (BIOMD0000000576,592-595).

Maxwell Neal and John Gennari (University of Washington): Analysis of qualifiers use in BioModels that resulted in corrections to several models.

Mike Hucka: For the successful conversion of the FIRM model to SBML, using the MOCCASIN software tool (the updated version, which was used for conversion is yet to be published), which allowed the model to be published in the curated branch. This model was also selected as the May Model of the Month article.

nonSBML Models

BioModels now hosts models encoded in formats other than SBML. These models are available from the uncurated branch and can currently be retrieved through a search using the string "non-SBML" (quotes required). User interface improvements to fetch these models directly will be implemented prior to the next release. Since the current infrastructure for BioModels is tied to support the SBML format, a 'dummy' SBML file is generated to accomodate models that are not natively encoded as SBML. The original source for these model files, such as matlab, mathematica, and R code are made available for download from the model page. The current list of nonSBML models in BioModels is, MODEL1505130000, MODEL1505130001, MODEL1604260000, MODEL1604270000, MODEL1604270001, MODEL1604270002, MODEL1604270003 and MODEL1604270004

When BioModels migrates to the new platform that is being developed, this feature will become more flexible. In the interim, authors may send their nonSBML models to us, following the information in the submission interface.

SBML L3 packages support

BioModels now provides some initial support for models making use of SBML L3 packages. Information on the packages used for such models is available from the model display page.

For example, we recently made available the logical models BIOMD0000000562, BIOMD0000000592 and BIOMD0000000593 in the curation branch.

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. This growing list of models can be directly accessed.

Disease Related Models

In addition, BioModels also provides a direct link to models describing other disease mechanisms.

Download

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

Statistics

Models published in the literature

Releases Models Species Relations Cross-references
10 May 2016 1483 1081311 1021641 2273907
16 April 2015 1296 808868 763927 2004125
16 September 2014 1212 563536 557291 1729513
11 April 2014 1183 560902 555024 1724801
04 November 2013 1085 401352 341011 1117506
18 June 2013 963 156665 174986 171432
12 December 2012 923 145746 165473 134852
11 August 2012 867 133559 154456 108345
20 May 2012 854 133263 154145 107074
08 February 2012 829 130800 151274 106210
01 September 2011 764 119745 135889 24666
15 April 2011 699 92112 113925 22969
30 September 2010 630 79224 98745 20426
27 April 2010 473 37852 51525 18950
26 January 2010 453 33702 47608 17228
02 September 2009 429 32014 45386 16492
16 June 2009 412 28901 42274 14611
25 March 2009 335 28726 38465 13818
03 December 2008 293 27238 35451 13206
21 August 2008 259 21783 28032 10811
28 March 2008 244 20945 26555 10498
25 September 2007 192 10482 13068 9810
05 June 2007 145 6027 7347 7692
05 January 2007 128 5697 6733 5651
03 October 2006 96 4125 5020 3074
05 June 2006 54 837 1404 3542
31 January 2006 50 761 1219 3126
28 July 2005 44 596 995 2373
01 June 2005 30 425 782 1609
11 April 2005 20 322 658 1084

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.

  Metabolic Non-metabolic Whole genome metabolism Total
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 information.