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Cytoscape Systems Biology Markup Language CySBML

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Designed to work with Systems Biology Markup Language (SBML) in Cytoscape. CySBML includes an importer for BioModels to load SBML from standard repositories. Cytoscape has already been used in numerous applications for visualization and graphical network analyses, whereas the BioModels database collects and annotates structural and mathematical models in SBML format that provide insights into the dynamic behavior of biological networks. CySBML makes it possible to combine these two important system biological resources in a convenient and easy-to-use way with special focus on the semantic layer defining the models.

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CySBML forum

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CySBML versioning

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CySBML classification

CySBML specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Java
Version:
1.2
Requirements:
Cytoscape
Maintained:
Yes
Interface:
Graphical user interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Medium
Stability:
Stable

CySBML support

Documentation

Maintainer

  • Matthias König <>

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Publications

Institution(s)

Department of Biochemistry, University Medicine Charité Berlin, Berlin; Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany

Funding source(s)

Supported by the Federal Ministry of Education and Research (BMBF, Germany) within the Virtual Liver Network (0315756 and 0315741).

Link to literature

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