Standardized visualization of differences between model versions

Abstract

Simulation models change over time. Reasons may include typo corrections, parameter updates, specification updates orimproved semantic annotations. The BiVeS tool is a Java library to detect differences between simulation models encoded in SBML or CellML. It returns a list of changes between two versions of a model. BiVeS provides both human-readable and computer-readable output formats. One output type is JSON, a data-interchange format that is based onJacaScript and easy to parse. SBGN is a visual standard to display biological networks. It defines sets of glyphs to use for the representation of biological entities (macromolecules, simple chemicals, complexed etc.) and relations between them (catalysis, inhibition, association, dissociation etc.).In our talk, we will introduce the BiVeS tool and its output types. We will focus on the novel JSON format. Contrary to the previous formats, BiVeS now exports all information necessary to generate the difference map using SBGN-compliant glyphs. The differences are furthermore highlighted in the SBGN map, using a specific color encoding. The support of SBGN for the visualisation of difference further improves the readability and interpretation of changes in simulation models, and it aids users in understanding the evolution of a model.

Date
Location
Newcastle, UK