Visualisation and annotation tools

Model Visualisation


Complicated relationships often exist between biological processes and the mathematical model(s) describing these processes. A biological concept may be represented using several mathematical equations and variables, spread across multiple components, to form a CellML model with a complex structure. In such cases it is often difficult to pull together all the relevant information required to discover the underlying biological process being described by the model. To help elucidate the underlying biology we have developed an ontological framework for annotating CellML models with biophysical concepts. In the paper referenced below we demonstrate that, by using these ontological mappings, in combination with a set of graph reduction rules, it is possible to represent the underlying biological process described in a CellML model.

Wimalaratne, S. M., Halstead, M.D.B., Lloyd, C.M., Crampin, E.J., and Nielsen, P.F.  Biophysical annotation and representation of CellML models. Bioinformatics, 2009, 25, 2263–2270. Pubmed ID: 19564239.

Tools: CellMLViewer

CellMLViewer is a prototype tool which combines a visual language, together with CellML ontologies, to support the visualisation of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model.

Wimalaratne, S. M., Halstead, M.D.B., Lloyd, C.M., Cooling, M.T., Crampin, E.J., and Nielsen, P.F. A method for visualizing CellML models. Bioinformatics, 2009, 25, 3012-3019. Pubmed ID: 19703920

Model Annotation


The efficient exchange, reuse, and integration of models is aided by the presence of biological information in the model. Model annotations are necessary to describe how the model has been generated and to define the meaning of the components that make up the model in a computationally-accessible fashion. If biological information about a model is added consistently and thoroughly, the model becomes useful not just for simulation, but also as an input in other computational tasks such as data integration and as a reference for researchers.

Lister, A. L., Pocock, M., Taschuk, M. & Wipat, A. Saint: a lightweight integration environment for model annotation. Bioinformatics 25, 3026-3027 (2009).

Tools: Saint

Saint logo 60pxSaint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Saint currently supports SBML, while CellML compatibility is awaiting development of MIRIAM annotation functionality in the CellML specification and API. Saint is freely available for use and development.