@inproceedings{HeinerHeiselHateburetal., author = {Heiner, Monika and Heisel, Maritta and Hatebur, Denis and Rottke, Thomas}, title = {A Problem-Oriented Approach to common Criteria Certification}, series = {Computer safety, reliability and security, 21st international conference, SAFECOMP 2002, Catania, Italy, September 10 - 13, 2002}, booktitle = {Computer safety, reliability and security, 21st international conference, SAFECOMP 2002, Catania, Italy, September 10 - 13, 2002}, editor = {Anderson, Stuart}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {3-540-44157-3}, pages = {334 -- 346}, abstract = {Abstract. There is an increasing demand to certify the security of systems according to the Common Criteria (CC). The CC distinguish several evaluation assurance levels (EALs), level EAL7 being the highest and requiring the application of formal techniques. We present a method for requirements engineering an (semi-formal and formal) modeling of systems to be certified according to the higher evaluation assurance levels of the CC. The method is problem oriented, i.e. it is driven by the environment in which the system will operate and by a mission statement. We illustrate our approach by an industrial case study, namely an electronic purse card (EPC) to be implemented on a Java Smart Card. As a novelty, we treat the mutual asymmetric authentication of the card an the terminal into which the card is inserted.}, language = {en} } @inproceedings{MertkeDeussenHeiner, author = {Mertke, Thomas and Deussen, Peter H. and Heiner, Monika}, title = {Eine anwenderorientierte Sicherheitsfachsprache zur Verifikation von Steuerungsprogrammen}, language = {de} } @incollection{Heiner, author = {Heiner, Monika}, title = {Understanding Network Behavior by Structured Representations of Transition Invariants}, language = {en} } @incollection{HeinerDonaldsonGilbert, author = {Heiner, Monika and Donaldson, Robin and Gilbert, David}, title = {Petri Nets for Systems Biology}, series = {Symbolic systems biology}, booktitle = {Symbolic systems biology}, editor = {Iyengar, M. Sriram}, publisher = {Jones and Bartlett Learning}, address = {Sudbury, Mass. [u.a.]}, isbn = {978-0-7637-5370-2}, language = {en} } @incollection{HeinerGilbertBreitlingetal., author = {Heiner, Monika and Gilbert, David and Breitling, Rainer and Orton, Richard}, title = {Computation modelling of kinase signalling cascades}, language = {en} } @incollection{HeinerGilbert, author = {Heiner, Monika and Gilbert, David}, title = {How Might Petri Nets Enhance Your Systems Biology Toolkit}, 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} } @incollection{Heiner, author = {Heiner, Monika}, title = {Understanding Network Behaviour by Structured Representations of Transition Invariants - A Petri Net Perspective on Systems and Synthetic Biology}, language = {en} } @incollection{HeinerLehrackGilbertetal., author = {Heiner, Monika and Lehrack, Sebastian and Gilbert, David and Marwan, Wolfgang}, title = {Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments}, series = {Transactions on Computational Systems Biology XI}, booktitle = {Transactions on Computational Systems Biology XI}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-04185-3}, pages = {138 -- 163}, language = {en} } @misc{GrafahrendBelauSchreiberHeineretal., author = {Grafahrend-Belau, Eva and Schreiber, Falk and Heiner, Monika and Sackmann, Andrea and Junker, Bj{\"o}rn H. and Grunwald, Stefanie and Speer, Astrid and Winder, Katja and Koch, Ina}, title = {Modularization of biochemical networks based on classification of Petri net T-invariants}, series = {BMC Bioinformatics}, volume = {Vol. 9}, journal = {BMC Bioinformatics}, issn = {1471-2105}, doi = {10.1186/1471-2105-9-90}, language = {en} } @misc{BreitlingGilbertHeineretal., author = {Breitling, Rainer and Gilbert, David and Heiner, Monika and Orton, Richard}, title = {A structured approach for the engineering of biochemical network models, illustrated for signalling pathways}, series = {Briefings in Bioinformatics}, volume = {9}, journal = {Briefings in Bioinformatics}, number = {5}, issn = {1477-4054}, doi = {10.1093/bib/bbn026}, pages = {404 -- 421}, language = {en} } @misc{SackmannHeinerKoch, author = {Sackmann, Andrea and Heiner, Monika and Koch, Ina}, title = {Application of Petri net based analysis techniques to signal transduction pathways}, series = {BMC Bioinformatics}, volume = {Vol. 7}, journal = {BMC Bioinformatics}, issn = {1471-2105}, doi = {10.1186/1471-2105-7-482}, language = {en} } @misc{PopovaZeugmannHeinerKoch, author = {Popova-Zeugmann, Louchka and Heiner, Monika and Koch, Ina}, title = {Time Petri Nets for Modelling and Analysis of Biochemical Networks}, series = {Fundamenta Informaticae}, volume = {67}, journal = {Fundamenta Informaticae}, number = {1-3}, issn = {1875-8681}, pages = {149 -- 162}, language = {en} } @misc{KochJunkerHeiner, author = {Koch, Ina and Junker, Bj{\"o}rn H. and Heiner, Monika}, title = {Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber}, series = {Bioinformatics}, volume = {21}, journal = {Bioinformatics}, number = {7}, issn = {1460-2059}, pages = {1219 -- 1226}, language = {en} } @misc{KochSchuelerHeiner, author = {Koch, Ina and Sch{\"u}ler, Markus and Heiner, Monika}, title = {STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks}, series = {In silico biology}, volume = {Vol. 5}, journal = {In silico biology}, issn = {1434-3207}, language = {en} } @misc{HeinerKochWill, author = {Heiner, Monika and Koch, Ina and Will, J{\"u}rgen}, title = {Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis}, series = {BioSystems}, volume = {75}, journal = {BioSystems}, number = {1-3}, doi = {10.1016/j.biosystems.2004.03.003}, pages = {15 -- 28}, language = {en} } @misc{VossHeinerKoch, author = {Voss, Klaus and Heiner, Monika and Koch, Ina}, title = {Steady State Analysis of Metabolic Pathways Using Petri Nets}, series = {In silico biology}, volume = {Vol. 3}, journal = {In silico biology}, issn = {1434-3207}, language = {en} } @misc{HeinerGilbert, author = {Heiner, Monika and Gilbert, David}, title = {BioModel Engineering for Multiscale Systems Biology}, series = {Progress in Biophysics and Molecular Biology}, volume = {111}, journal = {Progress in Biophysics and Molecular Biology}, number = {2-3}, issn = {1873-1732}, doi = {10.1016/j.pbiomolbio.2012.10.001}, pages = {119 -- 128}, language = {en} } @misc{LiuHeiner, author = {Liu, Fei and Heiner, Monika}, title = {Modeling membrane systems using colored stochastic Petri nets}, series = {Natural Computing}, volume = {12}, journal = {Natural Computing}, number = {4}, issn = {1572-9796}, doi = {10.1007/s11047-013-9367-8}, pages = {617 -- 629}, language = {en} } @incollection{HerajySchwarickHeiner, author = {Herajy, Mostafa and Schwarick, Martin and Heiner, Monika}, title = {Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle}, 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_7}, pages = {123 -- 141}, language = {en} } @misc{LiuHeiner, author = {Liu, Fei and Heiner, Monika}, title = {Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets}, series = {IET Systems Biology}, volume = {7}, journal = {IET Systems Biology}, number = {4}, issn = {1751-8849}, pages = {106 -- 113}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Hybrid Representation and Simulation of Stiff Biochemical Networks}, series = {Nonlinear Analysis: Hybrid Systems}, volume = {6}, journal = {Nonlinear Analysis: Hybrid Systems}, number = {4}, issn = {1751-570X}, pages = {942 -- 959}, language = {en} } @incollection{HeinerBreitlingDonaldsonetal., author = {Heiner, Monika and Breitling, Rainer and Donaldson, Robin and Gilbert, David}, title = {Biomodel Engineering - From Structure to Behavior}, series = {Transactions on Computational Systems Biology XII : Special Issue on Modeling Methodologies}, booktitle = {Transactions on Computational Systems Biology XII : Special Issue on Modeling Methodologies}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-11711-4}, doi = {10.1007/978-3-642-11712-1}, pages = {1 -- 12}, language = {en} } @misc{HeinerSriram, author = {Heiner, Monika and Sriram, K.}, title = {Structural Analysis to Determine the Core of Hypoxia Response Network}, series = {PLoS ONE}, volume = {5}, journal = {PLoS ONE}, number = {1}, issn = {1932-6203}, doi = {10.1371/journal.pone.0008600}, 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} } @misc{HeinerSoliman, author = {Heiner, Monika and Soliman, Sylvain}, title = {A Unique Transformation from Ordinary Differential Equations to Reaction Networks}, series = {PLoS one}, volume = {5}, journal = {PLoS one}, number = {12}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014284}, language = {en} } @misc{HeinerYangLiu, author = {Heiner, Monika and Yang, Ming and Liu, Fei}, title = {Modeling and analyzing biological systems using colored hierarchical Petri nets illustrated by C. elegans vulval development}, series = {Journal of Biological Systems}, volume = {22}, journal = {Journal of Biological Systems}, number = {3}, issn = {1793-6470}, doi = {10.1142/S0218339014500181}, pages = {463 -- 493}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks}, series = {Fundamenta Informaticae}, volume = {129}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {0169-2968}, pages = {49 -- 67}, 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} } @misc{HeinerVentreWikarski, author = {Heiner, Monika and Ventre, Giorgio and Wikarski, Dietmar}, title = {A Petri Net Based Methodology to Integrate Qaulitative and Quantitative Analysis}, series = {Information and Software Technology}, volume = {36}, journal = {Information and Software Technology}, number = {7}, issn = {0950-5849}, doi = {10.1016/0950-5849(94)90066-3}, pages = {435 -- 441}, language = {en} } @incollection{BlaetkeHeinerMarwan, author = {Bl{\"a}tke, Mary-Ann and Heiner, Monika and Marwan, Wolfgang}, title = {BioModel Engineering with Petri Nets}, series = {Algebraic and Discrete Mathematical Methods for Modern Biology}, booktitle = {Algebraic and Discrete Mathematical Methods for Modern Biology}, editor = {Robeva, Raina S.}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, isbn = {978-0-12-801213-0}, pages = {141 -- 193}, 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} } @incollection{LiuHeiner, author = {Liu, Fei and Heiner, Monika}, title = {Petri Nets for Modeling and Analyzing Biochemical Reaction Networks}, series = {Approaches in Integrative Bioinformatics}, booktitle = {Approaches in Integrative Bioinformatics}, editor = {Chen, Ming and Hofest{\"a}dt, Ralf}, publisher = {Springer}, address = {Heidelberg}, isbn = {978-3-642-41280-6}, doi = {10.1007/978-3-642-41281-3_9}, pages = {245 -- 272}, language = {en} } @misc{LiuHeinerYang, author = {Liu, Fei and Heiner, Monika and Yang, Ming}, title = {Representing Network Reconstruction Solutions with Colored Petri Nets}, series = {Neurocomputing}, volume = {174}, journal = {Neurocomputing}, number = {A}, issn = {0925-2312}, doi = {10.1016/j.neucom.2015.04.112}, pages = {483 -- 493}, language = {en} } @misc{SomekhPelegEranetal., author = {Somekh, Judith and Peleg, Mor and Eran, Alal and Koren, Itay and Feiglin, Ariel and Demishtein, Alik and Shiloh, Ruth and Heiner, Monika and Kong, Sek Won and Elazar, Zvulun and Kohane, Isaac}, title = {A Model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease}, series = {Biomedical Informatics}, volume = {63}, journal = {Biomedical Informatics}, issn = {1532-0464}, doi = {10.1016/j.jbi.2016.08.008}, pages = {366 -- 378}, language = {en} } @misc{BertensKleijnHilleetal., author = {Bertens, Laura M. F. and Kleijn, Jetty and Hille, Sander C. and Heiner, Monika and Koutny, Maciej and Verbeek, Fons J.}, title = {Modeling biological gradient formation: combining partial differential equations and Petri nets}, series = {Natural Computing}, volume = {15}, journal = {Natural Computing}, number = {4}, issn = {1567-7818}, doi = {10.1007/s11047-015-9531-4}, pages = {665 -- 675}, language = {en} } @misc{LiuHeinerYang, author = {Liu, Fei and Heiner, Monika and Yang, Ming}, title = {Fuzzy stochastic Petri nets for modeling biological systems with uncertain kinetic parameters}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {2}, issn = {1932-6203}, doi = {10.1371/journal.pone.0149674}, pages = {0149674}, 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} } @misc{ParvuGilbertHeineretal., author = {P{\^a}rvu, Ovidiu and Gilbert, David and Heiner, Monika and Liu, Fei and Saunders, Nigel and Shaw, Simon}, title = {Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes}, series = {ACM Transactions on Modeling and Computer Simulation (TOMACS)}, volume = {25}, journal = {ACM Transactions on Modeling and Computer Simulation (TOMACS)}, number = {2}, issn = {1558-1195}, doi = {10.1145/2742546}, pages = {13}, language = {en} } @misc{BarbotHaddadHeineretal., author = {Barbot, Benoit and Haddad, Serge and Heiner, Monika and Picaronny, Claudine}, title = {A Rare Event Method Applied to Signalling Cascades}, series = {International Journal on Advances in Systems and Measurements}, volume = {8}, journal = {International Journal on Advances in Systems and Measurements}, number = {1-2}, issn = {1942-261x}, pages = {69 -- 79}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets}, series = {Frontiers in Environmental Science}, volume = {3}, journal = {Frontiers in Environmental Science}, issn = {2296-665X}, doi = {10.3389/fenvs.2015.00053}, pages = {53}, language = {en} } @misc{LiuBlaetkeHeineretal., author = {Liu, Fei and Bl{\"a}tke, Mary-Ann and Heiner, Monika and Yang, Ming}, title = {Modelling and simulating reaction-diffusion systems using coloured Petri nets}, series = {Computers in Biology and Medicine}, volume = {53}, journal = {Computers in Biology and Medicine}, issn = {0010-4825}, doi = {10.1016/j.compbiomed.2014.07.004}, pages = {297 -- 308}, language = {en} } @misc{GaoGilbertHeineretal., author = {Gao, Quian and Gilbert, David and Heiner, Monika and Liu, Fei and Maccagnola, Daniele and Tree, David}, title = {Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing}, series = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {10}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, number = {2}, issn = {1545-5963}, doi = {10.1109/TCBB.2012.101}, pages = {337 -- 351}, language = {en} } @inproceedings{HeinerSchwarickWegener, author = {Heiner, Monika and Schwarick, Martin and Wegener, Jan-Thierry}, title = {Charlie - an extensible Petri net analysis tool}, series = {Application and Theory of Petri Nets and Concurrency, 36th International Conference, PETRI NETS 2015, Brussels, Belgium, June 21-26, 2015, Proceedings}, booktitle = {Application and Theory of Petri Nets and Concurrency, 36th International Conference, PETRI NETS 2015, Brussels, Belgium, June 21-26, 2015, Proceedings}, publisher = {Springer International Publishing}, address = {Cham}, isbn = {978-3-319-19487-5}, doi = {10.1007/978-3-319-19488-2_10}, pages = {200 -- 211}, language = {en} } @inproceedings{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets}, series = {Hybrid Systems Biology, 5th International Workshop, HSB 2016, Grenoble, France, October 20-21, 2016, Proceedings}, booktitle = {Hybrid Systems Biology, 5th International Workshop, HSB 2016, Grenoble, France, October 20-21, 2016, Proceedings}, editor = {Cinquemani, Eugenio and Donz{\´e}, Alexandre}, publisher = {Springer}, address = {Cham}, isbn = {978-3-319-47150-1}, doi = {10.1007/978-3-319-47151-8_2}, pages = {20 -- 38}, language = {en} } @inproceedings{LiuHeinerYang, author = {Liu, Fei and Heiner, Monika and Yang, Ming}, title = {Colored Petri Nets for Multiscale Systems Biology - Current Modeling and Analysis Capabilities in Snoopy}, series = {7th International Conference on Systems Biology (ISB), 2013, 23 - 25 Aug. 2013, Huangshan, China}, booktitle = {7th International Conference on Systems Biology (ISB), 2013, 23 - 25 Aug. 2013, Huangshan, China}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-4799-1387-9}, doi = {10.1109/ISB.2013.6623788}, pages = {24 -- 30}, language = {en} } @misc{HerajyLiuHeiner, author = {Herajy, Mostafa and Liu, Fei and Heiner, Monika}, title = {Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights}, series = {Nonlinear analysis: Hybrid systems}, volume = {27}, journal = {Nonlinear analysis: Hybrid systems}, issn = {1751-570X}, doi = {10.1016/j.nahs.2017.09.002}, pages = {191 -- 212}, language = {en} } @misc{LiuHeinerGilbert, author = {Liu, Fei and Heiner, Monika and Gilbert, David}, title = {Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems}, series = {Briefings in Bioinformatics}, volume = {20}, journal = {Briefings in Bioinformatics}, number = {3}, issn = {1477-4054}, doi = {10.1093/bib/bbx150}, pages = {877 -- 886}, 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} } @incollection{Heiner, author = {Heiner, Monika}, title = {From Petri Nets to Partial Differential Equations: A Petri Net Perspective on Systems and Synthetic Biology}, series = {DNA computing and molecular programming, 22nd international conference, DNA 22, Munich, Germany, September 4-8, 2016, proceedings}, booktitle = {DNA computing and molecular programming, 22nd international conference, DNA 22, Munich, Germany, September 4-8, 2016, proceedings}, editor = {Rondelez, Yannick and Woods, Damien}, publisher = {Springer}, address = {Cham}, isbn = {978-3-319-43993-8}, language = {en} } @inproceedings{HeinerMenzel, author = {Heiner, Monika and Menzel, Thomas}, title = {Modellierung und Analyse von SPS-Anwenderprogrammen mit Petri-Netzen}, series = {EKA '99, 6. Fachtagung, Braunschweig, May 1999}, booktitle = {EKA '99, 6. Fachtagung, Braunschweig, May 1999}, pages = {247 -- 265}, language = {en} } @misc{HeinerDeussenSpranger, author = {Heiner, Monika and Deussen, Peter H. and Spranger, Jochen}, title = {A Case Study in Design and Verification of Manufacturing Systems with Hierarchical Petri Nets}, series = {The International Journal of Advanced Manufacturing Technology}, volume = {15}, journal = {The International Journal of Advanced Manufacturing Technology}, number = {2}, issn = {1433-3015}, pages = {139 -- 152}, language = {en} } @inproceedings{HeinerMenzel, author = {Heiner, Monika and Menzel, Thomas}, title = {Time-related Modelling of PLC Systems with Time-less Petri Nets}, series = {Discrete event systems : analysis and control, proceedings of the 5th Workshop on Discrete Event Systems, held in Ghent, Belgium, on August 21 - 23, 2000}, booktitle = {Discrete event systems : analysis and control, proceedings of the 5th Workshop on Discrete Event Systems, held in Ghent, Belgium, on August 21 - 23, 2000}, editor = {Boel, Rene and Stremerch, G. Geert}, publisher = {Kluwer Academic Publishers}, address = {Boston [u.a.]}, isbn = {0-7923-7897-0}, pages = {275 -- 282}, language = {en} } @inproceedings{GilbertHeinerLiuetal., author = {Gilbert, David and Heiner, Monika and Liu, Fei and Saunders, Nigel}, title = {Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology}, series = {Application and Theory of Petri Nets and Concurrency, 34th International Conference, PETRI NETS 2013, Milan, Italy, June 24-28, 2013}, booktitle = {Application and Theory of Petri Nets and Concurrency, 34th International Conference, PETRI NETS 2013, Milan, Italy, June 24-28, 2013}, publisher = {Springer}, address = {Berlin [u.a.]}, pages = {230 -- 249}, language = {en} } @misc{XuCurtisPowersetal., author = {Xu, Hongwei and Curtis, Tanya Y. and Powers, Stephen J. and Raffan, Sarah and Gao, Runhong and Huang, Jianhua and Heiner, Monika and Gilbert, David and Halford, Nigel G.}, title = {Genomic, biochemical and modelling analyses of asparagine synthetases from wheat}, series = {Frontiers in Plant Science}, volume = {8}, journal = {Frontiers in Plant Science}, issn = {1664-462X}, doi = {10.3389/fpls.2017.02237}, pages = {12}, 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} } @inproceedings{Heiner, author = {Heiner, Monika}, title = {Petri Net Based Software Dependability Engineering}, series = {Proceedings, Ninth Symposium on Quality and Reliability in Electronics, 16th - 18th October, 1995, Budapest, Hungary}, booktitle = {Proceedings, Ninth Symposium on Quality and Reliability in Electronics, 16th - 18th October, 1995, Budapest, Hungary}, address = {Budapest}, pages = {181 -- 186}, language = {en} } @inproceedings{LindnerHeinerKobienia, author = {Lindner, G. and Heiner, Monika and Kobienia, Thomas}, title = {Deadlock Detection in a Distributed Implementation of a Visualization System for Medical Measurement Signals}, series = {IEEE International Conference on Systems, Man and Cybernetics, 14-17 Oct. 1996 Beijing, China, vol. 3}, booktitle = {IEEE International Conference on Systems, Man and Cybernetics, 14-17 Oct. 1996 Beijing, China, vol. 3}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {0-7803-3280-6}, doi = {10.1109/ICSMC.1996.565526}, pages = {2299 -- 2304}, language = {en} } @inproceedings{HeinerDeussenSpranger, author = {Heiner, Monika and Deussen, Peter H. and Spranger, Jochen}, title = {A Case Study in Developing Control Software of Manufacturing Systems with Hierarchical Petri Nets}, series = {Proceedings 1st International Workshop on Manufacturing and Petri Nets held at International Conference on Application and Theory of Petri Nets (ICATPN '96, Osaka, June 1996)}, booktitle = {Proceedings 1st International Workshop on Manufacturing and Petri Nets held at International Conference on Application and Theory of Petri Nets (ICATPN '96, Osaka, June 1996)}, pages = {177 -- 196}, language = {en} } @inproceedings{HeinerDeussen, author = {Heiner, Monika and Deussen, Peter H.}, title = {A Case Study in Design and Validation of Reactive Systems by Means of Petri Nets}, series = {CESA '96 IMACS Multiconference, Computational Engineering in Systems Applications, Symposium "Discrete Events and Manufacturing Systems", Lille, July 1996}, booktitle = {CESA '96 IMACS Multiconference, Computational Engineering in Systems Applications, Symposium "Discrete Events and Manufacturing Systems", Lille, July 1996}, pages = {121 -- 126}, language = {en} } @inproceedings{HeinerDeussen, author = {Heiner, Monika and Deussen, Peter H.}, title = {Petri Net Based Design and Analysis of Reactive Systems}, series = {International Workshop on Discrete Event Systems, WODES '96, 19 - 21 August 1996, John McIntyre Centre, Pollock Halls, University of Edinburgh, UK}, booktitle = {International Workshop on Discrete Event Systems, WODES '96, 19 - 21 August 1996, John McIntyre Centre, Pollock Halls, University of Edinburgh, UK}, publisher = {IEE}, address = {London}, isbn = {0-85296-664-4}, pages = {308 -- 313}, language = {en} } @inproceedings{PopovaZeugmannHeiner, author = {Popova-Zeugmann, Louchka and Heiner, Monika}, title = {Worst-case Analysis of Concurrent Systems with Duration Interval Petri Nets}, series = {EKA '97, Entwurf komplexer Automatisierungssysteme, 5. Fachtagung mit Tutorium, 21. bis 23. Mai 1997, Braunschweig}, booktitle = {EKA '97, Entwurf komplexer Automatisierungssysteme, 5. Fachtagung mit Tutorium, 21. bis 23. Mai 1997, Braunschweig}, editor = {Schnieder, Eckehard}, publisher = {Inst. f{\"u}r Regelungs- und Automatisierungstechnik}, address = {Braunschweig}, isbn = {3-9803363-4-4}, pages = {162 -- 179}, language = {en} } @inproceedings{KoenigUlrichHeiner, author = {K{\"o}nig, Hartmut and Ulrich, Andreas and Heiner, Monika}, title = {Design for Testability: A Step-wise Approach to Protocol Testing}, series = {Testing of Communicating Systems, IFIP TC6 10th International Workshop on Testing of Communicating Systems, 8-10 September 1997, Cheju Island, Korea}, booktitle = {Testing of Communicating Systems, IFIP TC6 10th International Workshop on Testing of Communicating Systems, 8-10 September 1997, Cheju Island, Korea}, editor = {Kim, Myungchul and Kang, Sungwon and Hong, Keesoo}, publisher = {Springer}, address = {Boston}, isbn = {978-1-4757-6701-8}, doi = {10.1007/978-0-387-35198-8_9}, pages = {125 -- 140}, language = {en} } @inproceedings{Heiner, author = {Heiner, Monika}, title = {Verification and Optimization of Control Programs by Petri Nets without State Explosion}, series = {Proceedings 2nd International Workshop on Manufacturing and Petri Nets held at International Conference on Application and Theory of Petri Nets (ICATPN '97, Toulouse, June 1997)}, booktitle = {Proceedings 2nd International Workshop on Manufacturing and Petri Nets held at International Conference on Application and Theory of Petri Nets (ICATPN '97, Toulouse, June 1997)}, pages = {69 -- 84}, language = {en} } @inproceedings{Heiner, author = {Heiner, Monika}, title = {On Exploiting the Analysis Power of Petri nets for the Validation of Discrete Event Systems}, series = {Proceedings, IMACS Symposium on Mathematical Modelling, February 5 - 7, 1997, Technical Univ. Vienna, Austria, 2nd Mathmod Vienna}, booktitle = {Proceedings, IMACS Symposium on Mathematical Modelling, February 5 - 7, 1997, Technical Univ. Vienna, Austria, 2nd Mathmod Vienna}, publisher = {ARGESIM}, address = {Vienna}, isbn = {3-901608-11-7}, pages = {171 -- 176}, language = {en} } @inproceedings{HeinerMenzel, author = {Heiner, Monika and Menzel, Thomas}, title = {A Petri Net Semantics for the PLC Language Instruction List}, series = {Proceedings IEE Workshop on Discrete Event Systems (WODES '98), Cagliari, August 1998}, booktitle = {Proceedings IEE Workshop on Discrete Event Systems (WODES '98), Cagliari, August 1998}, pages = {161 -- 165}, language = {en} } @inproceedings{HeinerMenzel, author = {Heiner, Monika and Menzel, Thomas}, title = {Instruction List Verification Using a Petri Net Semantics}, series = {1998 IEEE International Conference on Systems, Man and Cybernetics, San Diego, Calif., USA, October 11 - 14, 1998}, booktitle = {1998 IEEE International Conference on Systems, Man and Cybernetics, San Diego, Calif., USA, October 11 - 14, 1998}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {0-7803-4778-1}, doi = {10.1109/ICSMC.1998.725498}, pages = {716 -- 721}, language = {en} } @inproceedings{Heiner, author = {Heiner, Monika}, title = {Petri Net Based System Analysis without State Explosion}, series = {Proceedings High Performance Computing '98, Boston, April 1998, SCS Int. San Diego 1998}, booktitle = {Proceedings High Performance Computing '98, Boston, April 1998, SCS Int. San Diego 1998}, pages = {394 -- 403}, language = {en} } @misc{LiuChenHeineretal., author = {Liu, Fei and Chen, Siyuan and Heiner, Monika and Song, Hengjie}, title = {Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets}, series = {BMC Systems Biology}, volume = {12}, journal = {BMC Systems Biology}, number = {Supplement 4}, issn = {1752-0509}, doi = {10.1186/s12918-018-0568-8}, pages = {64 -- 74}, language = {en} } @misc{BaldanBocciBrigolinetal., author = {Baldan, Paolo and Bocci, Martina and Brigolin, Daniele and Cocco, Nicoletta and Heiner, Monika and Simeoni, Marta}, title = {Petri Nets for modelling and analysing Trophic Networks}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {0169-2968}, doi = {10.3233/FI-2018-1673}, pages = {27 -- 52}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {1875-8681}, doi = {10.3233/FI-2018-1674}, pages = {53 -- 80}, language = {en} } @misc{ColomboDamianiGilbertetal., author = {Colombo, Riccardo and Damiani, Chiara and Gilbert, David and Heiner, Monika and Mauri, Giancarlo and Pescini, Dario}, title = {Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes}, series = {BMC bioinformatics}, volume = {19}, journal = {BMC bioinformatics}, number = {Suppl. 7}, issn = {1471-2105}, doi = {10.1186/s12859-018-2181-7}, pages = {46 -- 59}, 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} } @inproceedings{ChodakHeiner, author = {Chodak, Jacek and Heiner, Monika}, title = {Spike - a command line tool for continuous, stochastic \& hybrid simulation of (coloured) Petri nets}, series = {Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018}, booktitle = {Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018}, editor = {Lorenz, Robert and Metzger, Johannes}, publisher = {Universit{\"a}t, Institut f{\"u}r Informatik}, address = {Augsburg}, pages = {1 -- 6}, language = {en} } @incollection{IsmailHerajyHeiner, author = {Ismail, Amr and Herajy, Mostafa and Heiner, Monika}, title = {A Graphical Approach for the Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets}, series = {Automated Reasoning for Systems Biology and Medicine}, booktitle = {Automated Reasoning for Systems Biology and Medicine}, editor = {Li{\`o}, Pietro and Zuliani, Paolo}, publisher = {Springer}, address = {Cham}, isbn = {978-3-030-17296-1}, doi = {10.1007/978-3-030-17297-8_13}, pages = {349 -- 367}, language = {en} } @misc{GilbertHeinerGhanbaretal., author = {Gilbert, David and Heiner, Monika and Ghanbar, Leila and Chodak, Jacek}, title = {Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking}, series = {BMC Bioinformatics}, volume = {20 supplement 4}, journal = {BMC Bioinformatics}, issn = {1471-2105}, doi = {10.1186/s12859-019-2690-z}, 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} } @techreport{AssafHeinerLiu, author = {Assaf, George and Heiner, Monika and Liu, Fei}, title = {Fuzzy Petri nets}, pages = {34}, abstract = {This document explains the procedure of modelling and simulating FPN and FPNC in Snoopy; please compare Figure 1 . Please note that the same steps for one net class can be equally applied to the other classes, just differentiate between uncoloured Petri nets (PN) and coloured Petri nets (PNC). Furthermore, we give more details about Latin Hybercube Sampling strategies supported by Snoopy's FPN.}, language = {en} } @misc{LiuHeinerGilbert, author = {Liu, Fei and Heiner, Monika and Gilbert, David}, title = {Hybrid modelling of biological systems: current progress and future prospects}, series = {Briefings in Bioinformatics}, volume = {23}, journal = {Briefings in Bioinformatics}, number = {3}, issn = {1477-4054}, doi = {10.1093/bib/bbac081}, pages = {1 -- 15}, abstract = {Integrated modelling of biological systems is becoming a necessity for constructing models containing the major biochemical processes of such systems in order to obtain a holistic understanding of their dynamics and to elucidate emergent behaviours. Hybrid modelling methods are crucial to achieve integrated modelling of biological systems. This paper reviews currently popular hybrid modelling methods, developed for systems biology, mainly revealing why they are proposed, how they are formed from single modelling formalisms and how to simulate them. By doing this, we identify future research requirements regarding hybrid approaches for further promoting integrated modelling of biological systems.}, language = {en} } @inproceedings{SelfGilbertHeiner, author = {Self, Timothy and Gilbert, David and Heiner, Monika}, title = {Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models}, series = {Computational Methods in Systems Biology, 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings}, booktitle = {Computational Methods in Systems Biology, 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings}, editor = {Češka, Milan and Šafr{\´a}nek, David}, publisher = {Springer}, address = {Cham}, isbn = {978-3-319-99428-4}, doi = {10.1007/978-3-319-99429-1_3}, pages = {39 -- 58}, language = {en} } @inproceedings{BadawyHerajyAwadetal., author = {Badawy, Asmaa and Herajy, Mostafa and Awad, Wael and Heiner, Monika}, title = {Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets}, series = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, booktitle = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-5386-5111-7}, doi = {10.1109/ICCES.2018.8639484}, pages = {268 -- 272}, language = {en} } @inproceedings{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets}, series = {Proceedings of the 2018 Winter Simulation Conference, (WSC 2018) Gothenburg, Sweden}, booktitle = {Proceedings of the 2018 Winter Simulation Conference, (WSC 2018) Gothenburg, Sweden}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-5386-6572-5}, doi = {10.1109/WSC.2018.8632514}, pages = {1346 -- 1357}, language = {en} } @inproceedings{IsmailHerajyHeineretal., author = {Ismail, Amr and Herajy, Mostafa and Heiner, Monika and Atlam, Elsayed}, title = {An Efficient Approach for the Hybrid Simulation of Intracellular Calcium Dynamics}, series = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, booktitle = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-5386-5111-7}, doi = {10.1109/ICCES.2018.8639261}, pages = {665 -- 670}, language = {en} } @inproceedings{HeinerHeisel, author = {Heiner, Monika and Heisel, Maritta}, title = {Modelling Safety-Critical Systems with Z and Petri Nets}, series = {Computer safety, reliability and security, 18th International Conference, SAFECOMP '99, Toulouse, France, September 27 - 29, 1999, proceedings}, booktitle = {Computer safety, reliability and security, 18th International Conference, SAFECOMP '99, Toulouse, France, September 27 - 29, 1999, proceedings}, editor = {Felici, Massimo}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {3-540-66488-2}, doi = {10.1007/3-540-48249-0_31}, pages = {361 -- 374}, language = {en} } @inproceedings{HeinerPopovaZeugmann, author = {Heiner, Monika and Popova-Zeugmann, Louchka}, title = {On Integration of Qualitative and Quantitative Analysis of Manufacturing Systems Using Petri Nets}, series = {Informatik und Automatisierung im Zeitalter der Informationsgesellschaft, 42. Internationales Wissenschaftliches Kolloquium, 22. bis 25. September 1997, Band 1}, booktitle = {Informatik und Automatisierung im Zeitalter der Informationsgesellschaft, 42. Internationales Wissenschaftliches Kolloquium, 22. bis 25. September 1997, Band 1}, publisher = {Technische Universit{\"a}t}, address = {Ilmenau}, pages = {557 -- 562}, 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} } @inproceedings{BarbotHaddadHeineretal., author = {Barbot, Benoit and Haddad, Serge and Heiner, Monika and Picaronny, Claudine}, title = {Rare Event Handling in Signalling Cascades}, series = {Proceedings, SIMUL 2014, Sixth International Conference on Advances in System Simulation}, booktitle = {Proceedings, SIMUL 2014, Sixth International Conference on Advances in System Simulation}, publisher = {IARIA}, isbn = {978-1-61208-371-1}, pages = {126 -- 131}, language = {en} } @inproceedings{LiuHeiner, author = {Liu, Fei and Heiner, Monika}, title = {Coloured Petri Nets to Model and simulate Biological Systems}, series = {Proceedings of the Workshops of the 31st International Conference on Application and Theory of Petri Nets and Other Models of Concurrency (PETRI NETS 2010)}, booktitle = {Proceedings of the Workshops of the 31st International Conference on Application and Theory of Petri Nets and Other Models of Concurrency (PETRI NETS 2010)}, pages = {70 -- 84}, 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{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {A Steering Server for Collaborative Simulation of Quantitative Petri Nets}, series = {Application and Theory of Petri Nets and Concurrency, 35th International Conference, PETRI NETS 2014, Tunis, Tunisia, June 23-27, 2014, Proceedings}, booktitle = {Application and Theory of Petri Nets and Concurrency, 35th International Conference, PETRI NETS 2014, Tunis, Tunisia, June 23-27, 2014, Proceedings}, editor = {Ciardo, Gianfranco and Kindler, Ekkart}, publisher = {Springer}, address = {Cham [u.a.]}, isbn = {978-3-319-07733-8}, pages = {374 -- 384}, language = {en} } @incollection{HeinerGilbertDonaldson, author = {Heiner, Monika and Gilbert, David and Donaldson, Robin}, title = {Petri Nets for Systems and Synthetic Biology}, language = {en} } @misc{ConnollyGilbertHeiner, author = {Connolly, Shannon and Gilbert, David and Heiner, Monika}, title = {From Epidemic to Pandemic Modelling}, series = {Frontiers in Systems Biology}, volume = {2}, journal = {Frontiers in Systems Biology}, issn = {2674-0702}, doi = {10.3389/fsysb.2022.861562}, pages = {1 -- 23}, abstract = {We present a methodology for systematically extending epidemic models to multilevel and multiscale spatio-temporal pandemic ones. Our approach builds on the use of coloured stochastic and continuous Petri nets facilitating the sound component-based extension of basic SIR models to include population stratification and also spatio-geographic information and travel connections, represented as graphs, resulting in robust stratified pandemic metapopulation models. The epidemic components and the spatial and stratification data are combined together in these coloured models and built in to the underlying expanded models. As a consequence this method is inherently easy to use, producing scalable and reusable models with a high degree of clarity and accessibility which can be read either in a deterministic or stochastic paradigm. Our method is supported by a publicly available platform PetriNuts; it enables the visual construction and editing of models; deterministic, stochastic and hybrid simulation as well as structural and behavioural analysis. All models are available as Supplementary Material, ensuring reproducibility. All uncoloured Petri nets can be animated within a web browser at https://www-dssz.informatik.tu-cottbus.de/DSSZ/Research/ModellingEpidemics, assisting the comprehension of those models. We aim to enable modellers and planners to construct clear and robust models by themselves.}, language = {en} } @misc{LiuAssafChenetal., author = {Liu, Fei and Assaf, George and Chen, Ming and Heiner, Monika}, title = {A Petri nets-based framework for whole-cell modeling}, series = {Biosystems}, volume = {210}, journal = {Biosystems}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2021.104533}, abstract = {Whole-cell modeling aims to incorporate all main genes and processes, and their interactions of a cell in one model. Whole-cell modeling has been regarded as the central aim of systems biology but also as a grand challenge, which plays essential roles in current and future systems biology. In this paper, we analyze whole-cell modeling challenges and requirements and classify them into three aspects (or dimensions): heterogeneous biochemical networks, uncertainties in components, and representation of cell structure. We then explore how to use different Petri net classes to address different aspects of whole-cell modeling requirements. Based on these analyses, we present a Petri nets-based framework for whole-cell modeling, which not only addresses many whole-cell modeling requirements, but also offers a graphical, modular, and hierarchical modeling tool. We think this framework can offer a feasible modeling approach for whole-cell model construction.}, language = {en} } @misc{AssafHeinerLiu, author = {Assaf, George and Heiner, Monika and Liu, Fei}, title = {Colouring Fuzziness for Systems Biology}, series = {Theoretical Computer Science}, volume = {875}, journal = {Theoretical Computer Science}, issn = {1879-2294}, doi = {10.1016/j.tcs.2021.04.011}, pages = {52 -- 64}, abstract = {Snoopy is a powerful modelling and simulation tool for various types of Petri nets, which have been applied to a wide range of biochemical reaction networks. We present an enhanced version of Snoopy, now supporting coloured and uncoloured stochastic, continuous and hybrid Petri Nets with fuzzy kinetic parameters. Colour helps to cope with modelling challenges imposed by larger and more complex networks. Fuzzy parameters are specifically useful when kinetic parameter values can not be precisely measured or estimated. By running fuzzy simulation we obtain output bands of the variables of interest induced by the effect of the fuzzy kinetic parameters. Simulation is always done on the uncoloured level. For this purpose, coloured fuzzy Petri nets are automatically unfolded to their corresponding uncoloured counterparts. Combining the power of fuzzy kinetic parameters with the modelling convenience of coloured Petri nets provides a new quality in user support with sophisticated modelling and analysis features.}, language = {en} } @misc{PretschnerPabelHaasetal., author = {Pretschner, Anna and Pabel, Sophie and Haas, Markus and Heiner, Monika and Marwan, Wolfgang}, title = {Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells}, series = {Frontiers in Genetics}, journal = {Frontiers in Genetics}, number = {11}, issn = {1664-8021}, doi = {10.3389/fgene.2020.612256}, pages = {17}, abstract = {Dynamics of cell fate decisions are commonly investigated by inferring temporal sequences of gene expression states by assembling snapshots of individual cells where each cell is measured once. Ordering cells according to minimal differences in expression patterns and assuming that differentiation occurs by a sequence of irreversible steps, yields unidirectional, eventually branching Markov chains with a single source node. In an alternative approach, we used multi-nucleate cells to follow gene expression taking true time series. Assembling state machines, each made from single-cell trajectories, gives a network of highly structured Markov chains of states with different source and sink nodes including cycles, revealing essential information on the dynamics of regulatory events. We argue that the obtained networks depict aspects of the Waddington landscape of cell differentiation and characterize them as reachability graphs that provide the basis for the reconstruction of the underlying gene regulatory network.}, language = {en} } @misc{AssafHeinerLiu, author = {Assaf, George and Heiner, Monika and Liu, Fei}, title = {Coloured fuzzy Petri nets for modelling and analysing membrane systems}, series = {Biosystems}, volume = {212}, journal = {Biosystems}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2021.104592}, pages = {1 -- 10}, abstract = {Membrane systems are a very powerful computational modelling formalism inspired by the internal organisation of living cells. Modelling of membrane systems is challenged by composing many structurally similar components, which may result in very large models. Furthermore, some components may suffer from a lack of precise kinetic parameters. Coloured fuzzy Petri nets combine coloured Petri nets with fuzzy kinetic parameters, and thus offer an approach to address these challenges. In this paper, we use coloured fuzzy Petri nets to model and simulate membrane systems which are enriched by fuzzy kinetic parameters. We also introduce a methodology and workflow utilising coloured fuzzy Petri nets for modelling and simulating general biological systems which have to cope with incomplete knowledge of their kinetic data.}, language = {en} } @techreport{ConnollyGilbertHeiner, author = {Connolly, Shannon and Gilbert, David and Heiner, Monika}, title = {From Epidemic to Pandemic Modelling}, publisher = {Cornell University}, address = {arXiv}, doi = {10.48550/arXiv.2107.00835}, pages = {79}, abstract = {We present a methodology for systematically extending epidemic models to multilevel and multiscale spatio-temporal pandemic ones. Our approach builds on the use of coloured stochastic and continuous Petri nets facilitating the sound component-based extension of basic SIR models to include population stratification and also spatio-geographic information and travel connections, represented as graphs, resulting in robust stratified pandemic metapopulation models. This method is inherently easy to use, producing scalable and reusable models with a high degree of clarity and accessibility which can be read either in a deterministic or stochastic paradigm. Our method is supported by a publicly available platform PetriNuts; it enables the visual construction and editing of models; deterministic, stochastic and hybrid simulation as well as structural and behavioural analysis. All the models are available as supplementary material, ensuring reproducibility.}, language = {en} } @misc{IsmailHerajyAtlametal., author = {Ismail, Amr and Herajy, Mostafa and Atlam, Elsayed and Heiner, Monika}, title = {A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets}, series = {Modelling and Simulation in Engineering}, journal = {Modelling and Simulation in Engineering}, editor = {Hong, Jing-song}, issn = {1687-5605}, doi = {10.1155/2020/4715172}, pages = {14}, abstract = {Three-dimensional modelling of biological systems is imperative to study the behaviour of dynamic systems that require the analysis of how their components interact in space. However, there are only a few formal tools that offer a convenient modelling of such systems. The traditional approach to construct and simulate 3D models is to build a system of partial differential equations (PDEs). Although this approach may be computationally efficient and has been employed by many researchers over the years, it is not always intuitive since it does not provide a visual depiction of the modelled systems. Indeed, a visual modelling can help to conceive a mental image which eventually contributes to the understanding of the problem under study. Coloured Hybrid Petri Nets () are a high-level representation of classical Petri nets that offer hybrid as well as spatial modelling of biological systems. In addition to their graphical representations, models are also scalable. This paper shows how can be used to construct and simulate systems that require three-dimensional as well as hybrid (stochastic/continuous) modelling. We use calcium diffusion in three dimensions to illustrate our main ideas. More specifically, we show that creating 3D models using can yield more flexible models as the structure can be easily scaled up and down by just modifying a few parameters. This advantage of convenient model configuration facilitates the design of different experiments without the need to alter the model structure.}, language = {en} } @inproceedings{HeinerSchwarick, author = {Heiner, Monika and Schwarick, Martin}, title = {CSL model checking of biochemical networks with Interval Decision Diagrams}, language = {en} }