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News

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2014

  • 16th September 2014
    We are proud to announce the 28th release of BioModels Database!
    The resource now provides a total of 144,282 models and introduces additional features and an easier access to its content thanks to an updated homepage.
    For more information about this release, please refer to the release notes.
    [Download models archives]
  • 8th August 2014
    BioModels' homepage has been updated to provide a clearer view of the various sets of models (curated, non-curated and automatically generated from pathway resources) which make the content of the repository. Additionally, this should make the several ways to access models of interest easier to find and use.
    Also, a Gene Ontology classification has been implemented as a new browsing tool for models from the literature. Based on the chart provided in our release notes, this allows you to find models based on the type of processes being modelled.
    Finally, various updates have been implemented for non-curated models: model annotations are now displayed on the model page, and non-kinetic models are indicated (on the browse and model display pages) by the following network icon: Network icon for non-kinetic models.
  • 25th April 2014
    Our recent review "The impact of mathematical modeling on the understanding of diabetes and related complications" has been the most downloaded this month from the CPT: Pharmacometrics & Systems Pharmacology website!
  • 24th April 2014
    The interview of Dr. Vijayalakshmi Chelliah, lead curator of BioModels Database, in the pharmacometrics and systems pharmacology podcast from the journal CPT: Pharmacometrics & Systems Pharmacology, produced in association with Nature Publishing Group (PSPod) is now online. Listen it.
  • 11th April 2014
    We are proud to announce the 27th release of BioModels Database!
    The resource now provides a total of 144,253 models, with new ones available in all branches (curated, non-curated and Path2Models). That includes more than 500 models manually curated.
    Additionally, we now have a new logo. We hope you will like it, and encourage you to use it!
    For more information about this release, please refer to the release notes.
    [Download models archives]

2013

  • 4th November 2013
    We are proud to announce the 'Movember' 26th release of BioModels Database!
    This release marks a new landmark: the distribution of over 1000 models published in the literature! With models coming from the Path2Models project, the resource now publicly provides a total of 143,135 models.
    In addition to a number of new models, this release includes a completely updated set of the genome-scale metabolic reconstruction models. Moreover, a SPARQL endpoint, giving access to the models using Semantic Web technologies, is now available.
    For more information about this release, please refer to the release notes.
    [Download models archives]
  • 8th October 2013
    The EBI launched a RDF platform. This provides access to various bioinformatics resources (including BioModels Database) using Semantic Web technologies (SPARQL endpoints and RDF dumps are available).
    For BioModels Database, the following services are available:
    For more information about this platform and access the other datasets, please follow http://www.ebi.ac.uk/rdf/.
  • 18th June 2013
    We are pleased to announce the twenty-fifth release of BioModels Database! The resource now publicly provides 143013 models. This corresponds to 963 models published in the literature and 142050 models coming from the Path2Models project.
    This release sees the publication of the first models making use of the latest version of SBML (L3 V1), in addition to some packages. That required the upgrade of our curation pipeline. Moreover, the behaviour of the generic search feature has been slightly modified to be more encompassing. Finally, efforts were made to clean and improve numerous older models' notes and annotations.
    For more information about this release, please refer to the release notes.
    [Download models archives]
  • 13th May 2013
    We are seeking an outstanding bioinformatician to join the BioModels.net team.
    For more information and application instructions, please refer to the job description page (closing date: 9 June 2013).
  • 1st April 2013
    Horse meat and impending zombie infestation of Earth? Discover why in our seasonal model of the month.
    Will you dare to read this model of month, published on 1st April?
  • 5 March 2013
    The user interface was slightly refreshed, in order to follow the new EBI look and feel.
  • 3 March 2013
    The latest and most comprehensive representation of human metabolism that is applicable to computational modelling, which was published in the journal Nature Biotechnology, is now available in BioModels Database: MODEL1109130000.

2012

  • 12 December 2012
    We are pleased to announce the twenty-fourth release of BioModels Database! BioModels Database now publicly provides 142972 models. This corresponds to 922 models published in the literature and 142050 models coming from the Path2Models project.
    With this release, several new models have been published and numerous have been updated. Moreover, new versions of the metabolic and non-metabolic models were generated by the Path2Models project, as well as graphical representations in SBGN for the metabolic ones. Finally we are introducing, for testing and feedback purposes, a RDF/XML version of the models published in the literature.
    For more information about this release, please refer to the release notes.
    [Download models archives]
  • 16 November 2012
    The Biotechnology and Biological Sciences Research Council (BBSRC) announced today a £5.5M investment to ensure that the bioscience community is equipped to help meet some of the biggest challenges that we face as a society. The ten selected projects will be supported through the Bioinformatics and Biological Resources fund and will help researchers develop and maintain the infrastructure and resources that are vital for modern bioscience.
    We are glad to report that BioModels Database is one of the projects which are being funded. We would like to use this opportunity to gratefully acknowledge the BBSRC for this ongoing support!
  • 15 November 2012
    The BioModels.net team, which maintains, at the EMBL-EBI, services such as BioModels Database, Identifiers.org, MIRIAM Registry, SBO, has now a Twitter account. Please follow us Twitter small logo for regular news and updates!
  • 7 November 2012
    We are seeking an experienced Software Developer to work on the software infrastructure behind BioModels Database. For more information and application instructions, please refer to the job description page (closing date: 30 November 2012).
  • 6 September 2012
    The EBI online training platform, Train online, now features an introduction to BioModels Database.
  • 11 August 2012
    We are pleased to announce the twenty-third release of BioModels Database. BioModels Database now publicly provides 142916 models. This corresponds to 867 models published in the literature and 142050 models coming from the Path2Models project.
    With this release, several new models have been published and numerous have been updated. Moreover new services are now available (for example related to the access to models from the Path2Models project) while others have been improved (such as the model browsing feature based on a tree of Gene Ontology terms or the BioPAX export).
    For more information about this release, please refer to the release notes.
    [Download models archives]
  • 31 July 2012
    The way to browse the curated models via Gene Ontology terms has been updated. The tree now fully works on all main web browsers. Moreover, when clicking on one GO term, the list of relevant models is displayed in the right panel.
  • 23 July 2012
    The Java library provided to access the web services is now available via the EBI Maven repository (in addition to the download from SourceForge). For more information about this library and how to configure your Maven configuration file, please refer to the web services documentation page.
  • 20 May 2012
    We are pleased to announce the twenty-second release of BioModels Database. BioModels Database now publicly provides 142904 models. This corresponds to 421 models in the curated branch, 433 models in the non-curated branch and 142050 models coming from the Path2Models project.
    In addition to the typical work on the curated and non-curated branches, where several new models have been made available and numerous others updated, this release sees the availability of the models generated by the Path2Models project, a change in the terms of use and several improvements and new features.
    For more information about this release, please refer to the release notes.
    [Download models archives]
  • 30 April 2012
    An alternative way to find models of interest is now available: a Taxonomy cloud allows users to retrieve all curated models related to a given organism.
  • 12 April 2012
    The web services have been updated and new methods are now provided: getAuthorsByModelId, getDateLastModifByModelId, getEncodersByModelId, getPublicationByModelId, getSimpleModelsByIds. Moreover all the methods returning a SimpleModel (when using the Java library) have been updated and now provide more information (such as the list of encoders, the list of authors, the date of last modification, ...). Please refer to the list of web services for up-to-date documentation.
    The version 1.20 of the Java library to access the web services has been released. This gives access to all the new services that are now provided.
  • 08 February 2012
    We are pleased to announce the twenty-first release of BioModels Database. In this release, 68 new models have been published and numerous existing models have been updated. BioModels Database now publicly provides 409 models in the curated and 420 in the non-curated branch. Together, these 829 models comprise 130800 species, 151274 relationships (which include reactions, rate rules, events and assignment rules), and 106210 cross-references.
    Important changes are happening or announced, please read more...
    [Download models archives]

2011

  • 1st September 2011
    We are pleased to announce the twentieth release of BioModels Database. In this release, 65 new models have been published and numerous existing models have been updated. BioModels Database now publicly provides 366 models in the curated and 398 in the non-curated branch. Together, these 764 models comprise 119745 species, 135889 relationships (which include reactions, rate rules, events and assignment rules), and 24666 cross-references. Read more...
    [Download all models in the SBML format]
  • 15 April 2011
    We are pleased to announce the nineteenth release of BioModels Database. In this release, 69 new models have been published. Moreover, numerous existing models have been updated. BioModels Database now publicly provides 326 models in the curated and 373 in the non-curated branch. Together, these 699 models comprise 92112 species, 113925 relationships (which include reactions, rate rules, events and assignment rules), and 22969 cross-references. Read more...
    [Download All Models Under SBML Format]
  • 4 February 2011
    To provide the worldwide community with a modern tool for the collaborative creation and sharing of models in an efficient and secured way, the Jürgen Eils and Nicolas Le Novère groups are announcing the JUMMP project. It is planned that JUMMP will be used as the software infrastructure running BioModels Database. We are open for further contribution from -and collaboration with- the global community interested in model development and sharing. Read more...

2010

2009

2008

2007

2006

2005

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