TY - THES A1 - Spranger, Jochen T1 - Symbolische LTL-Verifikation von Petrinetzen KW - nebenläufige Systeme KW - Modelchecking KW - Petrinetze KW - Stellen/Transaktionsnetze KW - 1-Stellen-Invarianten KW - symbolische Verfahren KW - reduzierte geordnete binäre Entscheidungsgraphen KW - ROBDD KW - linear-time temporale Logik KW - LTL KW - Fixpunktiteration KW - Tiefensuche KW - Büchinetze KW - Büchiautomaten KW - on-the-fly Verfahren KW - symbolische Tiefensuche KW - Verifikation Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-000000179 UR - http://opus.kobv.de/btu/volltexte/2007/97/ 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 - 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 - CHAP A1 - Mertke, Thomas A1 - Deussen, Peter H. A1 - Heiner, Monika T1 - Eine anwenderorientierte Sicherheitsfachsprache zur Verifikation von Steuerungsprogrammen Y1 - 2001 ER - TY - CHAP A1 - Heiner, Monika T1 - Understanding Network Behavior by Structured Representations of Transition Invariants KW - Petri Nets Y1 - 2009 UR - http://www.springerlink.com/content/m8t30720r141442m ER - TY - CHAP A1 - Heiner, Monika A1 - Donaldson, Robin A1 - Gilbert, David ED - Iyengar, M. Sriram T1 - Petri Nets for Systems Biology T2 - Symbolic systems biology Y1 - 2009 UR - http://www.jblearning.com/catalog/9780763753702/ SN - 978-0-7637-5370-2 PB - Jones and Bartlett Learning CY - Sudbury, Mass. [u.a.] 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 - 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 - CHAP A1 - Heiner, Monika A1 - Marwan, Wolfgang A1 - Rohr, Christian T1 - Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks Y1 - 2012 UR - http://www.springerlink.com/content/978-1-61779-361-5 ER - TY - CHAP A1 - Heiner, Monika T1 - Understanding Network Behaviour by Structured Representations of Transition Invariants - A Petri Net Perspective on Systems and Synthetic Biology Y1 - 2009 UR - http://www.springerlink.com/content/m8t30720r141442m 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 - 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 - 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 - 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 - 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 - Popova-Zeugmann, Louchka A1 - Heiner, Monika A1 - Koch, Ina T1 - Time Petri Nets for Modelling and Analysis of Biochemical Networks T2 - Fundamenta Informaticae Y1 - 2005 UR - http://iospress.metapress.com/content/84vabcc0venbcgwv/ SN - 1875-8681 VL - 67 IS - 1-3 SP - 149 EP - 162 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 - Koch, Ina A1 - Schüler, Markus A1 - Heiner, Monika T1 - STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks T2 - In silico biology Y1 - 2004 UR - http://www.bioinfo.de/isb/2004/05/0014/ SN - 1434-3207 VL - Vol. 5 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 - Voss, Klaus A1 - Heiner, Monika A1 - Koch, Ina T1 - Steady State Analysis of Metabolic Pathways Using Petri Nets T2 - In silico biology Y1 - 2003 UR - http://www.bioinfo.de/isb/2003/03/0031/ SN - 1434-3207 VL - Vol. 3 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 - 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 - Rohr, Christian T1 - Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators 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_8 N1 - referiert SP - 142 EP - 158 PB - Springer CY - Berlin [u.a.] 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 - 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 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 - 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 - Sriram, K. T1 - Structural Analysis to Determine the Core of Hypoxia Response Network T2 - PLoS ONE Y1 - 2010 U6 - https://doi.org/10.1371/journal.pone.0008600 SN - 1932-6203 VL - 5 IS - 1 ER - TY - GEN A1 - Rohr, Christian A1 - Marwan, Wolfgang A1 - Heiner, Monika T1 - Snoopy - a unifying Petri net framework to investigate biomolecular networks T2 - Bioinformatics Y1 - 2010 UR - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/974?ct=ct SN - 1460-2059 VL - 26 IS - 7 SP - 974 EP - 975 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 - 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 - Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks T2 - Fundamenta Informaticae Y1 - 2014 UR - http://iospress.metapress.com/content/y8760m2p02256uw3 SN - 0169-2968 VL - 129 IS - 1-2 SP - 49 EP - 67 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 - 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 - 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 - 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 - CHAP A1 - Liu, Fei A1 - Heiner, Monika ED - Chen, Ming ED - Hofestädt, Ralf T1 - Petri Nets for Modeling and Analyzing Biochemical Reaction Networks T2 - Approaches in Integrative Bioinformatics KW - Petri nets KW - Biochemical reaction networks KW - Unifying Petri net frame- work KW - Qualitative KW - Stochastic KW - Conti nuous and hybrid Petri nets KW - Colored Petri nets KW - Repressilator Y1 - 2014 SN - 978-3-642-41280-6 SN - 978-3-642-41281-3 U6 - https://doi.org/10.1007/978-3-642-41281-3_9 SP - 245 EP - 272 PB - Springer CY - Heidelberg 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 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 - 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 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 - CHAP A1 - Barbot, Benoit A1 - Haddad, Serge A1 - Heiner, Monika A1 - Picaronny, Claudine T1 - Rare Event Handling in Signalling Cascades T2 - Proceedings, SIMUL 2014, Sixth International Conference on Advances in System Simulation Y1 - 2014 UR - http://www.thinkmind.org/index.php?view=instance&instance=SIMUL+2014 SN - 978-1-61208-371-1 N1 - ThinkMind Digital Library SP - 126 EP - 131 PB - IARIA 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 - 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 - 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 - CHAP A1 - Heiner, Monika A1 - Gilbert, David A1 - Donaldson, Robin T1 - Petri Nets for Systems and Synthetic Biology Y1 - 2008 UR - http://www.springerlink.com/content/j115442q6518j330/ 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 - 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 - 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 - CHAP A1 - Heiner, Monika A1 - Koch, Ina T1 - Petri Nets Y1 - 2008 UR - http://www.amazon.com/Analysis-Biological-Networks-Wiley-Bioinformatics/dp/0470041447/ref=sr_1_1?ie=UTF8%26s=books%26qid=1195812618%26sr=8-1 ER - TY - RPRT A1 - Will, Jürgen A1 - Heiner, Monika T1 - Petri nets in biology, chemistry, and medicine : bibliography KW - Petri-Netz KW - Naturwissenschaften Y1 - 2002 PB - BTU, Inst. of Computer Science CY - Cottbus ER - TY - JOUR A1 - Deussen, Peter H. T1 - Partial Order Verification of Programmable Logic Controllers Y1 - 2001 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 - 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 - 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 - 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 - 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 -