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Selected References - Conference Papers

69 entries

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2020 - 2019 - 2018 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2004 - 2003 - 2002 - 2001 - 2000 - 1999 - 1998 - 1997 - 1996 - 1995

2020

• [SRL+20]
  M Schwarick and C Rohr, F Liu, G Assaf, J Chodak, M Heiner:
  Efficient Unfolding of Coloured Petri Nets using Interval Decision Diagrams;
  In Proc. PETRI NETS 2020, Paris, Springer, Cham, LNCS, volume 12152, pages 324-344, June 2020. [ doi ] [ BibTeX ]

2019

• [CH19a]
  J Chodak and M Heiner:
  Spike – reproducible simulation experiments with configuration file branching;
  In Proc. CMSB 2019, Trento, Springer, LNCS/LNBI, volume 11773, pages 315-321, September 2019. [ doi ] [ BibTeX ]
• [AHL19]
  G Assaf, M Heiner and F Liu:
  Biochemical reaction networks with fuzzy kinetic parameters in Snoopy;
  In Proc. CMSB 2019, Trieste, Springer, LNCS/LNBI, volume 11773, pages 302-307, September 2019. [ doi ] [ BibTeX ]

2018

• [IHHA18]
  A Ismail, M Herajy, M Heiner and E Atlam:
  An Efficient Approach for the Hybrid Simulation of Intracellular Calcium Dynamics;
  In 13th International Conference on Computer Engineering and Systems (ICCES), IEEE, pages 665–670, 2018. [ doi ] [ BibTeX ]
• [BHAH18]
  A Badawy, M Herajy, W Awad and M Heiner:
  Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets;
  In 13th International Conference on Computer Engineering and Systems (ICCES), IEEE, pages 268–272, 2018. [ doi ] [ BibTeX ]
• [HH18]
  M Herajy and M Heiner:
  An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets;
  In Proceedings of the 2018 Winter Simulation Conference (WSC 2018), Gothenburg, Sweden, IEEE, 978-1-5386-6572-5/18, pages 1346-1357, December 2018. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [SGH18]
  T Self, D Gilbert and M Heiner:
  Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models;
  In Proc. CMSB 2018, Brno, Springer, LNCS/LNBI, volume 11095, pages 39-58, September 2018. [ doi ] [ BibTeX ]

2016

• [HH16]
  M Herajy and M Heiner:
  Accelerated Simulation of Hybrid Biological Models with Quasi-disjoint Deterministic and Stochastic Subnets;
  In Proc. 5th Int. Workshop on Hybrid Systems Biology (HSB 2016), Springer, LNBI, volume 9957, pages 20-38, October 2016. [ url ] [ doi ] [ BibTeX ]
• [Rohr16]
  Rohr, C:
  Discrete-Time Leap Method For Stochastic Simulation;
  In Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2016), CEUR-WS.org, CEUR Workshop Proceedings, volume 1591, pages 362–376, June 2016. [ url ] [ pdf ] [ BibTeX ]

2015

• [HSW15]
  M Heiner, M Schwarick and J Wegener:
  Charlie – an extensible Petri net analysis tool;
  In Proc. PETRI NETS 2015, Brussels, Springer, LNCS, volume 9115, pages 200–211, June 2015. [ url ] [ doi ] [ BibTeX ]
• [BR15]
  MA Blätke, C Rohr:
  A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit;
  In Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2015), CEUR-WS.org, CEUR Workshop Proceedings, volume 1373, pages 37–54, June 2015. [ url ] [ pdf ] [ BibTeX ]

2014

• [BHHP14]
  B Barbot, S Haddad, M Heiner and C Picaronny:
  Rare Event Handling in Signalling Cascades;
  In Proc. SIMUL 2014, The Sixth International Conference on Advances in System Simulation, Nice, France, ThinkMind Digital Library, pages 126–131, October 2014. [ url ] [ pdf ] [ BibTeX ]
• [HLR14]
  M Herajy, F Liu and C Rohr:
  Coloured hybrid Petri nets for systems biology;
  In Proc. of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 60-76, June 2014. [ url ] [ pdf ] [ BibTeX ]
• [HH14b]
  M Herajy and M Heiner:
  A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
  In Proc. PETRI NETS 2014, Tunis, Springer, LNCS, volume 8489, pages 374–384, June 2014. [ url ] [ doi ] [ BibTeX ]

2013

• [PGH+13]
  O Parvu, D Gilbert, M Heiner, F Liu and N Saunders:
  Modelling and Analysis of Phase Variation in Bacterial Colony Growth;
  In Proc. CMSB 2013, Vienna, Springer, LNCS/LNBI, volume 8130, pages 78–-91, September 2013. [ doi ] [ BibTeX ]
• [LHY13]
  F Liu, M Heiner and M Yang:
  Colored Petri Nets for Multiscale Systems Biology – Current Modeling and Analysis Capabilities in Snoopy;
  In Proc. 7th International Conference on Systems Biology (ISB 2013), Huangshan/China, IEEE, pages 24 - 30, August 2013. [ url ] [ doi ] [ BibTeX ]
• [GHLS13]
  D Gilbert, M Heiner, F Liu and N Saunders:
  Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology;
  In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 230–249, June 2013. [ url ] [ doi ] [ BibTeX ]
• [HRS13]
  M Heiner, C Rohr and M Schwarick:
  MARCIE - Model checking And Reachability analysis done effiCIEntly;
  In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 389–399, June 2013. [ url ] [ pdf ] [ doi ] [ BibTeX ]

2012

• [LHY12]
  F Liu, M Heiner and M Yang:
  An efficient method for unfolding colored Petri nets;
  In Proceedings of the 2012 Winter Simulation Conference (WSC 2012), Berlin, IEEE, 978-1-4673-4781-5/12, 2012. [ url ] [ pdf ] [ BibTeX ]
• [BDH+12]
  MA Blätke, A Dittrich, M Heiner, F Schaper and W Marwan:
  JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept;
  In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI, volume 7605, pages 362–365, 2012. [ url ] [ doi ] [ BibTeX ]
• [BHM12]
  MA Blätke, M Heiner and W Marwan:
  Predicting Phenotype from Genotype Through Automatically Composed Petri Nets;
  In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI, volume 7605, pages 87–106, 2012. [ url ] [ doi ] [ BibTeX ]
• [Schw12]
  M Schwarick:
  Symbolic model checking of stochastic reward nets;
  In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2012), CEUR-WS.org, CEUR Workshop Proceedings, volume 928, pages 343–357, September 2012. [ url ] [ pdf ] [ BibTeX ]
• [HH12.csp]
  M Herajy and M Heiner:
  Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks;
  In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2012), CEUR-WS.org, CEUR Workshop Proceedings, volume 928, pages 147–159, September 2012. [ url ] [ pdf ] [ BibTeX ]
• [HH+12]
  M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
  Snoopy – a unifying Petri net tool;
  In Proc. PETRI NETS 2012, Hamburg, Springer, LNCS, volume 7347, 398–407, June 2012. [ url ] [ doi ] [ BibTeX ]
• [HS12]
  M Herajy and M Schwarick:
  A Hybrid Petri Net Model of the Eukaryotic Cell Cycle;
  In Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2012, CEUR-WS.org, CEUR Workshop Proceedings, volume 852, pages 29-43, June 2012. [ url ] [ pdf ] [ BibTeX ]
• [Rohr12]
  C Rohr:
  Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
  In Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2012, CEUR-WS.org, CEUR Workshop Proceedings, volume 852, pages 62-75, June 2012. [ url ] [ pdf ] [ BibTeX ]

2011

• [GLT+11]
  Q Gao, F Liu, D Tree and D Gilbert:
  Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity;
  In Proc. of the 2nd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 135–150, June 2011. [ pdf ] [ BibTeX ]
• [GLG+11]
  Q Gao, F Liu, D Gilbert, M Heiner and D Tree:
  A Multiscale Approach to Modelling Planar Cell Polarity in Drosophila Wing using Hierarchically Coloured Petri Nets;
  In Proc. 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, ACM digital library, pages 209–218, September 2011. [ url ] [ pdf ] [ BibTeX ]
• [SRH11]
  M Schwarick , C Rohr and M Heiner:
  MARCIE - Model checking And Reachability analysis done effiCIEntly;
  In Proc. 8th International Conference on Quantitative Evaluation of SysTems (QEST 2011), Aachen, Germany, IEEE CS Press, pages 91–100, September 2011. [ url ] [ pdf ] [ BibTeX ]
• [WSH11]
  J Wegener, M Schwarick and M Heiner:
  A Plugin System for Charlie;
  In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2011), Biaystok University of Technology, ISBN: 978-83-62582-06-8, pages 531–554, September 2011. [ url ] [ pdf ] [ BibTeX ]

2010

• [HMS10]
  M Heiner, C Mahulea and M Silva:
  On the Importance of the Deadlock Trap Property for Monotonic Liveness;
  In Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pages 39-54, June 2010. [ pdf ] [ BibTeX ]
• [HRSS10]
  M Heiner, C Rohr, M Schwarick and S Streif:
  A Comparative Study of Stochastic Analysis Techniques;
  In Proc. 8th International Conference on Computational Methods in Systems Biology (CMSB 2010), Trento, ACM digital library, pages 96–106, September 2010. [ pdf ] [ doi ] [ BibTeX ]
• [LH10]
  F Liu and M Heiner:
  Colored Petri nets to model and simulate biological systems;
  In Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pages 70-84, June 2010. [ pdf ] [ BibTeX ]

2009

• [HST09]
  M Heiner, M Schwarick and A Tovchigrechko:
  DSSZ-MC – A Tool for Symbolic Analysis of Extended Petri Nets;
  In Proc. PETRI NETS 2009, Paris, Springer, LNCS, volume 5606, pages 323–332, June 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [SH09]
  M Schwarick and M Heiner:
  CSL model checking of biochemical networks with Interval Decision Diagrams;
  In Proc. 7th International Conference on Computational Methods in Systems Biology (CMSB 2009), Bologna, Italy, Springer, LNCS/LNBI, volume 5688, pages 296–312, September 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [GBHD08]
  D Gilbert, R Breitling, M Heiner and R Donaldson:
  An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways;
  In Proc. 9th International Workshop on Membrane Computing (WMC 2008), Springer, LNCS, volume 5391, pages 13–28, 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]

2008

• [GHR+08]
  D Gilbert, M Heiner, S Rosser, R Fulton, X Gu and M Trybio:
  A Case Study in Model-driven Synthetic Biology;
  In IFIP WCC 2008, 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC 2008), Milano, Springer, IFIP, volume 268, pages 163–175, September 2008. [ url ] [ pdf ] [ BibTeX ]
• [HRS08]
  M Heiner, R Richter and M Schwarick:
  Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
  In Proc. International Workshop on Petri Nets Tools and APplications (PNTAP 2008, associated to SIMUTools 2008), ACM digital library, 2008. [ url ] [ pdf ] [ BibTeX ]

2007

• [GHL07b]
  D Gilbert, M Heiner and S Lehrack:
  A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
  In Proc. 5th International Conference on Computational Methods in Systems Biology (CMSB 2007), Edinburgh, Springer, LNCS/LNBI, volume 4695, pages 200-216, 2007. [ url ] [ pdf ] [ BibTeX ]
• [PH07]
  L Popova and M Heiner:
  Quantitative Evaluation of Time Petri Nets and Applications to Technical and Biochemical Networks);
  In Proc. International Workshop on Concurrency, Specification and Programming (CS&P 2007), Lagów, September 2007, volume 2, pages 473-484, 2007. [ BibTeX ]

2006

• [GH06]
  Gilbert, D. and Heiner, M.:
  From Petri nets to differential equations - an integrative approach for biochemical network analysis;
  In Proc. ICATPN 2006, LNCS 4024, Springer, pages 181–200, 2006. [ url ] [ pdf ] [ BibTeX ]

2004

• [HK04]
  M Heiner and I Koch:
  Petri Net Based System Validation in Systems Biology;
  In Proc. ICATPN 2004, Bologna, June, Springer, LNCS, volume 3099, pages 216-237, 2004. [ pdf ] [ doi ] [ BibTeX ]
• [Runge04b]
  T Runge:
  Application of Coloured Petri Nets in Systems Biology;
  In Proc. 5th Workshop CPN, Univ. of Aarhus, October 2004, pages 77-95, 2004. [ pdf ] [ BibTeX ]

2003

• [HKW03]
  M Heiner, I Koch and J Will:
  Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
  In Proc. First Int. Workshop on Computational Methods in Systems Biology (CMSB 2003), Rovereto, Febr. 2003, Springer, LNCS, volume 2602, page 173, 2003. [ pdf ] [ doi ] [ BibTeX ]

2002

• [RHHH02]
  T Rottke, D Hatebur, M Heisel and M Heiner:
  A Problem-Oriented Approach to Common Criteria Certification);
  In Proc. SafeComp ’02, Catania, Sept. 2002, Springer, LNCS, volume 2434, pages 334 - 346, 2002. [ pdf ] [ BibTeX ]

2001

• [Deus01]
  P Deussen:
  Partial Order Verification of Programmable Logic Controllers;
  In Proc. 22nd International Conference, ICATPN 2001, Newcastle upon Tyne, Juni 2001, Springer, LNCS, volume 2075, pages 144 - 163, 2001. [ url ] [ pdf ] [ BibTeX ]
• [HKV01]
  M Heiner, I Koch and K Voss:
  Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets;
  In Proc. Third Workshop CPN, Univ. of Aarhus, volume 08/2001, pages 15-34, 2001. [ pdf ] [ BibTeX ]
• [MDH01]
  T Mertke, P Deussen and M Heiner:
  Eine anwenderorientierte Sicherheitsfachsprache zur Verifikation von Steuerungsprogrammen;
  In Proc. EKA 2001, 7. Fachtagung, TU Braunschweig, volume April 2001, pages 275 - 282, 2001. [ pdf ] [ BibTeX ]

2000

• [HKS00]
  M Heiner, I Koch and S Schuster:
  Using Time-dependent Petri Nets for the Analysis of Metabolic Networks;
  In Proc. DFG-Workshop Modelling and Simulation of Metabolic Networks, May 2000, O.-v.-Guericke-Uni Magdeburg, pages 15 - 21, 2000. [ BibTeX ]
• [HM00]
  M Heiner and T Menzel:
  Time-related Modelling of PLC Systems with Time-less Petri Nets;
  In Discrete Event Systems, Analysis and Control, Boel, R.; Stremerch, G. (eds.) Kluwer Academic Publishers, volume 2000, pages 275 - 282, 2000. [ pdf ] [ BibTeX ]

1999

• [HH99]
  M Heiner and M Heisel:
  Modelling Safety-Critical Systems with Z and Petri Nets;
  In Proc. SafeComp '99, Toulouse 1999, Springer, LNCS, volume 1698, pages 361 - 374, 1999. [ url ] [ pdf ] [ BibTeX ]
• [HDS99]
  M Heiner, P Deussen and J Spranger:
  A Case Study in Design and Verification of Manufacturing Systems with Hierarchical Petri Nets;
  In The International Journal of Advanced Manufacturing Technology 1999, volume 15, pages 139-152, 1999. [ pdf ] [ BibTeX ]
• [HMS99]
  M Heiner and T Menzel:
  Modellierung und Analyse von SPS-Anwenderprogrammen mit Petri-Netzen;
  In Proc. EKA '99, 6. Fachtagung, Braunschweig, May 1999, pages 247-265, 1999. [ pdf ] [ BibTeX ]

1998

• [Deus98]
  P Deussen:
  Algorithmic Aspects of Concurrent Automata;
  In Proc. Workshop on Concurrency, Specification &Programming 1998, Berlin, Sept. 1998), Humbolt Univ. at Berlin, Informatik-Bericht, volume 110, pages 39-70, 1998. [ pdf ] [ BibTeX ]
• [H98]
  M Heiner:
  Petri Net Based System Analysis without State Explosion;
  In Proc. Hight Performance Computing '98, Boston, April 1998, SCS Int. San Diego 1998), pages 394-403, 1998. [ pdf ] [ BibTeX ]
• [HM98a]
  M Heiner and T Menzel:
  Instruction List Verification Using a Petri Net Semantics;
  In Proc. IEEE Int. Conf. on Systems, Man, and Cybernetics, San Diego, October 1998), pages 716-721, 1998. [ pdf ] [ BibTeX ]
• [HM98b]
  M Heiner and T Menzel:
  A Petri Net Semantics for the PLC Language Instruction List;
  In Proc. IEE Workshop on Discrete Event Systems (WODES '98), Cagliari, August 1998), pages 161-165, 1998. [ pdf ] [ BibTeX ]
• [Spra98]
  J Spranger:
  Combining structural properties and symbolic representation for efficient analysis of Petri nets;
  In Proc. Workshop on Concurrency, Specification &Programming 1998, Berlin, Sept. 1998), Humbolt Univ. at Berlin, Informatik-Bericht, volume 110, pages 236-244, 1998. [ pdf ] [ BibTeX ]

1997

• [H97a]
  M Heiner:
  On Exploiting the Analysis Power of Petri nets for the Validation of Discrete Event Systems;
  In Proc. 2nd IMACS Symposium on Mathematical Modelling (MATHMOD VIENNA '97), ARGESIM Report, volume 11, pages 171 – 176, 1997. [ pdf ] [ BibTeX ]
• [H97b]
  M Heiner:
  Verification and Optimization of Control Programs by Petri Nets without State Explosion;
  In Proc. 2nd Int. Workshop on Manufacturing and Petri Nets held at Int. Conf. on Application and Theory of Petri Nets (ICATPN '97, Toulouse, June 1997), pages 69–84, 1997. [ pdf ] [ BibTeX ]
• [HP97]
  M Heiner and L Popova-Zeugmann:
  On Integration of Qualitative and Quantitative Analysis of Manufacturing Systems Using Petri Nets;
  In Proc. 42. Int. wissenschaftliches Kolloquium (IWK '97), Ilmenau, September 1997), TU Ilmenau, volume 1, pages 557-562, 1997. [ pdf ] [ BibTeX ]
• [KUH97]
  H König, A Ulrich and M Heiner:
  Design for Testability: A Step-wise Approach to Protocol Testing;
  In Proc. 10th Int. Workshop on Testing of Communicating Systems (IWTCS '97), Seoul, Sept. 1997), Chapman &Hall, Kim, M.; Kang, S.; Hong, K. (eds.), pages 125-140, 1997. [ pdf ] [ BibTeX ]
• [PH97]
  L Popova-Zeugmann and M Heiner:
  Worst-case Analysis of Concurrent Systems with Duration Interval Petri Nets;
  In Proc. 5. Fachtagung EKA '97, Braunschweig, May 1997, IfRA 1997), Schnieder, E.; Abel, D. (eds.), Entwurf komplexer Automatisierungssysteme `97, pages 162–179, 1997. [ pdf ] [ BibTeX ]
• [Spra97]
  J Spranger:
  FUNlite - A Parallel Petri Net Simulator;
  In Proc. 42. IWK Ilmenau, September 1997), IWK Ilmenau, page 6, 1997. [ pdf ] [ BibTeX ]

1996

• [HD96a]
  M Heiner and P Deussen:
  Petri Net Based Design and Analysis of Reactive Systems;
  In Proc. Int. Workshop on Discrete Event Systems (WODES '96), Edinburgh, August 1996. [ pdf ] [ BibTeX ]
• [HD96b]
  M Heiner and P Deussen:
  A Case Study in Design and Validation of Reactive Systems by Means of Petri Nets;
  In Proc. IMACS Multiconference on Computational Engineering in Systems Applications (CESA '96), Symposium "Discrete Events and Manufacturing Systems", Lille, France, July 1996. [ pdf ] [ BibTeX ]
• [HDS96]
  M Heiner, P Deussen and J Spranger:
  A Case Study in Developing Control Software of Manufacturing Systems with Hierarchical Petri Nets;
  In Proc. 1st Int. Workshop on Manufacturing and Petri Nets held at Int. Conf. on Application and Theory of Petri Nets (ICATPN '96), Osaka, Japan, June 1996. [ pdf ] [ BibTeX ]
• [LHK96]
  G Lindner, M Heiner and T Kobienia:
  Deadlock Detection in a Distributed Implementation of a Visualization System for Medical Measurement Signals;
  In Proc. IEEE In. Conf. on Systems, Man and Cybernetics, Beijing, China, IEEE Press, volume 3, pages 2299–2304, Oct. 1996. [ pdf ] [ BibTeX ]

1995

• [H95]
  M Heiner:
  Petri Net Based Software Dependability Engineering;
  In Proc. 9th Symposium on Quality and Reliability in Electronics (RELECTRONIC '95), Budapest, Hungary, pages 181–186, October 1995. [ pdf ] [ BibTeX ]