A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Discrete, Continuous, and Hybrid Petri Nets
Discrete, Continuous, and Hybrid Petri Nets
From petri nets to differential equations – an integrative approach for biochemical network analysis
ICATPN'06 Proceedings of the 27th international conference on Applications and Theory of Petri Nets and Other Models of Concurrency
DSSZ-MC --- A Tool for Symbolic Analysis of Extended Petri Nets
PETRI NETS '09 Proceedings of the 30th International Conference on Applications and Theory of Petri Nets
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Steady-state solution of biochemical systems, beyond S-systems via T-invariants
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
IDD-based model validation of biochemical networks
Theoretical Computer Science
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We sketch the fundamental properties and features of Snoopy, a tool to model and execute (animate, simulate) hierarchical graph-based system descriptions. The tool comes along with several pre-fabricated graph classes, especially some kind of Petri nets and other related graphs, and facilitates a comfortable integration of further graph classes due to its generic design. To support an aspect-oriented model engineering, different graph classes may be used simultaneously. Snoopy provides some features (hierarchical nodes, logical nodes), which are particularly useful for larger models, or models with an higher connectivity degree. There are several Petri net classes available, among them the purely qualitative place/transition nets in its standard definition and in a version enhanced by four special arcs as well as two quantitative extensions of it - stochastic Petri nets and continuous Petri nets. Each of these classes enjoys dedicated animation or simulation features. Our tool runs on Windows and Linux operating systems, and it is available free of charge for non-commercial use.