We are pleased to announce the release of CySBML available for download from https://github.com/matthiaskoenig/cy2sbml/releases.

CySBML is a Cytoscape plugin for the import and work with SBML files in Cytoscape providing the visualisation of SBML annotations within the network context. The main features are

• Java based SBML parser for Cytoscape based on the java SBML library JSBML
• simple access to SBML models and SBML annotations via BioModel and MIRIAM WebServices
• supports all versions of SBML
• support of SBML Layout Package
• support of SBML Qualitative Models Package
• provides SBML validation (SBML warnings and errors accessible)
• creates standard network layout based on the SBML species/reaction model
• provides access to RDF based annotation information within the network context
• Navigation menu based on the SBML structure linked to layout and annotation information
• succesfully tested with all SBML.org and Biomodels.org test cases (sbml-test-cases-2.0.2, BioModels_Database-r21-sbml_files)

A detailed tutorial is available covering the topics

• Installation
• CySBML interface
• Import of SBML models
• Access to annotation information
• SBML validation in CySBML
• Programmatic Interaction with CySBML

Thanks and have fun

The CySBML team.

CySBML was developed by Matthias König in cooperation with Andreas Dräger from the Center of Bioinformatics Tuebingen (ZBIT) and was funded by the Virtual Liver Network.

We thank Camille Laibe for implementing additional BioModel WebService functionality, the Qual Team and Finja Büchel, Florian Mittag, and Nicolas Rodriguez (Qual implementation in JSBML), Sebastian Fröhlich and Clemens Wrzodek (Layout support in JSBML) as well as Sonia Villegas, Michael Weidlich and Christian Bölling for testing CySBML.

• Matthias König (Humboldt-University Berlin, Institute for Biology, Institute for Theoretical Biology)
• Andreas Dräger (Center of Bioinformatics Tuebingen (ZBIT))