Group of Clinical Genomic Networks

CAS-MPG Partner Institute for Computational Biology


The signalling Petri net (SPN) simulator, designed to provide insights into the trends of molecules’ activity-levels in response to an external stimulus, contributes to the systems biology necessity of analyzing the dynamics of large-scale cellular networks. Implemented into the freely available software, BioLayout Express3D, the simulator is publically available, distributed under the GNU General Public License Version 3 and easy to use, providing the input files are prepared in .graphML format, typically using the network editing software, yEd, and standards specific to the software. However, analysis of complex networks represented using other systems biology formatting languages (on which popular software, such as CellDesigner and Cytoscape are based) requires manual manipulation; a step that is prone to error and limits the use of the SPN simulator in BioLayout Express3D. To overcome this, we here present a Cytoscape plugin that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language (SBML). The automation of this step opens the SPN simulator to a far-larger user-group than has previously been possible.


Examples (from the same network):

CellDesigner examples can be downloaded here

Cytoscape examples can be downloaded here

SPN input graphs can be downloaded here


Software: SPNConverter.jar and ReadMe