FG Datenstrukturen und Softwarezuverlässigkeit
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- Automatic network reconstruction (1)
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Institute
BTU
BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models
(2018)
Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks
(2018)
We consider coloured Petri nets, qualitative and quantitative ones alike, as supported by our PetriNuts tool family, comprising, among others, Snoopy, Marcie and Spike. Currently, most analysis and simulation techniques require to unfold the given coloured Petri net into its corresponding plain, uncoloured Petri net representation. This unfolding step is rather straightforward for finite discrete colour sets, but tends to be time-consuming due to the potentially huge number of possible transition bindings. We present an unfolding approach building on a special type of symbolic data structures, called Interval Decision Diagram, and compare its runtime performance with an unfolding engine employing an off-the-shelf library to solve constraint satisfaction problems. For this comparison we use the 22 scalable coloured models from the MCC benchmark suite, complemented by a few from our own collection.