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What is BioModels?

BioModels is an invaluable core resource for the systems biology/pharmacology community (4, 5, 6). It stores a vast collection of the literature-based mechanistic models in standard formats, many of which are physiologically and pharmaceutically relevant, and describe a wide range of biological/biomedical processes at different biological scales.

BioModels provides two sets of models:

  1. Models described in scientific literature (Individual / All models under quick search options)
  2. Models generated automatically from pathway resources (a branch of BioModels called Autogenerated Models)

We have manually validated the model components, as well as the structure and behaviour of a large proportion of literature-based models. This is done to ensure the models correspondence with the original publication. In Figure 2 you can see the general BioModels curation workflow.

After models are submitted to BioModels they pass through a rigorous curation procedure involving analysis and data extraction, encoding the model in standard format, literature result reproduction and annotation.
Figure 2 BioModels curation workflow. After models are submitted to BioModels they pass through a rigorous curation procedure involving literature result reproduction and annotation using known ontologies or databases (4).

Figure 3 shows a specific example of the curation procedure for a mitogen-activated protein kinase cascades model.

Curation procedure for mitogen-activated protein kinase cascades model. Following representation of the biological process with mathematical rate laws, the model is encoded in standards, followed by model simulation which uncovers the dynamics of the system.
Figure 3 Model curation procedure. View the original model in BioModels Database. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades (7).

The model elements are also cross-linked to external database resources and ontologies, which enables you to precisely search models from the repository. BioModels is accessible through a web interface and programmatically through web services. Hosted models are freely available for use, modification and redistribution to all users under the terms of Creative Commons CC0.