What is BioModels?
BioModels is an invaluable core resource for the systems biology/pharmacology community. 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:
- Models described in scientific literature.
- Models generated automatically from pathway resources (a branch of BioModels called Path2Models).
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. 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.
Figure 2 BioModels production pipeline. After models are submitted to BioModels they pass through a rigorous curation procedure and are distributed to their respective branches based on the model type, and the curation status.
Figure 3 Model curation procedure. View the original model in BioModels Database. Reference: Kholodenko (2000), Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 2000 Mar; 267(6): 1583-1588.