BioModels Database
Encyclopedia
BioModels Database is a free and open-source database for storing, exchanging and retrieving published quantitative models of biological interest. Deposition of models upon publication is currently supported by Nature Publishing Group
, PLoS and BioMed Central
.
The models stored in the curated branch of BioModels Database are compliant with MIRIAM
, the standard of model curation and annotation. The models have been simulated by curators to check that when run in simulations, they provide the same results as described in the publication. Model components are annotated, so the users can conveniently identify each model element and retrieve further information from other resources.
Modellers can submit the models in SBML
and CellML
. Models can subsequently be downloaded in SBML
, CellML
, VCML, XPP, SciLab
, Octave
, BioPAX
. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java
applet
, in which some networks were presented by following Systems Biology Graphical Notation
. And a summary of model is available in PDF.
BioModels Database has two branches, one is called curated-branch, another is non-curated-branch. The models in curated-branch are all well curated and annotated. The models that are still not curated, non-curatable (spatial models, steady-state models etc), or too huge to be curated, are put into non-curated-branch. Non-curated models can be later moved into the curated branch. All these models are open to the public and can be easily accessed via web interface or BioModels Web Services. On the homepage, there is also a link for downloading an archive of all the models in SBML
format.
BioModels Database announced its 20th release on September 1, 2011. It now provides 366 curated models and 398 non-curated models to the public. These models amount to 119745 species, 135889 relationships (which include reactions, rate rules, events and assignment rules), and 24666 cross-references to other data resources.
Deposition of models in BioModels Database is now advocated by many scientific journals, included Molecular Systems Biology
, all the journals of the Public Library of Science
and all the journals of BioMed Central
.
, UK and the SBML
Team in Caltech, USA. Past and present collaborating groups include DOQCS at the National Center for Biological Sciences, India, JWS Online at Stellenbosch University, ZA, the CellML
team at the Auckland Bioengineering Institute, NZ, the Virtual Cell, USA, Herbert Sauro's team at the University of Washington, Seattle, and the Systems Biology Institute, Japan.
, the Biotechnology and Biological Sciences Research Council
, the National Institute of General Medical Sciences
, the DARPA, and the National Center for Research Resources
.
Nature Publishing Group
Nature Publishing Group is an international publishing company that publishes academic journals, online databases, and services across the life, physical, chemical and applied sciences and clinical medicine...
, PLoS and BioMed Central
BioMed Central
BioMed Central is a UK-based, for-profit scientific publisher specialising in open access journal publication. BMC, and its sister companies Chemistry Central and PhysMath Central, publish over 200 scientific journals. Most BMC journals are now published only online. BMC describes itself as the...
.
What is BioModels Database
BioModels Database is an online resource for storing and serving quantitative models of biomedical interest. All the models in the curated section of BioModels Database have been described in the peer-reviewed scientific literature.The models stored in the curated branch of BioModels Database are compliant with MIRIAM
MIRIAM
MIRIAM , is an effort to standardize the annotation and curation process of quantitative models of biological systems...
, the standard of model curation and annotation. The models have been simulated by curators to check that when run in simulations, they provide the same results as described in the publication. Model components are annotated, so the users can conveniently identify each model element and retrieve further information from other resources.
Modellers can submit the models in SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
and CellML
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology...
. Models can subsequently be downloaded in SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
, CellML
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology...
, VCML, XPP, SciLab
Scilab
Scilab is an open source, cross-platform numerical computational package and a high-level, numerically oriented programming language. Itcan be used for signal processing, statistical analysis, image enhancement, fluid dynamics simulations, numerical optimization, and modeling and simulation of...
, Octave
Octave
In music, an octave is the interval between one musical pitch and another with half or double its frequency. The octave relationship is a natural phenomenon that has been referred to as the "basic miracle of music", the use of which is "common in most musical systems"...
, BioPAX
BioPAX
BioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....
. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...
applet
Applet
In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page...
, in which some networks were presented by following Systems Biology Graphical Notation
Systems Biology Graphical Notation
The Systems Biology Graphical Notation is a standard graphical representation crafted over several years by a community of biochemists, modelers and computer scientists....
. And a summary of model is available in PDF.
Content of BioModels Database
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
format.
BioModels Database announced its 20th release on September 1, 2011. It now provides 366 curated models and 398 non-curated models to the public. These models amount to 119745 species, 135889 relationships (which include reactions, rate rules, events and assignment rules), and 24666 cross-references to other data resources.
Deposition of models in BioModels Database is now advocated by many scientific journals, included Molecular Systems Biology
Molecular Systems Biology
Molecular Systems Biology is an open-access peer-reviewed scientific journal publishing research within systems biology at the molecular level, including genomics, proteomics, metabolomics, microbial systems, the integration of cell signaling and regulatory networks, and synthetic biology.The...
, all the journals of the Public Library of Science
Public Library of Science
The Public Library of Science is a nonprofit open-access scientific publishing project aimed at creating a library of open access journals and other scientific literature under an open content license...
and all the journals of BioMed Central
BioMed Central
BioMed Central is a UK-based, for-profit scientific publisher specialising in open access journal publication. BMC, and its sister companies Chemistry Central and PhysMath Central, publish over 200 scientific journals. Most BMC journals are now published only online. BMC describes itself as the...
.
Organization of BioModels Database development
BioModels Database is developed by the Computational Systems Neurobiology Group at the EMBL-EBIEuropean Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
, UK and the SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
Team in Caltech, USA. Past and present collaborating groups include DOQCS at the National Center for Biological Sciences, India, JWS Online at Stellenbosch University, ZA, the CellML
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology...
team at the Auckland Bioengineering Institute, NZ, the Virtual Cell, USA, Herbert Sauro's team at the University of Washington, Seattle, and the Systems Biology Institute, Japan.
Funding for BioModels Database
BioModels Development has benefited from the funds of the European Molecular Biology LaboratoryEuropean Molecular Biology Laboratory
The European Molecular Biology Laboratory is a molecular biology research institution supported by 20 European countries and Australia as associate member state. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states...
, the Biotechnology and Biological Sciences Research Council
Biotechnology and Biological Sciences Research Council
Biotechnology and Biological Sciences Research Council is a UK Research Council and NDPB and is the largest UK public funder of non-medical bioscience...
, the National Institute of General Medical Sciences
National Institute of General Medical Sciences
The National Institute of General Medical Sciences is a part of the National Institutes of Health that primarily supports research that lays the foundation for advances in disease diagnosis, treatment and prevention...
, the DARPA, and the National Center for Research Resources
National Center for Research Resources
The National Center for Research Resources or NCRR, is a United States government agency. NCRR provides funding to laboratory scientists and researchers for facilities and tools in the goal of curing and treating diseases.-Organization and history:...
.
External references
- Official website of BioModels Database (There is also a mirror site in the USA: Caltech Mirror site)
- Li C., Donizelli M., Rodriguez N., Dharuri H., Endler L., Chelliah V., Li L., He E., Henry A., Stefan M.I., Snoep J.L., Hucka M., Le Novère N. and Laibe C. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 2010, 4:92
- Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res., 34: D689-D691.
- Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM) Nature Biotechnology, 23: 1509-1515.
- Website of the BioModels.net initiative