NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
Java editor for petri nets, based on the ARP analyzer. Exports nets to GIF, JPEG, PNG, PPM, ARP and PNML (XML based) file format. Uses the excellent JHotDraw 5.2 framework.