TY - GEN A1 - George, Sandra A1 - Noack, M. A1 - Vanek, Monika A1 - Rentzsch, J. A1 - Röber, Nadja A1 - Roggenbuck, Dirk A1 - Conrad, Karsten A1 - Küpper, Jan-Heiner T1 - Expression of nicotinic acetylcholine receptor subunits in HEp-2 cells for immunodetection of autoantibody specificities in sera fro Myasthenia gravis patients T2 - Clinical Hemorheology and Microcirculation Y1 - 2015 U6 - https://doi.org/10.3233/CH-151999 SN - 1875-8622 SN - 1386-0291 VL - 61 IS - 2 SP - 385 EP - 396 ER - TY - CHAP A1 - Gilbert, David A1 - Heiner, Monika A1 - Liu, Fei A1 - Saunders, Nigel T1 - Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology T2 - Application and Theory of Petri Nets and Concurrency, 34th International Conference, PETRI NETS 2013, Milan, Italy, June 24-28, 2013 Y1 - 2013 UR - http://link.springer.com/chapter/10.1007%2F978-3-642-38697-8_13 N1 - referiert SP - 230 EP - 249 PB - Springer CY - Berlin [u.a.] ER - TY - GEN A1 - Heiner, Monika T1 - Petri Nets Research at BTU in Cottbus, Germany T2 - Petri Net Newsletter Y1 - 2014 SN - 0391-1804 SN - 0931-1084 VL - 83 SP - 19 EP - 25 ER - TY - GEN A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Heiner, Monika T1 - Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights T2 - Nonlinear analysis: Hybrid systems Y1 - 2017 UR - https://www.sciencedirect.com/science/article/pii/S1751570X17300808 U6 - https://doi.org/10.1016/j.nahs.2017.09.002 SN - 1751-570X VL - 27 SP - 191 EP - 212 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 - 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 - TY - GEN A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian A1 - Heiner, Monika T1 - Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models T2 - BMC Systems Biology Y1 - 2017 UR - https://link.springer.com/epdf/10.1186/s12918-017-0449-6?author_access_token=54a9mC7bl_t-6TjlSqdqNG_BpE1tBhCbnbw3BuzI2RMKIgJAZ9nr6Hm0LME2XT_scd04D6IjdxN2SajBh1-bYG6TDIkKQYJrtczMPmCV290rFO3LRZ0YPUqCBRlezXRq1AJVJo-7YPWMt0G3LF52OA%3D%3D U6 - https://doi.org/10.1186/s12918-017-0449-6 SN - 1752-0509 VL - 11 ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Ghanbar, Leila T1 - Personalised models for human – gut microbiota interaction T2 - PeerJ preprints Y1 - 2017 UR - https://peerj.com/preprints/3267/ U6 - https://doi.org/10.7287/peerj.preprints.3267v1 SN - 2167-9843 VL - 5 IS - e3267v1 ER - TY - CHAP A1 - Heiner, Monika ED - Rondelez, Yannick ED - Woods, Damien T1 - From Petri Nets to Partial Differential Equations: A Petri Net Perspective on Systems and Synthetic Biology T2 - DNA computing and molecular programming, 22nd international conference, DNA 22, Munich, Germany, September 4-8, 2016, proceedings Y1 - 2016 UR - http://link.springer.com/book/10.1007%2F978-3-319-43994-5 SN - 978-3-319-43993-8 SN - 978-3-319-43994-5 PB - Springer CY - Cham ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Rohr, Christian T1 - Petri-net-based 2D Design of DNA Walker Circuits T2 - Natural Computing Y1 - 2018 U6 - https://doi.org/10.1007/s11047-018-9671-4 SN - 1572-9796 SN - 1567-7818 VL - 17 IS - 1 SP - 161 EP - 182 ER - TY - GEN A1 - Xu, Hongwei A1 - Curtis, Tanya Y. A1 - Powers, Stephen J. A1 - Raffan, Sarah A1 - Gao, Runhong A1 - Huang, Jianhua A1 - Heiner, Monika A1 - Gilbert, David A1 - Halford, Nigel G. T1 - Genomic, biochemical and modelling analyses of asparagine synthetases from wheat T2 - Frontiers in Plant Science Y1 - 2018 U6 - https://doi.org/10.3389/fpls.2017.02237 SN - 1664-462X VL - 8 ER - TY - CHAP A1 - Heiner, Monika T1 - Petri Net Based Software Dependability Engineering T2 - Proceedings, Ninth Symposium on Quality and Reliability in Electronics, 16th - 18th October, 1995, Budapest, Hungary Y1 - 1995 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1995_budapest.pdf SP - 181 EP - 186 CY - Budapest ER - TY - CHAP A1 - Lindner, G. A1 - Heiner, Monika A1 - Kobienia, Thomas T1 - Deadlock Detection in a Distributed Implementation of a Visualization System for Medical Measurement Signals T2 - IEEE International Conference on Systems, Man and Cybernetics, 14-17 Oct. 1996 Beijing, China, vol. 3 Y1 - 1996 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1996_bejing.pdf SN - 0-7803-3280-6 U6 - https://doi.org/10.1109/ICSMC.1996.565526 N1 - referiert SP - 2299 EP - 2304 PB - IEEE CY - Piscataway, NJ ER - TY - CHAP A1 - Heiner, Monika A1 - Deussen, Peter H. A1 - Spranger, Jochen T1 - A Case Study in Developing Control Software of Manufacturing Systems with Hierarchical Petri Nets T2 - 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) Y1 - 1996 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1996_osaka.pdf N1 - referiert SP - 177 EP - 196 ER - TY - CHAP A1 - Heiner, Monika A1 - Deussen, Peter H. T1 - A Case Study in Design and Validation of Reactive Systems by Means of Petri Nets T2 - CESA '96 IMACS Multiconference, Computational Engineering in Systems Applications, Symposium "Discrete Events and Manufacturing Systems", Lille, July 1996 Y1 - 1996 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1996_lille.pdf N1 - referiert SP - 121 EP - 126 ER - TY - CHAP A1 - Heiner, Monika A1 - Deussen, Peter H. T1 - Petri Net Based Design and Analysis of Reactive Systems T2 - International Workshop on Discrete Event Systems, WODES '96, 19 - 21 August 1996, John McIntyre Centre, Pollock Halls, University of Edinburgh, UK Y1 - 1996 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1996_edingburgh.pdf SN - 0-85296-664-4 N1 - referiert SP - 308 EP - 313 PB - IEE CY - London ER - TY - CHAP A1 - Popova-Zeugmann, Louchka A1 - Heiner, Monika ED - Schnieder, Eckehard T1 - Worst-case Analysis of Concurrent Systems with Duration Interval Petri Nets T2 - EKA '97, Entwurf komplexer Automatisierungssysteme, 5. Fachtagung mit Tutorium, 21. bis 23. Mai 1997, Braunschweig Y1 - 1997 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1997_popova_heiner_eka97.pdf SN - 3-9803363-4-4 N1 - referiert SP - 162 EP - 179 PB - Inst. für Regelungs- und Automatisierungstechnik CY - Braunschweig ER - TY - CHAP A1 - König, Hartmut A1 - Ulrich, Andreas A1 - Heiner, Monika ED - Kim, Myungchul ED - Kang, Sungwon ED - Hong, Keesoo T1 - Design for Testability: A Step-wise Approach to Protocol Testing T2 - Testing of Communicating Systems, IFIP TC6 10th International Workshop on Testing of Communicating Systems, 8-10 September 1997, Cheju Island, Korea Y1 - 1997 SN - 978-1-4757-6701-8 SN - 978-0-387-35198-8 U6 - https://doi.org/10.1007/978-0-387-35198-8_9 N1 - referiert SP - 125 EP - 140 PB - Springer CY - Boston ER - TY - CHAP A1 - Heiner, Monika A1 - Menzel, Thomas T1 - Modellierung und Analyse von SPS-Anwenderprogrammen mit Petri-Netzen T2 - EKA '99, 6. Fachtagung, Braunschweig, May 1999 Y1 - 1999 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1999_eka99.pdf N1 - referiert SP - 247 EP - 265 ER - TY - GEN A1 - Heiner, Monika A1 - Deussen, Peter H. A1 - Spranger, Jochen T1 - A Case Study in Design and Verification of Manufacturing Systems with Hierarchical Petri Nets T2 - The International Journal of Advanced Manufacturing Technology Y1 - 1999 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1999_heiner_deussen_spranger_journalAMT_productionCell.pdf SN - 1433-3015 SN - 0268-3768 VL - 15 IS - 2 SP - 139 EP - 152 ER - TY - CHAP A1 - Heiner, Monika A1 - Heisel, Maritta ED - Felici, Massimo T1 - Modelling Safety-Critical Systems with Z and Petri Nets T2 - Computer safety, reliability and security, 18th International Conference, SAFECOMP '99, Toulouse, France, September 27 - 29, 1999, proceedings Y1 - 1999 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1999_heiner_heisel_safecomp_lncs1698.pdf SN - 3-540-66488-2 U6 - https://doi.org/10.1007/3-540-48249-0_31 SP - 361 EP - 374 PB - Springer CY - Berlin [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Menzel, Thomas ED - Boel, Rene ED - Stremerch, G. Geert T1 - Time-related Modelling of PLC Systems with Time-less Petri Nets T2 - Discrete event systems : analysis and control, proceedings of the 5th Workshop on Discrete Event Systems, held in Ghent, Belgium, on August 21 - 23, 2000 Y1 - 2000 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/2000_gent_wodes.pdf SN - 0-7923-7897-0 N1 - referiert SP - 275 EP - 282 PB - Kluwer Academic Publishers CY - Boston [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Popova-Zeugmann, Louchka T1 - On Integration of Qualitative and Quantitative Analysis of Manufacturing Systems Using Petri Nets T2 - Informatik und Automatisierung im Zeitalter der Informationsgesellschaft, 42. Internationales Wissenschaftliches Kolloquium, 22. bis 25. September 1997, Band 1 Y1 - 1997 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1997_heiner_popova_ilmenau.pdf N1 - referiert SP - 557 EP - 562 PB - Technische Universität CY - Ilmenau ER - TY - CHAP A1 - Heiner, Monika T1 - Verification and Optimization of Control Programs by Petri Nets without State Explosion T2 - 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) Y1 - 1997 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1997_heiner_toulouse.pdf N1 - referiert SP - 69 EP - 84 ER - TY - CHAP A1 - Heiner, Monika T1 - On Exploiting the Analysis Power of Petri nets for the Validation of Discrete Event Systems T2 - Proceedings, IMACS Symposium on Mathematical Modelling, February 5 - 7, 1997, Technical Univ. Vienna, Austria, 2nd Mathmod Vienna Y1 - 1997 SN - 3-901608-11-7 N1 - referiert SP - 171 EP - 176 PB - ARGESIM CY - Vienna ER - TY - CHAP A1 - Heiner, Monika A1 - Menzel, Thomas T1 - A Petri Net Semantics for the PLC Language Instruction List T2 - Proceedings IEE Workshop on Discrete Event Systems (WODES '98), Cagliari, August 1998 Y1 - 1998 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1998_wodes.pdf N1 - referiert SP - 161 EP - 165 ER - TY - CHAP A1 - Heiner, Monika A1 - Menzel, Thomas T1 - Instruction List Verification Using a Petri Net Semantics T2 - 1998 IEEE International Conference on Systems, Man and Cybernetics, San Diego, Calif., USA, October 11 - 14, 1998 Y1 - 1998 SN - 0-7803-4778-1 U6 - https://doi.org/10.1109/ICSMC.1998.725498 N1 - referiert SP - 716 EP - 721 PB - IEEE CY - Piscataway, NJ ER - TY - CHAP A1 - Heiner, Monika T1 - Petri Net Based System Analysis without State Explosion T2 - Proceedings High Performance Computing '98, Boston, April 1998, SCS Int. San Diego 1998 Y1 - 1998 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1998_boston.pdf N1 - referiert SP - 394 EP - 403 ER - TY - GEN A1 - Gambin, Anna A1 - Heiner, Monika T1 - Advances in Biological processes and Petri nets (BioPPN) T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1671 SN - 0169-2968 SN - 1875-8681 VL - 160 IS - 1-2 SP - V EP - VII ER - TY - GEN A1 - Liu, Fei A1 - Chen, Siyuan A1 - Heiner, Monika A1 - Song, Hengjie T1 - Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets T2 - BMC Systems Biology Y1 - 2018 U6 - https://doi.org/10.1186/s12918-018-0568-8 SN - 1752-0509 VL - 12 IS - Supplement 4 SP - 64 EP - 74 ER - 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 - TY - GEN A1 - Ismail, Amr A1 - Herajy, Mostafa A1 - Atlam, Elsayed A1 - Heiner, Monika ED - Hong, Jing-song T1 - A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets T2 - Modelling and Simulation in Engineering N2 - 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. Y1 - 2020 UR - https://www.hindawi.com/journals/mse/2020/4715172/ U6 - https://doi.org/10.1155/2020/4715172 SN - 1687-5605 ER - TY - GEN A1 - Pretschner, Anna A1 - Pabel, Sophie A1 - Haas, Markus A1 - Heiner, Monika A1 - Marwan, Wolfgang T1 - Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells T2 - Frontiers in Genetics N2 - 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. KW - single cell time series KW - gene regulatory network KW - Petri net KW - Markov chain KW - systems biology KW - Waddington landscape Y1 - 2021 U6 - https://doi.org/10.3389/fgene.2020.612256 SN - 1664-8021 N1 - This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). IS - 11 ER - TY - RPRT A1 - Assaf, George A1 - Heiner, Monika A1 - Liu, Fei T1 - Fuzzy Petri nets N2 - 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. KW - Fuzzy Petri Nets coloured fuzzy Petri nets Snoopy Y1 - 2021 UR - https://www-dssz.informatik.tu-cottbus.de/publications/btu-reports/fpn_manual.pdf ER - TY - RPRT A1 - Connolly, Shannon A1 - Gilbert, David A1 - Heiner, Monika T1 - From Epidemic to Pandemic Modelling N2 - 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. KW - SIR model KW - coloured Petri nets KW - stochastic Petri nets KW - continuous Petri nets KW - ODEs KW - simulation KW - geographic spatio-temporal 20 modelling KW - multiscale models Y1 - 2021 U6 - https://doi.org/10.48550/arXiv.2107.00835 PB - Cornell University CY - arXiv ER - TY - GEN A1 - Connolly, Shannon A1 - Gilbert, David A1 - Heiner, Monika T1 - From Epidemic to Pandemic Modelling T2 - Frontiers in Systems Biology N2 - 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. KW - SIR model KW - coloured Petri nets KW - stochastic Petri nets KW - continuous Petri nets KW - ODEs KW - simulation KW - geographic spatio-temporal modelling KW - multiscale models Y1 - 2022 UR - https://www.frontiersin.org/articles/10.3389/fsysb.2022.861562/full U6 - https://doi.org/10.3389/fsysb.2022.861562 SN - 2674-0702 VL - 2 SP - 1 EP - 23 ER - TY - GEN A1 - Liu, Fei A1 - Heiner, Monika A1 - Gilbert, David T1 - Hybrid modelling of biological systems: current progress and future prospects T2 - Briefings in Bioinformatics N2 - 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. KW - biological modelling KW - hybrid modelling KW - modelling formalisms Y1 - 2022 UR - https://academic.oup.com/bib/article/23/3/bbac081/6555400 U6 - https://doi.org/10.1093/bib/bbac081 SN - 1477-4054 SN - 1467-5463 VL - 23 IS - 3 SP - 1 EP - 15 ER - TY - GEN A1 - Assaf, George A1 - Heiner, Monika A1 - Liu, Fei T1 - Coloured fuzzy Petri nets for modelling and analysing membrane systems T2 - Biosystems N2 - 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. KW - Fuzzy membrane systems KW - Parameter uncertainties KW - Coloured fuzzy stochastic Petri nets KW - Coloured fuzzy continuous Petri net KW - Coloured fuzzy hybrid Petri net KW - Modelling KW - Fuzzy simulation Y1 - 2022 UR - https://www.sciencedirect.com/science/article/pii/S0303264721002318?via%3Dihub U6 - https://doi.org/10.1016/j.biosystems.2021.104592 SN - 0303-2647 VL - 212 SP - 1 EP - 10 ER - TY - GEN A1 - Assaf, George A1 - Heiner, Monika A1 - Liu, Fei T1 - Colouring Fuzziness for Systems Biology T2 - Theoretical Computer Science N2 - 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. KW - fuzzy logic KW - Fuzzy kinetic parameters KW - Coloured fuzzy continuous, stochastic and hybrid Petri nets KW - Modelling and simulation KW - Modelling uncertainty Y1 - 2021 UR - https://www.sciencedirect.com/science/article/abs/pii/S0304397521002152?via%3Dihub U6 - https://doi.org/10.1016/j.tcs.2021.04.011 SN - 1879-2294 SN - 0304-3975 VL - 875 SP - 52 EP - 64 ER - TY - GEN A1 - Liu, Fei A1 - Assaf, George A1 - Chen, Ming A1 - Heiner, Monika T1 - A Petri nets-based framework for whole-cell modeling T2 - Biosystems N2 - 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. KW - Whole-cell modeling KW - Systems biology KW - Petri nets KW - Modeling framework Y1 - 2021 UR - https://www.sciencedirect.com/science/article/abs/pii/S0303264721001738?via%3Dihub U6 - https://doi.org/10.1016/j.biosystems.2021.104533 SN - 0303-2647 SN - 1872-8324 VL - 210 ER -