SPNConverter

SPNConverter converts SBML-formatted biological networks into GraphML within Cytoscape to enable analysis with the Signaling Petri Net (SPN) simulator in BioLayout Express3D.

Key Features:

• Automation: Automates the conversion of network files to eliminate manual file manipulation and reduce conversion errors.
• Cytoscape plug-in: Implements the conversion functionality as a Cytoscape plug-in to operate within Cytoscape sessions.
• SBML compatibility: Supports networks encoded in the Systems Biology Markup Language (SBML), including content produced by tools such as CellDesigner and Cytoscape.
• SPN simulator integration: Produces GraphML output required for direct use by the Signaling Petri Net (SPN) simulator in BioLayout Express3D.

Scientific Applications:

• Molecular activity trend analysis: Enables conversion of network models for SPN-based analysis of molecular activity trends in response to perturbations.
• Modeling and simulation of biological processes: Facilitates simulation of complex cellular processes by preparing network models for the SPN simulator.
• Large-scale network analysis: Supports preparation of large-scale cellular network models for reliable SPN simulation and analysis.

Methodology:

Interfaces with Cytoscape to automatically convert SBML-formatted networks into GraphML required by the Signaling Petri Net (SPN) simulator in BioLayout Express3D.