A symbolic reachability graph for coloured Petri nets
Theoretical Computer Science
An Introduction to the Theoretical Aspects of Coloured Petri Nets
A Decade of Concurrency, Reflections and Perspectives, REX School/Symposium
Bioinformatics
Electronic Notes in Theoretical Computer Science (ENTCS)
The Space and Motion of Communicating Agents
The Space and Motion of Communicating Agents
ESOP'03 Proceedings of the 12th European conference on Programming
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
A comparative study of stochastic analysis techniques
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
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From the phosphorylation state of a molecule to the volume of a cell, parameters are ubiquitous in systems biology. At the same time, most models involve static or dynamic compartments, for example to separate cells from their environment. We introduce coloured stochastic multilevel multiset rewriting, an expressive formalism for modelling systems with parameters and complex dynamic, multilevel compartment structures, and an extension of both multilevel multiset rewriting and coloured Petri nets. While being very expressive, it allows the direct and natural expression of biological ideas. We give some illustrative examples, demonstrating the use of parameters to handle cell states, position and volume, and variable rates. We further demonstrate the use of rules with complex right-hand sides for reproduction. We regard these examples as paving the way for more biologically relevant models.