Target driven biochemical network reconstruction based on petri nets and simulated annealing
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
A comparative study of stochastic analysis techniques
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Initial experience with a computational thinking course for computer science students
Proceedings of the 42nd ACM technical symposium on Computer science education
How might petri nets enhance your systems biology toolkit
PETRI NETS'11 Proceedings of the 32nd international conference on Applications and theory of Petri Nets
Quantitative evaluation of time-dependent Petri nets and applications to biochemical networks
Natural Computing: an international journal
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Snoopy --- a unifying petri net tool
PETRI NETS'12 Proceedings of the 33rd international conference on Application and Theory of Petri Nets
Petri nets approach to modeling of immune system and autism
ICARIS'12 Proceedings of the 11th international conference on Artificial Immune Systems
Predicting phenotype from genotype through automatically composed petri nets
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
JAK-STAT signalling as example for a database-supported modular modelling concept
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
An efficient method for unfolding colored Petri nets
Proceedings of the Winter Simulation Conference
A module-based approach to biomodel engineering with Petri nets
Proceedings of the Winter Simulation Conference
A new object-oriented Petri net simulation environment based on modelica
Proceedings of the Winter Simulation Conference
Toward a language for the flexible observation of simulations
Proceedings of the Winter Simulation Conference
Stochastic simulation of the coagulation cascade: a petri net based approach
Euro-Par'12 Proceedings of the 18th international conference on Parallel processing workshops
Mining for variability in the coagulation pathway: a systems biology approach
EvoBIO'13 Proceedings of the 11th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Colouring space - a coloured framework for spatial modelling in systems biology
PETRI NETS'13 Proceedings of the 34th international conference on Application and Theory of Petri Nets and Concurrency
Efficient recovery of missing events
Proceedings of the VLDB Endowment
Modeling membrane systems using colored stochastic Petri nets
Natural Computing: an international journal
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Summary: To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the graphical user interface adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools. Snoopy facilitates the addition of new Petri net classes thanks to its generic design. Availability: Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions). Contact: snoopy@informatik.tu-cottbus.de