2016 Conference on Computational Modelling with COPASI
Manchester Institute of Biotechnology, 12th – 13th May, 2016

BioModels: a public model sharing resource for computational models of biological/biomedical systems

Vijayalakshmi Chelliah1, Nick Juty1, Mihai Glont1, Nicolas Le Novère2, Henning Hermjakob1

1 - EMBL - European Bioinformatics Institute, UK; 2 - Babraham Institute, UK

Keywords: BioModels, mathematical modelling, resource, database, mechanistic models, biological process, COPASI


Mechanistic models are becoming one of the cornerstones of the computational life sciences. Coupled with high-throughput 'omics' and network analysis, hypothesis design and the use of predictive models is becoming standard practice to understand the mechanisms underlying complex biological systems.

BioModels [1, 2] 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 processes at different biological scales. These models can also serve as a comprehensive body of knowledge on existing processes or be used as building blocks, facilitating the repurposing of a model through further development, refinement or merging.

BioModels provides two sets of models: (i) models described in scientific literature, and (ii) models generated from pathway resources (path2models [3]). The components, structure and behaviour of a large proportion of these models are manually verified ensuring correspondence to the original reference publication. This verification process is conducted using a tool other than that used in the original publication, thus precluding tool specific errors or hidden dependencies; the simulation results of more than 60% of the curated models have been verified using COPASI.

The model elements are cross-referenced (annotated) to records from external database resources to precisely relate them to the corresponding biological processes or physical entities they represent. Over 40 external database resources and ontologies are used to cross-reference the model components. This facilitates efficient search and retrieval of the models from the database, and also helps in model comparison, merging and expansion with novel information.

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.

  1. Chelliah et al. (2015). BioModels: ten year anniversary. Nucleic Acids Research 43(D1): D542-D548.
  2. Juty et al. (2015). BioModels: Content, Features, Functionality, and Use. CPT: Pharmacometrics Systems Pharmacology. 4(2): e3.
  3. Büchel et al. (2013). Path2Models: Large-scale generation of computational models from biochemical pathway maps.BMC Systems Biology. 7:116.

Conference Program