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 - 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 - 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 - Liu, Fei A1 - Heiner, Monika A1 - Gilbert, David T1 - Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems T2 - Briefings in Bioinformatics Y1 - 2019 U6 - https://doi.org/10.1093/bib/bbx150 SN - 1477-4054 SN - 1467-5463 VL - 20 IS - 3 SP - 877 EP - 886 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 - 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 - 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 - 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 - 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 - 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 - Gilbert, David A1 - Heiner, Monika A1 - Jayaweera, Yasoda A1 - Rohr, Christian T1 - Towards dynamic genome scale models T2 - Briefings in Bioinformatics Y1 - 2019 U6 - https://doi.org/10.1093/bib/bbx096 SN - 1477-4054 SN - 1467-5463 VL - 20 IS - 4 SP - 1167 EP - 1180 ER -