Talks

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.

Graph databases can be successfully applied in Systems Biology for managing extensive and complex heterogeneous information. Ultimately, graphs are a natural way of representing biological networks. A graph database like Neo4j can thus often provide a better response time and it enables efficient storage, processing and querying of biological networks. Here we present STON (SBGN TO Neo4j), a Java-based framework to import and translate metabolic, signalling and gene regulatory pathways presented in SBGN Process Description and SBGN Activity Flow languages to a graph-oriented format compatible with Neo4j. Exploiting the power of a graph database opens new opportunities for combining different layers of granularity and for identifying functional sub-modules in the network. Further extensions are planned and will allow merging pathways into larger networks while taking into account possible overlapping areas of the network. The framework is freely available on SourceForge: http://sourceforge.net/projects/ston/.