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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Chen Li1, Marco Donizelli, Nicolas Rodriguez
1European Bioinformatics Institute, Hinxton, UK.
BMC Systems Biology
|July 1, 2010
Summary
Centralized repositories like BioModels Database are essential for managing and reusing quantitative biological models. This resource facilitates model sharing, analysis, and integration with other biological data, advancing systems biology research.
Area of Science:
- Systems Biology
- Computational Biology
- Biochemistry
Background:
- Quantitative models are crucial for understanding complex biological systems.
- The growing number of models necessitates centralized repositories for efficient dissemination and reuse.
- Standardized formats and cross-referencing are key for maximizing model utility.
Purpose of the Study:
- To establish a centralized, accessible repository for quantitative biological models.
- To facilitate the storage, retrieval, analysis, and reuse of peer-reviewed models.
- To promote standardization and interoperability within the systems biology community.
Main Methods:
- BioModels Database provides a freely accessible online platform for quantitative models.
- Models undergo thorough checking of structure and behavior, with annotation using controlled vocabularies.
- Features include online examination, various download formats, reaction network diagrams, online simulation, and submodel extraction.
Main Results:
- BioModels Database serves as a recognized reference resource for systems biology.
- It supports benchmarking of simulation systems and analysis of model clustering.
- Model deposition is encouraged by scientific journal publishers.
Conclusions:
- BioModels Database effectively addresses the need for a centralized model repository.
- The freely distributed and reusable models, along with open-source software, foster community engagement.
- The resource enhances the advancement and application of systems biology research.
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