TY - GEN A1 - Baldan, Paolo A1 - Bocci, Martina A1 - Brigolin, Daniele A1 - Cocco, Nicoletta A1 - Heiner, Monika A1 - Simeoni, Marta T1 - Petri Nets for modelling and analysing Trophic Networks T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1673 SN - 0169-2968 SN - 1875-8681 VL - 160 IS - 1-2 SP - 27 EP - 52 ER - TY - GEN A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1674 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 53 EP - 80 ER - TY - GEN A1 - Colombo, Riccardo A1 - Damiani, Chiara A1 - Gilbert, David A1 - Heiner, Monika A1 - Mauri, Giancarlo A1 - Pescini, Dario T1 - Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes T2 - BMC bioinformatics KW - Ensembles KW - Fluxes KW - Kinetic parameters KW - Mechanistic simulations KW - Metabolism KW - ODEs KW - Steady state KW - Systems biology Y1 - 2018 UR - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2181-7 U6 - https://doi.org/10.1186/s12859-018-2181-7 SN - 1471-2105 VL - 19 IS - Suppl. 7 SP - 46 EP - 59 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 - CHAP A1 - Chodak, Jacek A1 - Heiner, Monika ED - Lorenz, Robert ED - Metzger, Johannes T1 - Spike - a command line tool for continuous, stochastic & hybrid simulation of (coloured) Petri nets T2 - Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018 Y1 - 2018 UR - https://opus.bibliothek.uni-augsburg.de/opus4/frontdoor/deliver/index/docId/41861/file/awpn18-lorenz-metzger-OPUS.pdf#page=9 SP - 1 EP - 6 PB - Universität, Institut für Informatik CY - Augsburg ER - TY - CHAP A1 - Ismail, Amr A1 - Herajy, Mostafa A1 - Heiner, Monika ED - Liò, Pietro ED - Zuliani, Paolo T1 - A Graphical Approach for the Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets T2 - Automated Reasoning for Systems Biology and Medicine Y1 - 2019 UR - https://link.springer.com/chapter/10.1007/978-3-030-17297-8_13 SN - 978-3-030-17296-1 SN - 978-3-030-17297-8 U6 - https://doi.org/10.1007/978-3-030-17297-8_13 SP - 349 EP - 367 PB - Springer CY - Cham ER - TY - GEN A1 - Liu, Fei A1 - Heiner, Monika A1 - Gilbert, David T1 - Fuzzy Petri nets for modelling of uncertain biological systems T2 - Briefings in Bioinformatics Y1 - 2018 U6 - https://doi.org/10.1093/bib/bby118 SN - 1477-4054 SN - 1467-5463 VL - 2018 ER - TY - CHAP A1 - Ismail, Amr A1 - Herajy, Mostafa A1 - Heiner, Monika A1 - Atlam, Elsayed T1 - An Efficient Approach for the Hybrid Simulation of Intracellular Calcium Dynamics T2 - 13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt Y1 - 2018 SN - 978-1-5386-5111-7 U6 - https://doi.org/10.1109/ICCES.2018.8639261 SP - 665 EP - 670 PB - IEEE CY - Piscataway, NJ ER - TY - CHAP A1 - Badawy, Asmaa A1 - Herajy, Mostafa A1 - Awad, Wael A1 - Heiner, Monika T1 - Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets T2 - 13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt Y1 - 2018 SN - 978-1-5386-5111-7 U6 - https://doi.org/10.1109/ICCES.2018.8639484 SP - 268 EP - 272 PB - IEEE CY - Piscataway, NJ ER - TY - CHAP A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets T2 - Proceedings of the 2018 Winter Simulation Conference, (WSC 2018) Gothenburg, Sweden Y1 - 2018 SN - 978-1-5386-6572-5 U6 - https://doi.org/10.1109/WSC.2018.8632514 N1 - referierter Beitrag SP - 1346 EP - 1357 PB - IEEE CY - Piscataway, NJ ER - TY - CHAP A1 - Self, Timothy A1 - Gilbert, David A1 - Heiner, Monika ED - Češka, Milan ED - Šafránek, David T1 - Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models T2 - Computational Methods in Systems Biology, 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings Y1 - 2018 SN - 978-3-319-99428-4 U6 - https://doi.org/10.1007/978-3-319-99429-1_3 N1 - referierter Beitrag SP - 39 EP - 58 PB - Springer CY - Cham ER - TY - GEN A1 - Chodak, Jacek A1 - Heiner, Monika ED - Bergenthum, Robin ED - Kindler, Ekkart T1 - SPIKE – as a Supporting Tool for a Model Parameters Optimization via Branched Simulations T2 - Algorithms and Tools for Petri Nets : Proceedings of the Workshop AWPN 2019, Hagen, Germany, October 10–11, 2019, Tagungsband Y1 - 2019 UR - https://ub-deposit.fernuni-hagen.de/receive/mir_mods_00001564 SP - 18 EP - 23 PB - Uni Hagen CY - Hagen ER - TY - CHAP A1 - Heiner, Monika ED - Reisig, Wolfgang ED - Rozenberg, Grzegorz T1 - Petri Nets for BioModel Engineering: A Personal Perspective T2 - Carl Adam Petri: Ideas, Personality, Impact Y1 - 2019 UR - https://www.springer.com/de/book/9783319961538 SN - 978-3-319-96153-8 SN - 978-3-319-96154-5 U6 - https://doi.org/10.1007/978-3-319-96154-5_25 SP - 205 EP - 216 PB - Springer CY - Cham ER - TY - GEN A1 - Nickaeen, Niloofar A1 - Ghaisari, Jafar A1 - Heiner, Monika A1 - Moein, Shiva A1 - Gheisari, Yousof T1 - Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution T2 - Scientific Reports Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-48865-z SN - 2045-2322 IS - 9 ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Ghanbar, Leila A1 - Chodak, Jacek T1 - Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking T2 - BMC Bioinformatics Y1 - 2019 U6 - https://doi.org/10.1186/s12859-019-2690-z SN - 1471-2105 VL - 20 supplement 4 ER - TY - GEN A1 - Chodak, Jacek A1 - Heiner, Monika ED - Bortolussi, Luca ED - Sanguinetti, Guido T1 - Spike – reproducible simulation experiments with configuration file branching T2 - Computational Methods in Systems Biology : 17th International Conference, CMSB 2019, Trieste, Italy, September 18–20, 2019, Proceedings Y1 - 2019 SN - 978-3-030-31303-6 SN - 978-3-030-31304-3 U6 - https://doi.org/http://dx.doi.org/10.1007/978-3-030-31304-3_19 SP - 315 EP - 321 PB - Springer ER - TY - GEN A1 - Assaf, George A1 - Heiner, Monika A1 - Liu, Fei ED - Bortolussi, Luca ED - Sanguinetti, Guido T1 - Biochemical reaction networks with fuzzy kinetic parameters in Snoopy T2 - Computational Methods in Systems Biology : 17th International Conference, CMSB 2019, Trieste, Italy, September 18–20, 2019, Proceedings Y1 - 2019 SN - 978-3-030-31303-6 SN - 978-3-030-31304-3 U6 - https://doi.org/http://dx.doi.org/10.1007/978-3-030-31304-3_17 SP - 302 EP - 307 PB - Springer ER - TY - GEN A1 - Assaf, George A1 - Heiner, Monika ED - Bergenthum, Robin ED - Kindler, Ekkart T1 - Spatial Encoding of Systems Using Coloured Petri Nets T2 - Algorithms and Tools for Petri Nets : Proceedings of the Workshop AWPN 2019 Y1 - 2019 UR - https://ub-deposit.fernuni-hagen.de/receive/mir_mods_00001564 SP - 38 EP - 44 PB - Universität CY - Hagen ER - TY - GEN A1 - Liu, Fei A1 - Sun, Wujie A1 - Heiner, Monika A1 - Gilbert, David T1 - Hybrid modelling of biological systems using fuzzy continuous Petri nets T2 - Briefings in Bioinformatics N2 - Integrated modelling of biological systems is challenged by composing components with sufficient kinetic data and components with insufficient kinetic data or components built only using experts’ experience and knowledge. Fuzzy continuous Petri nets (FCPNs) combine continuous Petri nets with fuzzy inference systems, and thus offer an hybrid uncertain/certain approach to integrated modelling of such biological systems with uncertainties. In this paper, we give a formal definition and a corresponding simulation algorithm of FCPNs, and briefly introduce the FCPN tool that we have developed for implementing FCPNs. We then present a methodology and workflow utilizing FCPNs to achieve hybrid (uncertain/certain) modelling of biological systems illustrated with a case study of the Mercaptopurine metabolic pathway. We hope this research will promote the wider application of FCPNs and address the uncertain/certain integrated modelling challenge in the systems biology area. KW - systems biology KW - integrated modelling KW - fuzzy continuous Petri nets KW - uncertainties KW - hybrid simulation Y1 - 2019 U6 - https://doi.org/10.1093/bib/bbz114 VL - 22(2021) SP - 438 EP - 450 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 -