@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{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} } @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{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} } @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} } @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{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} } @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{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} } @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} } @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{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{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} } @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} } @phdthesis{Herajy, author = {Herajy, Mostafa}, title = {Computational Steering of Multi-Scale Biochemical Networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-27255}, pages = {159}, language = {en} }