Petri Net Based Descriptions for Systematic Understanding of Biological Pathways
IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences
Modelling coordination in biological systems
ISoLA'04 Proceedings of the First international conference on Leveraging Applications of Formal Methods
Modelling and analysing genetic networks: from boolean networks to petri nets
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Towards a petri net semantics for membrane systems
WMC'05 Proceedings of the 6th international conference on Membrane Computing
What Can Formal Methods Bring to Systems Biology?
FM '09 Proceedings of the 2nd World Congress on Formal Methods
Step coverability algorithms for communicating systems
Science of Computer Programming
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Petri nets are a widely used formalism to qualitatively model concurrent systems such as a biological cell. We present techniques for modelling biological processes as Petri nets for further analyses and in-silico experiments. Instead of extending the formalism with ,,colours" or rates, as is most often done, we focus on preserving the simplicity of the formalism and developing an execution semantics which resembles biology --- we apply a principle of maximal parallelism and introduce the novel concept of bounded execution with overshooting. A number of modelling solutions are demonstrated using the example of the well-studied C. elegansvulval development process. To date our model is still under development, but first results, based on Monte Carlo simulations, are promising.