@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} } @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{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{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} } @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} } @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} } @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{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} } @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{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} }