What is BioModels Database?

Computational models are essential for understanding the mechanisms of biological processes and for predicting their behaviour (Figure 1). Until recently, most of the published quantitative models in biology were lost to the community, either because they were not made available or because they were insufficiently characterised to allow them to be reused. The rise of systems biology has led to an increased interest in detailed mathematical models within the life sciences. As a consequence, academic and industrial scientists, as well as teachers of biological science, need to find, evaluate, compare and integrate models. BioModels Database not only provides a central repository for quantitative models of biological systems, but also instils confidence to users because a large number of models have been carefully simulated and verified based on their reference peer reviewed publications.

SBGN Process Description map representing a gene network

Figure 1 SBGN Process Description map representing a gene network (termed the 'repressilator' by the authors), which generates oscillating fluorescence patterns. From: Elowitz and Leibler (2000).
View the original model in BioModels Database.

About BioModels Database

BioModels Database allows biologists to store, search and retrieve published mathematical models of biological interest. Models present in the database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, and controlled vocabularies. BioModels Database provides access to a large diversity of models representing biochemical, cellular, tissular, and even population systems.

Many of the models are carefully checked by curators to verify that the models correspond to their reference publication and that they produce the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to relevant data resources. This allows you to search accurately for your models of interest, and to identify the components of models precisely - an important step towards model reuse and composition.

Models can be retrieved in standard formats such as the Systems Biology Markup Language (SBML), as well as several other representational formats.