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.
30th BioModels Release
Hinxton, Tuesday 10th May 2016
We are extremely pleased to announce the 30th release of BioModels
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 . 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
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.
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.
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.
All the models of this release are provided in the following archives from our FTP server:
- models published in the literature (SBML files and all converted exports)
- models published in the literature (SBML files only)
- models published in the literature (RDF/XML files only)
- metabolic models automatically generated from pathway resources (unchanged in this release)
- non-metabolic models automatically generated from pathway resources (unchanged in this release)
- whole genome metabolism models automatically generated from pathway resources (unchanged in this release)
Models published in the literature
|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|
|Metabolic||Non-metabolic||Whole genome metabolism||Total|
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.