cy3sbml

cy3sbml is an app for the Cytoscape network-analysis platform (Cytoscape 3) that imports, visualizes, and annotates computational biology models encoded in the Systems Biology Markup Language (SBML). It is the successor to the earlier Cytoscape 2 plugin CySBML, developed primarily by Matthias König (Humboldt-University Berlin, Systems Medicine of the Liver group) with contributions from Andreas Dräger and others, and released under the MIT license. The reference publication remains König, Dräger and Holzhütter, "CySBML: a Cytoscape plugin for SBML" (Bioinformatics, 2012).

Internally, cy3sbml parses SBML with the JSBML library and maps the model onto one or more Cytoscape networks. The core network follows the species-reaction structure of SBML: chemical species and reactions become nodes, and reactant, product and modifier relationships become directed edges, with compartments and other objects carried as attributes. Beyond this biochemical view, it can expose additional SBML constructs such as kinetic laws, function definitions and parameters as graph objects, so that the mathematical scaffolding of a model is browsable alongside its reaction topology. Because it rides on JSBML, it supports all SBML levels and versions and the qual (qualitative), comp (hierarchical composition) and fbc (flux balance constraints) extension packages, and it runs the SBML validator to surface errors and warnings in a readable form.

A distinctive strength is annotation handling: cy3sbml reads both RDF-based (MIRIAM) and non-RDF annotations and offers one-click resolution of identifiers through identifiers.org, the EBI Ontology Lookup Service and BioModels, letting users jump from a species or reaction to its database records. Models can be pulled directly from the BioModels and BiGG repositories, and sessions preserve layouts. It complements repository and standards tooling such as SBFC, and its networks can be exported through Cytoscape into interchange formats like Cytoscape CX2, SIF or GraphML for downstream analysis.

Its limitations follow from its scope. cy3sbml is a viewer and annotation browser, not a simulator, so it does not integrate SED-ML/COMBINE execution and pairs naturally with dedicated engines for that. Its species-reaction graph is a topological rendering rather than a standardized process diagram, so it does not render SBGN process maps the way Newt, SBGN-ED or SBGN-ML do. Being a JVM/JavaFX Cytoscape app, it depends on a compatible Cytoscape 3.x release and Java runtime.