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 - 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 - 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 - Blätke, Mary-Ann A1 - Rohr, Christian ED - Heiner, Monika ED - Wagler, Annegret K. T1 - A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit T2 - Proceedings of the 6th International Workshop on Biological Processes & Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015 Y1 - 2015 UR - http://ceur-ws.org/Vol-1373/ N1 - peer reviewed SP - 37 EP - 54 ER - TY - CHAP A1 - Heiner, Monika A1 - Rohr, Christian A1 - Schwarick, Martin A1 - Streif, Stefan ED - Quaglia, Paola T1 - A Comparative Study of Stochastic Analysis Techniques T2 - CMSB '10, 8th Conference on Computational Methods in Systems Biology, Trento, Italy — September 29 - October 01, 2010 Y1 - 2010 SN - 978-1-4503-0068-1 U6 - https://doi.org/10.1145/1839764.1839776 SP - 96 EP - 106 PB - ACM CY - New York, NY 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 - 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 - Somekh, Judith A1 - Peleg, Mor A1 - Eran, Alal A1 - Koren, Itay A1 - Feiglin, Ariel A1 - Demishtein, Alik A1 - Shiloh, Ruth A1 - Heiner, Monika A1 - Kong, Sek Won A1 - Elazar, Zvulun A1 - Kohane, Isaac T1 - A Model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease T2 - Biomedical Informatics Y1 - 2016 U6 - https://doi.org/10.1016/j.jbi.2016.08.008 SN - 1532-0464 VL - 63 SP - 366 EP - 378 ER - TY - CHAP A1 - Blätke, Mary-Ann A1 - Rohr, Christian A1 - Heiner, Monika A1 - Marwan, Wolfgang ED - Benner, Peter T1 - A Petri Net based Framework for Biomodel Engineering T2 - Large-Scale Networks in Engineering and Life Sciences KW - Automatic network reconstruction KW - Biomodel engineering KW - Dynamic systems modelling KW - Modular modelling KW - Petri nets KW - Molecular regulatory networks KW - Reverse engineering Y1 - 2014 SN - 978-3-319-08436-7 U6 - https://doi.org/10.1007/978-3-319-08437-4_6 SP - 317 EP - 366 PB - Springer CY - Heidelberg ER - TY - GEN A1 - Heiner, Monika A1 - Ventre, Giorgio A1 - Wikarski, Dietmar T1 - A Petri Net Based Methodology to Integrate Qaulitative and Quantitative Analysis T2 - Information and Software Technology Y1 - 1994 U6 - https://doi.org/10.1016/0950-5849(94)90066-3 SN - 0950-5849 VL - 36 IS - 7 SP - 435 EP - 441 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 - 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 - TY - CHAP A1 - Heiner, Monika A1 - Heisel, Maritta A1 - Hatebur, Denis A1 - Rottke, Thomas ED - Anderson, Stuart T1 - A Problem-Oriented Approach to common Criteria Certification T2 - Computer safety, reliability and security, 21st international conference, SAFECOMP 2002, Catania, Italy, September 10 - 13, 2002 N2 - Abstract. There is an increasing demand to certify the security of systems according to the Common Criteria (CC). The CC distinguish several evaluation assurance levels (EALs), level EAL7 being the highest and requiring the application of formal techniques. We present a method for requirements engineering an (semi-formal and formal) modeling of systems to be certified according to the higher evaluation assurance levels of the CC. The method is problem oriented, i.e. it is driven by the environment in which the system will operate and by a mission statement. We illustrate our approach by an industrial case study, namely an electronic purse card (EPC) to be implemented on a Java Smart Card. As a novelty, we treat the mutual asymmetric authentication of the card an the terminal into which the card is inserted. Y1 - 2002 SN - 3-540-44157-3 SP - 334 EP - 346 PB - Springer CY - Berlin [u.a.] ER - TY - GEN A1 - Barbot, Benoit A1 - Haddad, Serge A1 - Heiner, Monika A1 - Picaronny, Claudine T1 - A Rare Event Method Applied to Signalling Cascades T2 - International Journal on Advances in Systems and Measurements Y1 - 2015 UR - http://www.iariajournals.org/systems_and_measurements/sysmea_v8_n12_2015_paged.pdf SN - 1942-261x VL - 8 IS - 1-2 SP - 69 EP - 79 ER - TY - GEN A1 - Heiner, Monika A1 - Mertke, Thomas A1 - Deussen, Peter H. T1 - A Safety-Oriented Technical Language for the Requirement Specification in Control Engineering (Eine Sicherheitsfachsprache zur Formulierung steuerungstechnischer Anforderungen); in German Y1 - 2001 ER - TY - CHAP A1 - Herajy, Mostafa A1 - Heiner, Monika ED - Ciardo, Gianfranco ED - Kindler, Ekkart T1 - A Steering Server for Collaborative Simulation of Quantitative Petri Nets T2 - Application and Theory of Petri Nets and Concurrency, 35th International Conference, PETRI NETS 2014, Tunis, Tunisia, June 23-27, 2014, Proceedings Y1 - 2014 UR - http://link.springer.com/chapter/10.1007%2F978-3-319-07734-5_21 SN - 978-3-319-07733-8 SP - 374 EP - 384 PB - Springer CY - Cham [u.a.] ER - TY - GEN A1 - Breitling, Rainer A1 - Gilbert, David A1 - Heiner, Monika A1 - Orton, Richard T1 - A structured approach for the engineering of biochemical network models, illustrated for signalling pathways T2 - Briefings in Bioinformatics Y1 - 2008 U6 - https://doi.org/10.1093/bib/bbn026 SN - 1477-4054 VL - 9 IS - 5 SP - 404 EP - 421 ER - TY - GEN A1 - Heiner, Monika A1 - Soliman, Sylvain T1 - A Unique Transformation from Ordinary Differential Equations to Reaction Networks T2 - PLoS one Y1 - 2010 U6 - https://doi.org/10.1371/journal.pone.0014284 SN - 1932-6203 VL - 5 IS - 12 ER - TY - CHAP A1 - Herajy, Mostafa A1 - Heiner, Monika ED - Cinquemani, Eugenio ED - Donzé, Alexandre T1 - Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets T2 - Hybrid Systems Biology, 5th International Workshop, HSB 2016, Grenoble, France, October 20-21, 2016, Proceedings Y1 - 2016 UR - http://link.springer.com/chapter/10.1007/978-3-319-47151-8_2 SN - 978-3-319-47150-1 SN - 978-3-319-47151-8 U6 - https://doi.org/10.1007/978-3-319-47151-8_2 N1 - referierte Konferenzveröffentlichung SP - 20 EP - 38 PB - Springer CY - Cham 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 - 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 - 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 - CHAP A1 - Deussen, Peter H. T1 - Algorithmic Aspects of Concurrent Automata T2 - Workshop Concurrency, Specification & Programming, September 28 - 30, 1998 Y1 - 1998 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1998_pd_csp.pdf N1 - referiert SP - 39 EP - 70 PB - Professoren des Institutes für Informatik CY - Berlin 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 - 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 - GEN A1 - Gilbert, David A1 - Breitling, Rainer A1 - Heiner, Monika A1 - Donaldson, Robin T1 - An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways KW - Petri Nets Y1 - 2009 ER - TY - THES A1 - Deussen, Peter H. T1 - Analyse verteilter Systeme mit Hilfe von Prozeßautomaten KW - Verteilte Systeme KW - Prozeßautomaten KW - Modelchecking KW - Verifikation KW - DCTL KW - Petri-Netze Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-000000275 PB - Brandenburgische Techn. Univ. CY - Cottbus ER - TY - JOUR A1 - Heiner, Monika A1 - Koch, Ina A1 - Voss, Klaus T1 - Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets, Proc. Y1 - 2001 ER - TY - GEN A1 - Sackmann, Andrea A1 - Heiner, Monika A1 - Koch, Ina T1 - Application of Petri net based analysis techniques to signal transduction pathways T2 - BMC Bioinformatics Y1 - 2006 U6 - https://doi.org/10.1186/1471-2105-7-482 SN - 1471-2105 VL - Vol. 7 ER - TY - GEN A1 - Koch, Ina A1 - Junker, Björn H. A1 - Heiner, Monika T1 - Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber T2 - Bioinformatics Y1 - 2005 UR - http://bioinformatics.oupjournals.org/cgi/content/abstract/bti145?ijkey=58saZCDV5w9LY&keytype=ref SN - 1460-2059 VL - 21 IS - 7 SP - 1219 EP - 1226 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 - CHAP ED - Heiner, Monika T1 - Biological Processes & Petri Nets 5th International Workshop BioPPN 2014, Tunis, 23 June 2014, Proceedings KW - Petri nets Biological Processes Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1159-5 ER - TY - CHAP ED - Heiner, Monika ED - Wagler, Annegret K. T1 - Biological Processes & Petri Nets, 6th International Workshop BioPPN 2015, Brussels, 22 June 2015, Proceedings Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1373-4 ER - TY - CHAP ED - Balbo, Gianfranco ED - Heiner, Monika T1 - Biological Processes & Petri Nets, Proceedings of the International Workshop on Biological Processes & Petri Nets, BioPPN 2013, Milano, Italy, June 24, 2013 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-988-2 UR - http://ceur-ws.org/Vol-988/ SN - 1613-0073 PB - RWTH CY - Aachen ER - TY - CHAP A1 - Heiner, Monika A1 - Breitling, Rainer A1 - Donaldson, Robin A1 - Gilbert, David T1 - Biomodel Engineering - From Structure to Behavior T2 - Transactions on Computational Systems Biology XII : Special Issue on Modeling Methodologies Y1 - 2010 SN - 978-3-642-11711-4 SN - 978-3-642-11712-1 U6 - https://doi.org/10.1007/978-3-642-11712-1 SP - 1 EP - 12 PB - Springer CY - Berlin [u.a.] ER - TY - GEN A1 - Heiner, Monika A1 - Gilbert, David T1 - BioModel Engineering for Multiscale Systems Biology T2 - Progress in Biophysics and Molecular Biology Y1 - 2013 UR - http://www.sciencedirect.com/science/article/pii/S0079610712001071?v=s5 U6 - https://doi.org/10.1016/j.pbiomolbio.2012.10.001 SN - 1873-1732 VL - 111 IS - 2-3 SP - 119 EP - 128 ER - TY - CHAP A1 - Blätke, Mary-Ann A1 - Heiner, Monika A1 - Marwan, Wolfgang ED - Robeva, Raina S. T1 - BioModel Engineering with Petri Nets T2 - Algebraic and Discrete Mathematical Methods for Modern Biology Y1 - 2015 UR - http://store.elsevier.com/product.jsp?isbn=9780128012130 SN - 978-0-12-801213-0 SP - 141 EP - 193 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - GEN A1 - Blätke, Mary-Ann A1 - Rohr, Christian T1 - BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1682 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 221 EP - 254 ER - TY - CHAP A1 - Heiner, Monika A1 - Schwarick, Martin A1 - Wegener, Jan-Thierry T1 - Charlie – an extensible Petri net analysis tool T2 - Application and Theory of Petri Nets and Concurrency, 36th International Conference, PETRI NETS 2015, Brussels, Belgium, June 21-26, 2015, Proceedings Y1 - 2015 UR - http://link.springer.com/chapter/10.1007/978-3-319-19488-2_10 SN - 978-3-319-19487-5 U6 - https://doi.org/10.1007/978-3-319-19488-2_10 N1 - peer reviewed SP - 200 EP - 211 PB - Springer International Publishing CY - Cham ER - TY - CHAP A1 - Liu, Fei A1 - Heiner, Monika A1 - Yang, Ming T1 - Colored Petri Nets for Multiscale Systems Biology – Current Modeling and Analysis Capabilities in Snoopy T2 - 7th International Conference on Systems Biology (ISB), 2013, 23 - 25 Aug. 2013, Huangshan, China Y1 - 2013 SN - 978-1-4799-1387-9 U6 - https://doi.org/10.1109/ISB.2013.6623788 N1 - referiert SP - 24 EP - 30 PB - IEEE CY - Piscataway, NJ ER - TY - THES A1 - Liu, Fei T1 - Colored Petri Nets for Systems Biology Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-23656 UR - http://opus.kobv.de/btu/volltexte/2012/2365/pdf/LiuFei_Thesis_final.pdf 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 - CHAP A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian ED - Heiner, Monika T1 - Coloured hybrid Petri nets for systems biology T2 - Proceedings of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN) Y1 - 2014 UR - http://ceur-ws.org/Vol-1159/ SP - 60 EP - 76 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 - 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 - CHAP A1 - Liu, Fei A1 - Heiner, Monika T1 - Coloured Petri Nets to Model and simulate Biological Systems T2 - Proceedings of the Workshops of the 31st International Conference on Application and Theory of Petri Nets and Other Models of Concurrency (PETRI NETS 2010) Y1 - 2010 UR - http://ceur-ws.org/Vol-827 SP - 70 EP - 84 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 - 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 - CHAP A1 - Spranger, Jochen T1 - Combining structural properties and symbolic representation for efficient analysis of Petri nets T2 - Workshop Concurrency, Specification & Programming, September 28 - 30, 1998 Y1 - 1998 UR - http://www-dssz.informatik.tu-cottbus.de/publications/papers/1998_jsp_csp.pdf N1 - referiert SP - 236 EP - 244 PB - Professoren des Institutes für Informatik CY - Berlin ER - TY - CHAP A1 - Heiner, Monika A1 - Gilbert, David A1 - Breitling, Rainer A1 - Orton, Richard T1 - Computation modelling of kinase signalling cascades Y1 - 2010 UR - http://www.springerlink.com/content/w737003v17214214/#section=761974%26page=1 ER - TY - THES A1 - Herajy, Mostafa T1 - Computational Steering of Multi-Scale Biochemical Networks Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-27255 UR - http://opus.kobv.de/btu/volltexte/2013/2725/pdf/diss_Herajy_Final_2013.pdf ER - TY - CHAP A1 - Heiner, Monika A1 - Schwarick, Martin T1 - CSL model checking of biochemical networks with Interval Decision Diagrams KW - Petri Nets Y1 - 2009 UR - http://www.springerlink.com/content/n11g5021770h8k88/ 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 - 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 - 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 - GEN A1 - Rohr, Christian T1 - Discrete-Time Leap Method For Stochastic Simulation T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1680 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 181 EP - 198 ER - TY - GEN A1 - Rohr, Christian ED - Cabac, Lawrence ED - Kristensen, Lars Michael ED - Rölke, Heiko T1 - Discrete-Time Leap Method For Stochastic Simulation T2 - Proceedings of the International Workshop on Petri Nets and Software Engineering 2016, including the International Workshop on Biological Processes & Petri Nets 2016 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1591-5 UR - http://ceur-ws.org/Vol-1591/paper26.pdf SP - 362 EP - 376 PB - RWTH CY - Aachen 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 - Heiner, Monika A1 - Schwarick, Martin A1 - Tovchigrechko, Alexey A. T1 - DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets KW - Petri Nets Y1 - 2009 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 - THES A1 - Tovchigrechko, Alexey A. T1 - Efficient symbolic analysis of bounded petri nets using interval decision diagrams KW - Petri-Netz KW - Model Checking Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-10294 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 - CHAP A1 - Mertke, Thomas A1 - Deussen, Peter H. A1 - Heiner, Monika T1 - Eine anwenderorientierte Sicherheitsfachsprache zur Verifikation von Steuerungsprogrammen Y1 - 2001 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 - CHAP A1 - Heiner, Monika A1 - Lehrack, Sebastian A1 - Gilbert, David A1 - Marwan, Wolfgang T1 - Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments T2 - Transactions on Computational Systems Biology XI Y1 - 2009 UR - http://www.springerlink.com/content/5u8h68411657x827/?p=e806216818924093ad3bc526c8b3604d&pi=0 SN - 978-3-642-04185-3 SP - 138 EP - 163 PB - Springer CY - Berlin [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Breitling, Rainer A1 - Gilbert, David A1 - Priami, C. T1 - Formal Methods in Molecular Biology KW - Petri Nets Y1 - 2009 UR - http://drops.dagstuhl.de/portals/index.php?semnr=09091 ER - TY - THES A1 - Mertke, Thomas T1 - Formale Spezifikation reaktiver Systeme mit einer Sicherheitsfachsprache T1 - A Technical Language for Formal Safety Specification of Reactive Systems Y1 - 2004 SN - 3-8322-3085-8 PB - Shaker Verlag CY - Aachen 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 - 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 - 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 - CHAP A1 - Spranger, Jochen T1 - FUNlite - A Parallel Petri Net Simulator 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_jsp_ilmenau.pdf N1 - referiert PB - Technische Universität CY - Ilmenau ER - TY - THES A1 - Assaf, George T1 - Fuzzy coloured Petri nets for modelling biological systems with uncertain kinetic parameters N2 - Over the last twenty years, Petri nets have been increasingly adopted for modelling and simulating biological systems, as they offer an intuitive and graphical approach for this purpose. Their usability convenience comes from the fact that they offer many types of elements to describe systems in a qualitative and quantitative way. Coloured Petri nets are particularly useful to model systems with repeated components in a compact fashion. Our tool Snoopy for modelling and simulating Petri nets is one of the most well-known tools supporting a family of related Petri net classes comprising stochastic, continuous and hybrid Petri nets, and covering uncoloured and coloured Petri nets alike. However, kinetic information of a biological system, i.e. kinetic parameters may be uncertain, due to many reasons, e.g. environmental factors. Besides, coloured Petri nets as they were previously supported in Snoopy suffered from some inconsistencies. Due to these inconsistencies, exploring the model behaviour using different sizes (scaleability) was not feasible. Both challenges call for a new and more powerful approach integrating the modelling of uncertainties together with modelling features supporting repeated structures in a compact and scalable way. This thesis comprises two major contributions: Firstly, we introduce the definition and present the simulation algorithm for both uncoloured and coloured fuzzy Petri nets, by extending the existing quantitative uncoloured and coloured Petri nets in Snoopy. This includes discretising the uncertain kinetic parameters to crisp values by using sampling strategies. Secondly, we harmonise coloured Petri nets in Snoopy with their uncoloured counterparts and we extend the Snoopy’s coloured Petri nets by all the features, which are supported by the coloured abstract net description language - an exchange format of coloured Petri nets in our PetriNuts tool family. By performing fuzzy simulation, one can obtain two kinds of output: fuzzy bands of each output variable and their corresponding timed-membership functions. Each fuzzy band describes the uncertainties associated with the input, whereas membership functions give more accurate information about the associated uncertainties. The most important features that we obtain by harmonising coloured Petri nets are to develop scaleable models, by defining scaling factors as constants and unifying the usage of coloured Petri nets with the other tools in our PetriNuts tool family. KW - modelling KW - Colouring fuzziness KW - fuzzy logic KW - Petri nets KW - Uncertain biological systems KW - systems biology KW - Software harmonisation KW - coloured Petri nets Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-58516 PB - BTU CY - Cottbus 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 - 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 - GEN A1 - Liu, Fei A1 - Heiner, Monika A1 - Yang, Ming T1 - Fuzzy stochastic Petri nets for modeling biological systems with uncertain kinetic parameters T2 - PLoS ONE Y1 - 2016 UR - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149674 U6 - https://doi.org/10.1371/journal.pone.0149674 SN - 1932-6203 VL - 11 IS - 2 SP - 0149674 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 A1 - Gilbert, David T1 - How Might Petri Nets Enhance Your Systems Biology Toolkit Y1 - 2011 UR - http://www.springerlink.com/content/t21n70p613h75m64/ 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 - 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 - CHAP A1 - Herajy, Mostafa A1 - Schwarick, Martin A1 - Heiner, Monika T1 - Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle T2 - Transactions on petri nets and other models of concurrency VIII Y1 - 2013 SN - 978-3-642-40464-1 SN - 978-3-642-40465-8 U6 - https://doi.org/10.1007/978-3-642-40465-8_7 N1 - referiert SP - 123 EP - 141 PB - Springer CY - Berlin [u.a.] ER - TY - GEN A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - Hybrid Representation and Simulation of Stiff Biochemical Networks T2 - Nonlinear Analysis: Hybrid Systems Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S1751570X12000192 SN - 1751-570X VL - 6 IS - 4 SP - 942 EP - 959 ER - TY - GEN A1 - Schwarick, Martin A1 - Tovchigrechko, Alexey A. T1 - IDD-based model validation of biochemical networks T2 - Theoretical Computer Science Y1 - 2010 U6 - https://doi.org/10.1016/j.tcs.2010.06.030 SN - 0304-3975 VL - 412 IS - 26 SP - 2884 EP - 2908 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 - GEN A1 - Blätke, Mary-Ann A1 - Dittrich, Anna A1 - Rohr, Christian A1 - Heiner, Monika A1 - Schaper, Fred A1 - Marwan, Wolfgang T1 - JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology T2 - Molecular BioSystems Y1 - 2013 U6 - https://doi.org/10.1039/C3MB25593J SN - 1742-2051 VL - 9 IS - 6 SP - 1290 EP - 1307 ER - TY - CHAP A1 - Heiner, Monika A1 - Rohr, Christian A1 - Schwarick, Martin ED - Colom, José-Manuel ED - Desel, Jörg T1 - MARCIE - Model checking and Reachability analysis done effieciently T2 - Application and theory of petri nets and concurrency, 34th international conference, proceedings, PETRI NETS 2013, Milan, Italy, June 24 - 28, 2013 Y1 - 2013 UR - http://link.springer.com/chapter/10.1007/978-3-642-38697-8_21 SN - 978-3-642-38696-1 N1 - referiert SP - 389 EP - 399 PB - Springer CY - Heidelberg [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Rohr, Christian A1 - Schwarick, Martin A1 - Tovchigrechko, Alexey A. ED - Koutny, Maciej ED - Desel, Jörg ED - Kleijn, Jetty T1 - MARCIE’s secrets of efficient model checking T2 - Transactions on petri nets and other models of concurrency XI Y1 - 2016 SN - 978-3-662-53400-7 SN - 978-3-662-53401-4 U6 - https://doi.org/10.1007/978-3-662-53401-4_14 N1 - referiert SP - 286 EP - 296 PB - Springer CY - Berlin [u.a.] ER - TY - GEN A1 - Heiner, Monika A1 - Koch, Ina A1 - Will, Jürgen T1 - Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis T2 - BioSystems Y1 - 2004 U6 - https://doi.org/10.1016/j.biosystems.2004.03.003 VL - 75 IS - 1-3 SP - 15 EP - 28 ER - TY - GEN A1 - Heiner, Monika A1 - Yang, Ming A1 - Liu, Fei T1 - Modeling and analyzing biological systems using colored hierarchical Petri nets illustrated by C. elegans vulval development T2 - Journal of Biological Systems Y1 - 2014 U6 - https://doi.org/10.1142/S0218339014500181 SN - 1793-6470 VL - 22 IS - 3 SP - 463 EP - 493 ER - TY - GEN A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets T2 - Frontiers in Environmental Science Y1 - 2015 UR - http://www.frontiersin.org/environmental_informatics/10.3389/fenvs.2015.00053/abstract U6 - https://doi.org/10.3389/fenvs.2015.00053 SN - 2296-665X VL - 3 SP - 53 ER - TY - GEN A1 - Bertens, Laura M. F. A1 - Kleijn, Jetty A1 - Hille, Sander C. A1 - Heiner, Monika A1 - Koutny, Maciej A1 - Verbeek, Fons J. T1 - Modeling biological gradient formation: combining partial differential equations and Petri nets T2 - Natural Computing Y1 - 2016 UR - http://link.springer.com/article/10.1007/s11047-015-9531-4 U6 - https://doi.org/10.1007/s11047-015-9531-4 SN - 1567-7818 SN - 1572-9796 VL - 15 IS - 4 SP - 665 EP - 675 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 - Liu, Fei A1 - Heiner, Monika T1 - Modeling membrane systems using colored stochastic Petri nets T2 - Natural Computing Y1 - 2013 U6 - https://doi.org/10.1007/s11047-013-9367-8 SN - 1572-9796 VL - 12 IS - 4 SP - 617 EP - 629 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 - Liu, Fei A1 - Blätke, Mary-Ann A1 - Heiner, Monika A1 - Yang, Ming T1 - Modelling and simulating reaction–diffusion systems using coloured Petri nets T2 - Computers in Biology and Medicine Y1 - 2014 UR - http://www.sciencedirect.com/science/article/pii/S0010482514001693 U6 - https://doi.org/10.1016/j.compbiomed.2014.07.004 SN - 0010-4825 VL - 53 SP - 297 EP - 308 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 - GEN A1 - Grafahrend-Belau, Eva A1 - Schreiber, Falk A1 - Heiner, Monika A1 - Sackmann, Andrea A1 - Junker, Björn H. A1 - Grunwald, Stefanie A1 - Speer, Astrid A1 - Winder, Katja A1 - Koch, Ina T1 - Modularization of biochemical networks based on classification of Petri net T-invariants T2 - BMC Bioinformatics Y1 - 2008 U6 - https://doi.org/10.1186/1471-2105-9-90 SN - 1471-2105 VL - Vol. 9 ER - TY - GEN A1 - Gao, Quian A1 - Gilbert, David A1 - Heiner, Monika A1 - Liu, Fei A1 - Maccagnola, Daniele A1 - Tree, David T1 - Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing T2 - IEEE/ACM Transactions on Computational Biology and Bioinformatics Y1 - 2013 U6 - https://doi.org/10.1109/TCBB.2012.101 SN - 1545-5963 VL - 10 IS - 2 SP - 337 EP - 351 ER - TY - GEN A1 - Liu, Fei A1 - Heiner, Monika T1 - Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets T2 - IET Systems Biology Y1 - 2013 SN - 1751-8849 VL - 7 IS - 4 SP - 106 EP - 113 ER - TY - GEN ED - Gilbert, David ED - Heiner, Monika ED - Takahashi, Koichi ED - Uhrmacher, Adelinde M. T1 - Multiscale Spatial Computational Systems Biology N2 - This report documents the program and the outcomes of Dagstuhl Seminar 14481 "Multiscale Spatial Computational Systems Biology". This seminar explored challenges arising from the need to model and analyse complex biological systems at multiple scales (spatial and temporal), which falls within the general remit of Computational Systems Biology. A distinguishing factor of the seminar was the modelling exercise -- where teams explored different modelling paradigms, in order to better understand the details of the approaches, their challenges, potential applications, and their pros and cons. This activity was carried out in a collaborative and self-directed manner using the Open Space Technology approach as evidenced by a high degree of communication both within and between the teams. Eight teams were formed, and reports from five of them are included in this document. KW - Multiscale, multidimensional, computational modelling, space, time, systems biology, synthetic biology Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?nbn:de:0030-drops-49723 UR - http://drops.dagstuhl.de/opus/volltexte/2015/4972/ CY - Dagstuhl 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 -