@misc{WetterPfisterWerneretal., author = {Wetter, Oliver and Pfister, Christian and Werner, Johannes P. and Zorita, Eduardo and Wagner, Sebastian and Seneviratne, Sonia I. and Herget, J{\"u}rgen and Gr{\"u}newald, Uwe and Luterbacher, J{\"u}rg and Alcoforado, Maria Jo{\~a}o and Barriendos, Mariano and Bieber, Ursula and Br{\´a}zdil, Rudolf and Burmeister, Karl H. and Camenisch, Chantal and Contino, Antonio and Dobrovoln{\´y}, Petr and Glaser, R{\"u}diger and Himmelsbach, Iso and Kiss, Andrea and Kotyza, Oldřich and Labb{\´e}, Thomas and Liman{\´o}wka, Danuta and Litzenburger, Laurent and Nordl, {\O}yvind and Pribyl, Kathleen and Rets{\"o}, Dag and Riemann, Dirk and Rohr, Christian and Siegfried, Werner and S{\"o}derberg, Johan and Spring, Jean-Laurent}, title = {The year-long unprecedented European heat and drought of 1540 - a worst case}, series = {Climatic change}, volume = {125}, journal = {Climatic change}, number = {3-4}, issn = {1573-1480}, doi = {10.1007/s10584-014-1184-2}, pages = {349 -- 363}, abstract = {The heat waves of 2003 in Western Europe and 2010 in Russia, commonly labelled as rare climatic anomalies outside of previous experience, are often taken as harbingers of more frequent ex-tremes in the global warming-influenced future. However, a recent reconstruction of spring-summer temperatures for WE resulted in the likelihood of significantly higher temperatures in 1540. In order to check the plausibility of this result we investigated the severity of the 1540 drought by putting forward the argument of the known soil desiccation-temperature feedback. Based on more than 300 first-hand documentary weather report sources originating from an area of 2 to 3 million km2, we show that Europe was affected by an unprecedented 11-month-long Megadrought. The estimated number of precipitation days and precipitation amount for Central and Western Europe in 1540 is significantly lower than the 100-year minima of the in-strumental measurement period for spring, summer and autumn. This result is supported by independent documentary evidence about extremely low river flows and Europe-wide wild-, forestand settlement fires. We found that an event of this severity cannot be simulated by state-of-the-art climate models.}, language = {en} } @misc{PfisterWetterBrazdiletal., author = {Pfister, Christian and Wetter, Oliver and Br{\´a}zdil, Rudolf and Dobrovoln{\´y}, Petr and Glaser, R{\"u}diger and Luterbacher, J{\"u}rg and Seneviratne, Sonia I. and Zorita, Eduardo and Alcoforado, Maria Jo{\~a}o and Barriendos, Mariano and Bieber, Ursula and Burmeister, Karl H. and Camenisch, Chantal and Contino, Antonio and Gr{\"u}newald, Uwe and Herget, J{\"u}rgen and Himmelsbach, Iso and Labb{\´e}, Thomas and Liman{\´o}wka, Danuta and Litzenburger, Laurent and Kiss, Andrea and Kotyza, Oldřich and Nordl, {\O}yvind and Pribyl, Kathleen and Rets{\"o}, Dag and Riemann, Dirk and Rohr, Christian and Siegfried, Werner and Spring, Jean-Laurent and S{\"o}derberg, Johan and Wagner, Sebastian and Werner, Johannes P.}, title = {Tree-rings and people - different views on the 1540 Megadrought. Reply to B{\"u}ntgen et al. 2015}, series = {Climatic change}, volume = {131}, journal = {Climatic change}, number = {2}, issn = {0165-0009}, doi = {10.1007/s10584-015-1429-8}, pages = {191 -- 198}, language = {en} } @incollection{HeinerMarwanRohr, author = {Heiner, Monika and Marwan, Wolfgang and Rohr, Christian}, title = {Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks}, language = {en} } @misc{BlaetkeDittrichRohretal., author = {Bl{\"a}tke, Mary-Ann and Dittrich, Anna and Rohr, Christian and Heiner, Monika and Schaper, Fred and Marwan, Wolfgang}, title = {JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology}, series = {Molecular BioSystems}, volume = {9}, journal = {Molecular BioSystems}, number = {6}, issn = {1742-2051}, doi = {10.1039/C3MB25593J}, pages = {1290 -- 1307}, language = {en} } @incollection{Rohr, author = {Rohr, Christian}, title = {Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators}, series = {Transactions on petri nets and other models of concurrency VIII}, booktitle = {Transactions on petri nets and other models of concurrency VIII}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-40464-1}, doi = {10.1007/978-3-642-40465-8_8}, pages = {142 -- 158}, language = {en} } @misc{RohrMarwanHeiner, author = {Rohr, Christian and Marwan, Wolfgang and Heiner, Monika}, title = {Snoopy - a unifying Petri net framework to investigate biomolecular networks}, series = {Bioinformatics}, volume = {26}, journal = {Bioinformatics}, number = {7}, issn = {1460-2059}, pages = {974 -- 975}, language = {en} } @inproceedings{HerajyLiuRohr, author = {Herajy, Mostafa and Liu, Fei and Rohr, Christian}, title = {Coloured hybrid Petri nets for systems biology}, series = {Proceedings of the 5th International Workshop on Biological Processes \& Petri Nets (BioPPN)}, booktitle = {Proceedings of the 5th International Workshop on Biological Processes \& Petri Nets (BioPPN)}, editor = {Heiner, Monika}, pages = {60 -- 76}, language = {en} } @inproceedings{HeinerRohrSchwarick, author = {Heiner, Monika and Rohr, Christian and Schwarick, Martin}, title = {MARCIE - Model checking and Reachability analysis done effieciently}, series = {Application and theory of petri nets and concurrency, 34th international conference, proceedings, PETRI NETS 2013, Milan, Italy, June 24 - 28, 2013}, booktitle = {Application and theory of petri nets and concurrency, 34th international conference, proceedings, PETRI NETS 2013, Milan, Italy, June 24 - 28, 2013}, editor = {Colom, Jos{\´e}-Manuel and Desel, J{\"o}rg}, publisher = {Springer}, address = {Heidelberg [u.a.]}, isbn = {978-3-642-38696-1}, pages = {389 -- 399}, language = {en} } @inproceedings{HeinerRohrSchwaricketal., author = {Heiner, Monika and Rohr, Christian and Schwarick, Martin and Streif, Stefan}, title = {A Comparative Study of Stochastic Analysis Techniques}, series = {CMSB '10, 8th Conference on Computational Methods in Systems Biology, Trento, Italy — September 29 - October 01, 2010}, booktitle = {CMSB '10, 8th Conference on Computational Methods in Systems Biology, Trento, Italy — September 29 - October 01, 2010}, editor = {Quaglia, Paola}, publisher = {ACM}, address = {New York, NY}, isbn = {978-1-4503-0068-1}, doi = {10.1145/1839764.1839776}, pages = {96 -- 106}, language = {en} } @incollection{BlaetkeRohrHeineretal., author = {Bl{\"a}tke, Mary-Ann and Rohr, Christian and Heiner, Monika and Marwan, Wolfgang}, title = {A Petri Net based Framework for Biomodel Engineering}, series = {Large-Scale Networks in Engineering and Life Sciences}, booktitle = {Large-Scale Networks in Engineering and Life Sciences}, editor = {Benner, Peter}, publisher = {Springer}, address = {Heidelberg}, isbn = {978-3-319-08436-7}, doi = {10.1007/978-3-319-08437-4_6}, pages = {317 -- 366}, language = {en} } @misc{Rohr, author = {Rohr, Christian}, title = {Discrete-Time Leap Method For Stochastic Simulation}, series = {Proceedings of the International Workshop on Petri Nets and Software Engineering 2016, including the International Workshop on Biological Processes \& Petri Nets 2016}, journal = {Proceedings of the International Workshop on Petri Nets and Software Engineering 2016, including the International Workshop on Biological Processes \& Petri Nets 2016}, editor = {Cabac, Lawrence and Kristensen, Lars Michael and R{\"o}lke, Heiko}, publisher = {RWTH}, address = {Aachen}, url = {http://nbn-resolving.de/urn:nbn:de:0074-1591-5}, pages = {362 -- 376}, language = {en} } @incollection{HeinerRohrSchwaricketal., author = {Heiner, Monika and Rohr, Christian and Schwarick, Martin and Tovchigrechko, Alexey A.}, title = {MARCIE's secrets of efficient model checking}, series = {Transactions on petri nets and other models of concurrency XI}, booktitle = {Transactions on petri nets and other models of concurrency XI}, editor = {Koutny, Maciej and Desel, J{\"o}rg and Kleijn, Jetty}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-662-53400-7}, doi = {10.1007/978-3-662-53401-4_14}, pages = {286 -- 296}, language = {en} } @inproceedings{BlaetkeRohr, author = {Bl{\"a}tke, Mary-Ann and Rohr, Christian}, title = {A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit}, series = {Proceedings of the 6th International Workshop on Biological Processes \& Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015}, booktitle = {Proceedings of the 6th International Workshop on Biological Processes \& Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015}, editor = {Heiner, Monika and Wagler, Annegret K.}, pages = {37 -- 54}, language = {en} } @misc{GilbertHeinerJayaweeraetal., author = {Gilbert, David and Heiner, Monika and Jayaweera, Yasoda and Rohr, Christian}, title = {Towards dynamic genome scale models}, series = {Briefings in Bioinformatics}, volume = {20}, journal = {Briefings in Bioinformatics}, number = {4}, issn = {1477-4054}, doi = {10.1093/bib/bbx096}, pages = {1167 -- 1180}, language = {en} } @misc{HerajyLiuRohretal., author = {Herajy, Mostafa and Liu, Fei and Rohr, Christian and Heiner, Monika}, title = {Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models}, series = {BMC Systems Biology}, volume = {11}, journal = {BMC Systems Biology}, issn = {1752-0509}, doi = {10.1186/s12918-017-0449-6}, pages = {16}, language = {en} } @phdthesis{Rohr, author = {Rohr, Christian}, title = {Simulative analysis of coloured extended stochastic Petri nets}, address = {Cottbus}, pages = {171}, language = {en} } @misc{GilbertHeinerRohr, author = {Gilbert, David and Heiner, Monika and Rohr, Christian}, title = {Petri-net-based 2D Design of DNA Walker Circuits}, series = {Natural Computing}, volume = {17}, journal = {Natural Computing}, number = {1}, issn = {1572-9796}, doi = {10.1007/s11047-018-9671-4}, pages = {161 -- 182}, language = {en} } @misc{Rohr, author = {Rohr, Christian}, title = {Discrete-Time Leap Method For Stochastic Simulation}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {1875-8681}, doi = {10.3233/FI-2018-1680}, pages = {181 -- 198}, language = {en} } @misc{BlaetkeRohr, author = {Bl{\"a}tke, Mary-Ann and Rohr, Christian}, title = {BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {1875-8681}, doi = {10.3233/FI-2018-1682}, pages = {221 -- 254}, language = {en} } @misc{HerajyLiuRohretal., author = {Herajy, Mostafa and Liu, Fei and Rohr, Christian and Heiner, Monika}, title = {Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks}, series = {Computational Biology and Chemistry}, volume = {76}, journal = {Computational Biology and Chemistry}, issn = {1476-9271}, doi = {10.1016/j.compbiolchem.2018.05.023}, pages = {87 -- 100}, language = {en} } @misc{SchwarickRohrLiuetal., author = {Schwarick, Martin and Rohr, Christian and Liu, Fei and Assaf, George and Chodak, Jacek and Heiner, Monika}, title = {Efficient Unfolding of Coloured Petri Nets using Interval Decision Diagrams}, series = {Application and Theory of Petri Nets and Concurrency : 41st International Conference, PETRI NETS 2020, Paris, France, June 24-25, 2020, Proceedings}, journal = {Application and Theory of Petri Nets and Concurrency : 41st International Conference, PETRI NETS 2020, Paris, France, June 24-25, 2020, Proceedings}, publisher = {Springer}, address = {Cham}, isbn = {978-3-030-51830-1}, doi = {10.1007/978-3-030-51831-8_16}, pages = {324 -- 344}, abstract = {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.}, language = {en} }