SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers
ACM Transactions on Mathematical Software (TOMS) - Special issue on the Advanced CompuTational Software (ACTS) Collection
Bioinformatics
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments
Transactions on Computational Systems Biology XI
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
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
MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly
QEST '11 Proceedings of the 2011 Eighth International Conference on Quantitative Evaluation of SysTems
Predicting phenotype from genotype through automatically composed petri nets
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Proceedings of the Winter Simulation Conference
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
MARCIE: model checking and reachability analysis done efficiently
PETRI NETS'13 Proceedings of the 34th international conference on Application and Theory of Petri Nets and Concurrency
Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets
Journal of Biomedical Informatics
Modeling membrane systems using colored stochastic Petri nets
Natural Computing: an international journal
Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks
Fundamenta Informaticae - Dedicated to the Memory of Professor Manfred Kudlek
Hi-index | 0.00 |
The tool Snoopy provides a unifying Petri net framework which has particularly many application scenarios in systems and synthetic biology. The framework consists of two levels: uncoloured and coloured. Each level comprises a family of related Petri net classes, sharing structure, but being specialized by their kinetic information. Petri nets of all net classes within one level can be converted into each other, while changing the level involves user-guided folding or automatic unfolding. Models can be hierarchically structured, allowing for the mastering of larger networks. Snoopy supports the simultaneous use of several Petri net classes; the graphical user interface adapts dynamically to the active one. Built-in animation and simulation (depending on the net class) are complemented by export to various analysis tools. Snoopy facilitates the extension by new Petri net classes thanks to its generic design.