[cellml-discussion] 16th release of BioModels Database
Dear colleagues, We are pleased to announce the sixteenth release of BioModels Database. In this release, 10 new models have gained entry to the curated branch. The public version of BioModels Database now contains 241 models in the curated and 212 in the non-curated branch. Together, these 453 models comprise 33702 species and 41069 reactions. Some of the existing models have been curated again and updated to SBML Level 2 Version 4. And some have been slightly changed for correction and to enhance reusability. Also the annotations of several existing models have been updated. The database now features around 17228 cross-references. For more details, please check: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20100126 BioModels Database is being developed by the Computational Neurobiology group (EMBL-European Bioinformatics Institute, United-Kingdom) and the SBML Team (California Institute of Technology, USA). The collaborators are the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML team (Auckland Bioengineering Institute, NZ). BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Neurobiology group), the Biotechnology and Biological Sciences Research Council (Computational Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Neurobiology group), and the National Center for Research Resources (Virtual Cell team). BioModels Database also benefited from the help of Herbert Sauro (Washington University, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team). A big thanks to all collaborators and submitters. We also want to thank the SBML community for their support and the tools they provide and develop. The BioModels Database Team http://www.ebi.ac.uk/biomodels/ -- Camille Laibe BioModels.net Coordinator European Bioinformatics Institute, Cambridge (UK) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] 17th release of BioModels Database
Dear colleagues, We are pleased to announce the seventeenth release of BioModels Database. In this release, 20 new models have been published. The public version of BioModels Database now contains 249 models in the curated and 224 in the non-curated branch. Together, these 473 models comprise 37852 species and 44886 reactions. Some of the existing models have been converted to SBML Level 2 Version 4, while others have been corrected with annotational updates to enhance their reusability. The database now features 18950 cross-references. Along with the data release, there have been dramatic improvements to both the software availability and the documentation. This should greatly help users wishing to implement their own local version of the BioModels Database infrastructure. For more information, please refer to: http://www.ebi.ac.uk/biomodels-main/develop . For more details about this release, please check: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20100427 BioModels Database is being developed by the Computational Neurobiology group (EMBL-European Bioinformatics Institute, United-Kingdom) and the SBML Team (California Institute of Technology, USA). The collaborators are the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML team (Auckland Bioengineering Institute, NZ). BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Neurobiology group), the Biotechnology and Biological Sciences Research Council (Computational Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Neurobiology group), and the National Center for Research Resources (Virtual Cell team). BioModels Database also benefited from the help of Herbert Sauro (Washington University, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team). A big thanks to all collaborators and submitters. We also want to thank the SBML community for their support and the tools they provide and develop. The BioModels Database Team http://www.ebi.ac.uk/biomodels/ -- Camille Laibe BioModels.net Coordinator European Bioinformatics Institute, Cambridge (UK) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] 18th release of BioModels Database
Dear colleagues, We are pleased to announce the eighteenth release of BioModels Database. In this release, 157 new models have been published. The public version of BioModels Database now contains 269 models in the curated and 361 in the non-curated branch. Together, these 630 models comprise 79224 species and 109091 reactions. Some of the existing models have been converted to SBML Level 2 Version 4, while others have been corrected with annotational updates to enhance their reusability. The database now features 20426 cross-references. Along with the data release, we are introducing several new converters. Models in BioModels Database are now available in these new or updated formats (as well as in the previously supported formats): - XPP (updated) - BioPAX Level 2 (updated) - BioPAX Level 3 (new) - Octave (new) We will soon announce the availability of the source code of these new converters and the associated online service. Finally, we would like to give a special thank you to Kieran Smallbone, who single-handedly submitted several already annotated models! For more details about this release, please check: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20100930 Finally, for those of you who are going to the ICSB 2010 in Edinburgh, I would like to advertise the tutorial on BioModels Database that our team of curators will provide there. Cf. http://www.icsb2010.org.uk/tutorials/ . BioModels Database is being developed by the Computational Systems Neurobiology group (EMBL-European Bioinformatics Institute, United Kingdom) and the SBML Team (California Institute of Technology, USA). The collaborators are the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML Team (Auckland Bioengineering Institute, NZ). BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Systems Neurobiology group), the UK Biotechnology and Biological Sciences Research Council (Computational Systems Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Systems Neurobiology group), and the National Center for Research Resources (Virtual Cell team). BioModels Database also benefited from the help of Herbert Sauro (Washington University, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team). A big thank you to all collaborators and submitters. We also want to thank the SBML community for their support and the tools they provide and develop. The BioModels Database Team http://www.ebi.ac.uk/biomodels/ -- Camille Laibe BioModels.net Coordinator European Bioinformatics Institute, Cambridge (UK) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] 20th release of BioModels Database
Dear colleagues, We are pleased to announce the twentieth release of BioModels Database (http://www.ebi.ac.uk/biomodels/). In this release, 65 new models have been published. The public version of BioModels Database now contains 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. Along with the data release, various performance improvements were made: the loading speed of pages describing models in the non-curated branch should be greatly improved, especially for large models. For more details about this release, please refer to: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20110901 BioModels Database is being developed by the Computational Systems Neurobiology group (EMBL-European Bioinformatics Institute, United Kingdom) and the SBML Team (California Institute of Technology, USA). The collaborators are the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML Team (Auckland Bioengineering Institute, NZ). BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Systems Neurobiology group), the UK Biotechnology and Biological Sciences Research Council (Computational Systems Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Systems Neurobiology group), and the National Center for Research Resources (Virtual Cell team). BioModels Database also benefited from the help of Herbert Sauro (University of Washington, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team). A big thank you to all collaborators and submitters. We also want to thank the SBML community for their support and the tools they develop and provide. Camille Laibe on behalf of the BioModels.net team. -- Camille Laibe BioModels.net Coordinator European Bioinformatics Institute, Cambridge (UK) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] 21st release of BioModels Database
Dear colleagues, We are pleased to announce the twenty-first release of BioModels Database (http://www.ebi.ac.uk/biomodels/). Important changes are happening or announced in this message, so please read further. In this release, 68 new models have been published and numerous existing models have been updated. The public version of BioModels Database now contains 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. Along with the data release, we would like to announce several important changes. First of all, in addition to the SBML version of each model with annotations encoded with MIRIAM URNs, BioModels Database now provides a second SBML file with annotations encoded using Identifiers.org URLs. Those files can be accessed from the Download SBML menu displayed on the top left of any model page and from the models archives (now provided from the EBI FTP server). BioModels Database will serve the URN form as the default until the next release of the database. Then the URL form will be provided as the default. The files with the URN annotations will still be available for a while. We encourage software developers to consider the Identifiers.org version of MIRIAM URIs for any new development. Moreover, after consultation with BioModels Database's Scientific Advisory Board and to be more in agreement with the EBI terms of use, it was decided that from the next release, the BioModels.net Team will abandon its copyright on the encoded form of the models and release them in the public domain. Finally various improvements were made to the underlying software infrastructure. The main publicly visible change is the fact that a bug, dealing with the handling of annotations in the non-curated branch, has been discovered and subsequently fixed. This results in an major increase in the number of annotations from models in the non-curated branch. However, we would like to emphasise that those annotations were provided during submission and are not checked by our curators. For more information about this release, please refer to the release notes: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20120208 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: http://www.ebi.ac.uk/biomodels-main/acknowledgements Camille Laibe on behalf of the BioModels.net team. -- Camille Laibe BioModels.net Coordinator European Bioinformatics Institute, Cambridge (UK) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
