BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

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TitleBioModels.net Web Services, a free and integrated toolkit for computational modelling software.
Publication TypeJournal Article
Year of Publication2010
AuthorsLi, C, Courtot, M, Le Novère, N, Laibe, C
JournalBrief Bioinform
Volume11
Issue3
Pagination270-7
Date Published2010 May
ISSN1477-4054
KeywordsAlgorithms, Computer Simulation, Data Mining, Database Management Systems, Databases, Factual, Internet, Models, Biological, Programming Languages, Software, Software Design, Systems Integration
Abstract

<p>Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.</p>

DOI10.1093/bib/bbp056
Alternate JournalBrief. Bioinformatics
PubMed ID19939940
PubMed Central IDPMC2913671
Grant ListBB/E005748/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/E006248/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
GM070923-02 / GM / NIGMS NIH HHS / United States