open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in
peer-reviewed
Peer review is the evaluation of work by one or more people with similar competencies as the producers of the work (peers). It functions as a form of self-regulation by qualified members of a profession within the relevant field. Peer review ...
scientific literature.
The models stored in BioModels' curated branch are compliant with
MIRIAM
Miriam ( he, מִרְיָם ''Mīryām'', lit. 'Rebellion') is described in the Hebrew Bible as the daughter of Amram and Jochebed, and the older sister of Moses and Aaron. She was a prophetess and first appears in the Book of Exodus.
The Tor ...
, 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
The Systems Biology Markup Language (SBML) 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 use ...
and
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 re ...
. Models can subsequently be downloaded in
SBML
The Systems Biology Markup Language (SBML) 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 use ...
SciLab
Scilab is a free and open-source, cross-platform numerical computational package and a high-level, numerically oriented programming language. It can be used for signal processing, statistical analysis, image enhancement, fluid dynamics simulat ...
,
Octave
In music, an octave ( la, octavus: eighth) or perfect octave (sometimes called the diapason) is the interval between one musical pitch and another with double its frequency. The octave relationship is a natural phenomenon that has been refer ...
,
BioPAX BioPAX (Biological Pathway Exchange) is a RDF/OWL-based
standard language to represent biological pathways
at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data.
Pathway data captures our understanding of ...
and
RDF/XML
RDF/XML is a syntax,RDF/XML Syntax Specification
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...
applet
In computing, an applet is any small application that performs one specific task that runs within the scope of a dedicated widget engine or a larger program, often as a plug-in. The term is frequently used to refer to a Java applet, a program w ...
, in which some networks were presented by following
Systems Biology Graphical Notation
The Systems Biology Graphical Notation (SBGN) is a standard graphical representation intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst c ...
. And a human readable summary of each model is available in
PDF
Portable Document Format (PDF), standardized as ISO 32000, is a file format developed by Adobe in 1992 to present documents, including text formatting and images, in a manner independent of application software, hardware, and operating systems. ...
.
Content
BioModels is composed of several branches. The curated branch hosts models that are well curated and annotated. The non-curated-branch provides models that are still not curated, are non-curatable (spatial models, steady-state models etc.), or too huge to be curated. Non-curated models can be later moved into the curated branch. The repository also hosts models which were automatically generated from pathways databases.
All the models are freely available under the Creative Commons CC0 Public Domain Dedication, and can be easily accessed via the website o Web Services One can also download archives of all the models from th EBI FTP server
BioModels announced its 31st release on June 26, 2017. It now publicly provides 144,710 models. This corresponds to 1,640 models published in the literature and 143,070 models automatically generated from pathway resources.
Deposition of models in BioModels is advocated by many scientific journals, included
Molecular Systems Biology
''Molecular Systems Biology'' is a peer-reviewed open-access scientific journal covering systems biology at the molecular level (examples include: genomics, proteomics, metabolomics, microbial systems, the integration of cell signaling and r ...
, all the journals of the
Public Library of Science
PLOS (for Public Library of Science; PLoS until 2012 ) is a nonprofit publisher of open-access journals in science, technology, and medicine and other scientific literature, under an open-content license. It was founded in 2000 and launc ...
, all the journals of
BioMed Central
BioMed Central (BMC) is a United Kingdom-based, for-profit scientific open access publisher that produces over 250 scientific journals. All its journals are published online only. BioMed Central describes itself as the first and largest open a ...
and all the journals published by the
Royal Society of Chemistry
The Royal Society of Chemistry (RSC) is a learned society (professional association) in the United Kingdom with the goal of "advancing the chemistry, chemical sciences". It was formed in 1980 from the amalgamation of the Chemical Society, the Ro ...
.
Development
BioModels is developed by the BioModels.net Team at the
EMBL
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...
-
EBI
Ebrahim Hamedi ( fa, اِبراهیم حامدی, also Romanized as "Ebrāhim Hāmedi"; born 1949), better known by his stage name Ebi (Persian: ), is an Iranian pop singer who first started his career in Tehran, gaining fame as part of a ban ...
, UK, the Le Novère lab at the
Babraham Institute
The Babraham Institute is a life sciences research institution and a partner organisation of the University of Cambridge. The Babraham Institute is based on the Babraham Research Campus, partly occupying a former manor house, but also labora ...
, UK, and the
SBML
The Systems Biology Markup Language (SBML) 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 use ...
BioModels Development has benefited from the funds of the
European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...
, the
Biotechnology and Biological Sciences Research Council
Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds scientific rese ...
, the
Innovative Medicines Initiative
The Innovative Medicines Initiative (IMI) is a European initiative to improve the competitive situation of the European Union in the field of pharmaceutical research. The IMI is a joint initiative ( public-private partnership) of the DG Researc ...
National Institute of General Medical Sciences
The National Institute of General Medical Sciences (NIGMS) supports basic research that increases understanding of biological processes and lays the foundation for advances in disease diagnosis, treatment, and prevention. NIGMS-funded scientists ...
, the
DARPA
The Defense Advanced Research Projects Agency (DARPA) is a research and development agency of the United States Department of Defense responsible for the development of emerging technologies for use by the military.
Originally known as the Adv ...
, and the
National Center for Research Resources
The National Center for Research Resources (NCRR) was a center within the National Institutes of Health a United States government agency. NCRR provided funding to laboratory scientists and researchers for facilities and tools in the goal of curi ...