The PNK 2e
The PNK (Petri Net Kernel) 2e is a software environment for the modeling and simulation of biological processes. It was developed as part of a M.Sc. project at the University of Edinburgh, UK. The software uses Stochastic Petri Nets (SPNs), a graphical representation of Markov Jump Processes. SPNs are described by directed graphs and give an intuitive description of complex systems. PNK 2e has been developed with the aim of providing a software that is easy to use and has been applied successfully to model genetic oscillators.
PNK 2e is based on the software project the Petri Net Kernel, developed at the Humboldt University in Berlin, Germany. The original Petri Net Kernel is a framework for the development of Petri Net tools. PNK 2e uses the infrastructure of the Kernel and extends it by features that are thought to be useful for biological applications.
It offers the following features:
Extended Stochastic Petri Nets with simplifications for the representation of biological reactions.
Import and Export of biological models from / to SBML (Systems Biology Markup Language).
Stepwise simulation (“token game”) of the SPN.
Stochastic and deterministic simulation through the Systems Biology Workbench (SBW).
The Kernel also contains an interface to INA (Integrated Network Analyzer). It can be used to perform a structural analysis of the Petri Net such as the computation of invariants, deadlocks, etc. The INA software is available here.
More information is available on the web page of the Petri Net Kernel project.
PNK2e (The Systems Biology Workbench needs to be downloaded here)
PNK (The original Kernel, included in the package above)
Javadoc documentation (html) (zip)
Documentation created with doxygen (html) (zip)
Modeling the Randomness in Biological Systems (poster presenting PNK2e at the BioSysBio 05 conference in Edinburgh)