BioModels: Content, Features, Functionality, and Use.

Area of Science:

• Systems Biology
• Computational Biology
• Bioinformatics

Background:

• Mathematical models are essential for understanding complex biological systems.
• Access to curated and diverse biological models is crucial for research.
• Interoperability and reproducibility are key challenges in computational biology.

Purpose of the Study:

• To present the BioModels database, a key resource for biological modeling.
• To detail the content, features, and functionality of the BioModels repository.
• To provide guidance on the usage of BioModels for researchers.

Main Methods:

• The BioModels database aggregates manually curated and automatically generated mathematical models.
• Models cover various biological scales and are linked to external resources.
• A tutorial format is used to explain the database's structure and access methods.

Main Results:

• BioModels hosts over 1,200 literature-based models and over 140,000 pathway-derived models.
• Extensive cross-linking with external databases enhances model interoperability.
• Manual curation ensures the reproducibility of simulation results for a significant portion of models.

Conclusions:

• BioModels serves as a vital, centralized resource for biological mathematical models.
• The database facilitates research by providing accessible, interoperable, and reproducible models.
• This tutorial empowers users to effectively leverage BioModels for their research needs.