TY - CHAP A1 - Blätke, Mary-Ann A1 - Rohr, Christian ED - Heiner, Monika ED - Wagler, Annegret K. T1 - A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit T2 - Proceedings of the 6th International Workshop on Biological Processes & Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015 Y1 - 2015 UR - http://ceur-ws.org/Vol-1373/ N1 - peer reviewed SP - 37 EP - 54 ER - TY - CHAP A1 - Heiner, Monika A1 - Rohr, Christian A1 - Schwarick, Martin A1 - Streif, Stefan ED - Quaglia, Paola T1 - A Comparative Study of Stochastic Analysis Techniques T2 - CMSB '10, 8th Conference on Computational Methods in Systems Biology, Trento, Italy — September 29 - October 01, 2010 Y1 - 2010 SN - 978-1-4503-0068-1 U6 - https://doi.org/10.1145/1839764.1839776 SP - 96 EP - 106 PB - ACM CY - New York, NY ER - TY - CHAP A1 - Blätke, Mary-Ann A1 - Rohr, Christian A1 - Heiner, Monika A1 - Marwan, Wolfgang ED - Benner, Peter T1 - A Petri Net based Framework for Biomodel Engineering T2 - Large-Scale Networks in Engineering and Life Sciences KW - Automatic network reconstruction KW - Biomodel engineering KW - Dynamic systems modelling KW - Modular modelling KW - Petri nets KW - Molecular regulatory networks KW - Reverse engineering Y1 - 2014 SN - 978-3-319-08436-7 U6 - https://doi.org/10.1007/978-3-319-08437-4_6 SP - 317 EP - 366 PB - Springer CY - Heidelberg ER - TY - GEN A1 - Blätke, Mary-Ann A1 - Rohr, Christian T1 - BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1682 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 221 EP - 254 ER - TY - CHAP A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian ED - Heiner, Monika T1 - Coloured hybrid Petri nets for systems biology T2 - Proceedings of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN) Y1 - 2014 UR - http://ceur-ws.org/Vol-1159/ SP - 60 EP - 76 ER - TY - GEN A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian A1 - Heiner, Monika T1 - Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks T2 - Computational Biology and Chemistry KW - Coloured Petri nets KW - Hybrid Petri Nets KW - Multi-scale modelling KW - Bistable switch KW - Dendritic spines Y1 - 2018 U6 - https://doi.org/10.1016/j.compbiolchem.2018.05.023 SN - 1476-9271 VL - 76 SP - 87 EP - 100 ER - TY - GEN A1 - Rohr, Christian T1 - Discrete-Time Leap Method For Stochastic Simulation T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1680 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 181 EP - 198 ER - TY - GEN A1 - Rohr, Christian ED - Cabac, Lawrence ED - Kristensen, Lars Michael ED - Rölke, Heiko T1 - Discrete-Time Leap Method For Stochastic Simulation T2 - Proceedings of the International Workshop on Petri Nets and Software Engineering 2016, including the International Workshop on Biological Processes & Petri Nets 2016 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1591-5 UR - http://ceur-ws.org/Vol-1591/paper26.pdf SP - 362 EP - 376 PB - RWTH CY - Aachen 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 - GEN A1 - Blätke, Mary-Ann A1 - Dittrich, Anna A1 - Rohr, Christian A1 - Heiner, Monika A1 - Schaper, Fred A1 - Marwan, Wolfgang T1 - JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology T2 - Molecular BioSystems Y1 - 2013 U6 - https://doi.org/10.1039/C3MB25593J SN - 1742-2051 VL - 9 IS - 6 SP - 1290 EP - 1307 ER - TY - CHAP A1 - Heiner, Monika A1 - Rohr, Christian A1 - Schwarick, Martin ED - Colom, José-Manuel ED - Desel, Jörg T1 - MARCIE - Model checking and Reachability analysis done effieciently T2 - Application and theory of petri nets and concurrency, 34th international conference, proceedings, PETRI NETS 2013, Milan, Italy, June 24 - 28, 2013 Y1 - 2013 UR - http://link.springer.com/chapter/10.1007/978-3-642-38697-8_21 SN - 978-3-642-38696-1 N1 - referiert SP - 389 EP - 399 PB - Springer CY - Heidelberg [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Rohr, Christian A1 - Schwarick, Martin A1 - Tovchigrechko, Alexey A. ED - Koutny, Maciej ED - Desel, Jörg ED - Kleijn, Jetty T1 - MARCIE’s secrets of efficient model checking T2 - Transactions on petri nets and other models of concurrency XI Y1 - 2016 SN - 978-3-662-53400-7 SN - 978-3-662-53401-4 U6 - https://doi.org/10.1007/978-3-662-53401-4_14 N1 - referiert SP - 286 EP - 296 PB - Springer CY - Berlin [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Marwan, Wolfgang A1 - Rohr, Christian T1 - Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks Y1 - 2012 UR - http://www.springerlink.com/content/978-1-61779-361-5 ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Rohr, Christian T1 - Petri-net-based 2D Design of DNA Walker Circuits T2 - Natural Computing Y1 - 2018 U6 - https://doi.org/10.1007/s11047-018-9671-4 SN - 1572-9796 SN - 1567-7818 VL - 17 IS - 1 SP - 161 EP - 182 ER - TY - THES A1 - Rohr, Christian T1 - Simulative analysis of coloured extended stochastic Petri nets Y1 - 2017 UR - https://opus4.kobv.de/opus4-btu/files/4147/Rohr_Christian.pdf CY - Cottbus ER - TY - CHAP A1 - Rohr, Christian T1 - Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators T2 - Transactions on petri nets and other models of concurrency VIII Y1 - 2013 SN - 978-3-642-40464-1 SN - 978-3-642-40465-8 U6 - https://doi.org/10.1007/978-3-642-40465-8_8 N1 - referiert SP - 142 EP - 158 PB - Springer CY - Berlin [u.a.] ER - TY - GEN A1 - Rohr, Christian A1 - Marwan, Wolfgang A1 - Heiner, Monika T1 - Snoopy - a unifying Petri net framework to investigate biomolecular networks T2 - Bioinformatics Y1 - 2010 UR - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/974?ct=ct SN - 1460-2059 VL - 26 IS - 7 SP - 974 EP - 975 ER - TY - GEN A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian A1 - Heiner, Monika T1 - Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models T2 - BMC Systems Biology Y1 - 2017 UR - https://link.springer.com/epdf/10.1186/s12918-017-0449-6?author_access_token=54a9mC7bl_t-6TjlSqdqNG_BpE1tBhCbnbw3BuzI2RMKIgJAZ9nr6Hm0LME2XT_scd04D6IjdxN2SajBh1-bYG6TDIkKQYJrtczMPmCV290rFO3LRZ0YPUqCBRlezXRq1AJVJo-7YPWMt0G3LF52OA%3D%3D U6 - https://doi.org/10.1186/s12918-017-0449-6 SN - 1752-0509 VL - 11 ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Jayaweera, Yasoda A1 - Rohr, Christian T1 - Towards dynamic genome scale models T2 - Briefings in Bioinformatics Y1 - 2019 U6 - https://doi.org/10.1093/bib/bbx096 SN - 1477-4054 SN - 1467-5463 VL - 20 IS - 4 SP - 1167 EP - 1180 ER -