TY - CHAP A1 - Chodak, Jacek A1 - Heiner, Monika ED - Lorenz, Robert ED - Metzger, Johannes T1 - Spike - a command line tool for continuous, stochastic & hybrid simulation of (coloured) Petri nets T2 - Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018 Y1 - 2018 UR - https://opus.bibliothek.uni-augsburg.de/opus4/frontdoor/deliver/index/docId/41861/file/awpn18-lorenz-metzger-OPUS.pdf#page=9 SP - 1 EP - 6 PB - Universität, Institut für Informatik CY - Augsburg ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Ghanbar, Leila A1 - Chodak, Jacek T1 - Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking T2 - BMC Bioinformatics Y1 - 2019 U6 - https://doi.org/10.1186/s12859-019-2690-z SN - 1471-2105 VL - 20 supplement 4 ER - TY - GEN A1 - Schwarick, Martin A1 - Rohr, Christian A1 - Liu, Fei A1 - Assaf, George A1 - Chodak, Jacek A1 - Heiner, Monika T1 - Efficient Unfolding of Coloured Petri Nets using Interval Decision Diagrams T2 - Application and Theory of Petri Nets and Concurrency : 41st International Conference, PETRI NETS 2020, Paris, France, June 24–25, 2020, Proceedings N2 - 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. KW - Coloured Petri KW - Unfolding KW - Symbolic data structures KW - Interval decision diagrams Y1 - 2020 SN - 978-3-030-51830-1 SN - 978-3-030-51831-8 U6 - https://doi.org/10.1007/978-3-030-51831-8_16 SP - 324 EP - 344 PB - Springer CY - Cham ER - TY - THES A1 - Chodak, Jacek T1 - Spike – a tool for reproducible simulation experiments N2 - Reproducibility of simulation experiments is still a significant challenge and has attracted considerable attention in recent years. One cause of this situation is bad habits of the scientific community. Many results are published without data or source code, and only a textual description of the simulation set-up is provided. Other causes are: no complete simulation set-up, no proper output data analysis and inconsistency of published data, which makes it impossible to compare results. The progress of computational modelling, amount of data and complexity of models requires designing experiments in such a way that ensures reproducibility. A textual description does not provide all the needed details. A computer code is more reliable than a textual description. It is the precise specification that describes a simulation configuration, model, etc. When computer code, data, models and all parameters are provided, the simulation results become reproducible. The main goal of this thesis is to develop a tool that ensures reproducibility and efficient execution of simulation experiments, often involving many individual simulation runs. The tool should support a wide range of application scenarios, where the typical scenario is simulation of biochemical reaction networks, which are represented as (coloured) Petri nets interpreted in the stochastic, continuous or hybrid paradigm. The model to be simulated can be given in various formats, including SBML. The result is a command line tool called Spike, which can be used for various scenarios, including benchmarking, simulation of adaptive models and parameter optimization. It builds on a human-readable configuration script SPC, supporting the efficient specification of multiple model configurations as well as multiple simulator configurations in a single configuration file. KW - Parallel simulation KW - Parameter scanning KW - Petri nets KW - Reproducibility KW - Simulation of adaptive models Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-58509 PB - BTU CY - Cottbus ER - TY - GEN A1 - Chodak, Jacek A1 - Heiner, Monika ED - Bergenthum, Robin ED - Kindler, Ekkart T1 - SPIKE – as a Supporting Tool for a Model Parameters Optimization via Branched Simulations T2 - Algorithms and Tools for Petri Nets : Proceedings of the Workshop AWPN 2019, Hagen, Germany, October 10–11, 2019, Tagungsband Y1 - 2019 UR - https://ub-deposit.fernuni-hagen.de/receive/mir_mods_00001564 SP - 18 EP - 23 PB - Uni Hagen CY - Hagen ER - TY - GEN A1 - Chodak, Jacek A1 - Heiner, Monika ED - Bortolussi, Luca ED - Sanguinetti, Guido T1 - Spike – reproducible simulation experiments with configuration file branching T2 - Computational Methods in Systems Biology : 17th International Conference, CMSB 2019, Trieste, Italy, September 18–20, 2019, Proceedings Y1 - 2019 SN - 978-3-030-31303-6 SN - 978-3-030-31304-3 U6 - https://doi.org/http://dx.doi.org/10.1007/978-3-030-31304-3_19 SP - 315 EP - 321 PB - Springer ER -