BioModels: expanding horizons to include more modelling approaches and formats

Abstract

BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing.

Figure 1.

Shows some of the modelling approaches and formats that BioModels supports with its current JUMMP-based infrastructure. In addition to model files, the current platform also allows the submission of other supporting model related files.

Figure 2.

Models can be shared with specific users or teams. Submitters can search for collaborators through the text field on the left-hand-side of the page which provides autocompletion and can choose whether to grant them read-only or read-write permissions. Existing collaborators can be managed using the controls on the right-hand-side of the page.

Figure 3.

Representation of a sample life cycle for a model in the new portal of BioModels. The full modification history of the model, captured as a series of revisions, is available to the submitter. Only revisions that have been published are publicly available. Submitters can continue to revise models privately even after publishing them.

Figure 4.

Screenshot of the search results for logical models. The left-hand-side column allows users to progressively filter their models of interest. Long search results are broken into separate chunks (pages) of customisable size that can be accessed independently. Different sorting criteria are available. A subset of the search results can be selected for bulk download.

Figure 5.

The model display page offers a high-level summary of the model organised arranged into a series of tabs. The first three tabs are always shown, whilst subsequent ones depend on the model’s curation status and encoding format.