title: SPNConverter: a new link between static and dynamic complex network analysis.
abstract: CONCLUSIONS
  The signaling 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 Express(3D), the simulator is publicly available and easy to use, provided the input files are prepared in the 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 Express(3D). To overcome this, we present a Cytoscape plug-in that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language. The automation of this step opens the SPN simulator to a far larger user group than has previously been possible.
  
  
  METHODS
  Distributed under the GNU General Public License Version 3 at http://apps.cytoscape.org/apps/spnconverter.
authors.affiliation: Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, PR China and Division of Community Health Sciences, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Dent
authors.forename: Xinyi
authors.initials: X
authors.lastname: Yang
authors.forename: Christine
authors.initials: C
authors.lastname: Nardini
mesh_terms: D001331:Automation; D020407:Internet; D012984:Software; D049490:Systems Biology / Q000379:methods*