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

Chen Li¹, Mélanie Courtot, Nicolas Le Novère

¹Computational Neurobiology Group, at the European Bioinformatics Institute, Hinxton, UK.

Briefings in Bioinformatics

|November 27, 2009

Summary

Researchers can now easily access and analyze computational biology models using BioModels.net's standardized annotations and web services, facilitating systems biology research.

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Area of Science:

Computational biology
Systems biology
Bioinformatics

Background:

Sharing and exchanging scientific results are crucial for computational modeling research.
Standardized model curation is essential for reproducible research.
Existing resources lacked comprehensive programmatic access for model analysis.

Purpose of the Study:

To present the BioModels.net resources and their integrated web services.
To facilitate the programmatic access and analysis of curated biological models.
To support the adoption of standards like MIRIAM and SBO in systems biology.

Main Methods:

Development of MIRIAM Resources for standardized model annotation.
Creation of Systems Biology Ontology (SBO) for controlled vocabularies.
Implementation of BioModels Database for model storage and retrieval.
Provision of Web Services utilizing SOAP and WSDL for programmatic access.

Main Results:

BioModels.net offers a centralized database and standardized annotation system.
Web services enable remote querying, model retrieval, and annotation resolution.
Integration of MIRIAM annotations and SBO terms enhances model understanding.
Provided libraries simplify client software development for accessing resources.

Conclusions:

BioModels.net Web Services significantly advance researchers' ability to simulate and understand biological systems.
Programmatic access allows for model integration into workflows and efficient analysis.
Standardization through MIRIAM and SBO promotes data interoperability and research reproducibility.