Categories: data visualization, network dynamics, networks, petri nets, systems biology

**Description:** PIC is an app that implements Petri nets for Cytoscape. It can both load Petri nets from input files of several different formats as well as manually create Petri nets while ensuring their formal correctness, and finally, simulate or export them. **Features included:** - Loading Petri nets from input files - supported formats: SBML, PNT, APNN, RL, Metatool - Manual creation and modification of Petri nets - Export of created and/or modified Petri nets to SBML Level 3 Version 1 format - Verification of formal correctness - Simulation of Petri nets (synchronous / asynchronous firing, randomized firing order) - Import of Invariants and check their realizability - Computation of minimal Transition-Invariants with the Fourier-Motzkin-Elimination

Authors:

• Marcel Gehrmann (Molecular Bioinformatics, Goethe-University, Frankfurt am Main, Germany)
• Marius Kirchner (Molecular Bioinformatics, Goethe-University, Frankfurt am Main, Germany)
• Jens Rieser (Molecular Bioinformatics, Goethe-University, Frankfurt am Main, Germany)
• Jörg Ackermann (Molecular Bioinformatics, Goethe-University, Frankfurt am Main, Germany)
• Ina Koch (Molecular Bioinformatics, Goethe-University, Frankfurt am Main, Germany)