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:

  1. Models described in scientific literature.
  2. 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.

BioModels production pipeline

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.

Model curation procedure

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.