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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

Selected references

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342 entries:

editorships · journal papers · conference papers · book chapters · technical reports · further reports · talks · posters · PhD theses · students' theses

editorships

  • [GH18.fi]
    A Gambin and M Heiner (eds.):
    Advances in Biological processes and Petri nets (BioPPN);
    volume 160 of Fundamenta Informaticae, IOS Press, 2018. [ doi ] [ BibTeX ]
  • [GHTU15]
    D Gilbert, M Heiner, K Takahashi and AM Uhrmacher (eds.):
    Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481);
    volume 4, Dagstuhl, Germany, Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2015. [ url ] [ doi ] [ BibTeX ]
  • [HW15.bioppn]
    M Heiner and AK Wagler (eds.):
    Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2015), satellite event of Petri Nets 2015;
    volume 1373 of CEUR Workshop Proceedings, June 2015. [ url ] [ BibTeX ]
  • [GH15.tcs]
    D Gilbert and M Heiner (eds.):
    Special Issue 'Advances in CMSB';
    volume 599 of J. Theoretical Computer Science, Elsevier, 2015. [ doi ] [ BibTeX ]
  • [H14.bioppn]
    M Heiner (ed.):
    Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2014), satellite event of Petri Nets 2014;
    volume 1159 of CEUR Workshop Proceedings, June 2014. [ url ] [ BibTeX ]
  • [BH13.bioppn]
    G Balbo and M Heiner (eds.):
    Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2013), satellite event of Petri Nets 2013;
    volume 988 of CEUR Workshop Proceedings, June 2013. [ url ] [ BibTeX ]
  • [GH12.lncs]
    D Gilbert and M Heiner (eds.):
    Computational Methods in Systems Biology; Proc. 10th International Conference CMSB 2012;
    volume 7605 of LNCS/LNBI, Springer, 2012. [ url ] [ doi ] [ BibTeX ]
  • [HH12.bioppn]
    M Heiner and R Hofestädt (eds.):
    Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2012), satellite event of Petri Nets 2012;
    volume 852 of CEUR Workshop Proceedings, June 2012. [ url ] [ BibTeX ]
  • [H11.naco1]
    M Heiner (ed.):
    Special Issue 'Petri Nets for Systems and Synthetic Biology, Part I: Bridging Gaps';
    volume 10 of J. Nat. Computing, Springer, 2011. [ doi ] [ BibTeX ]
  • [H11.naco2]
    M Heiner (ed.):
    Special Issue 'Petri Nets for Systems and Synthetic Biology, Part II: Unifying Diversity';
    volume 10 of J. Nat. Computing, Springer, 2011. [ doi ] [ BibTeX ]
  • [HU11.tcs]
    M Heiner and A Uhrmacher (eds.):
    Special Issue 'Foundations of formal reconstruction of biochemical networks';
    volume 412, issue 26 of J. Theoretical Computer Science, Elsevier, 2011. [ doi ] [ BibTeX ]
  • [HM11.bioppn]
    M Heiner and H Matsuno (eds.):
    Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2011), satellite event of Petri Nets 2011;
    volume 724 of CEUR Workshop Proceedings, June 2011. [ url ] [ BibTeX ]
  • [SH10.awpn]
    M Schwarick and M Heiner (eds.):
    Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010);
    volume 643 of CEUR Workshop Proceedings, October 2010. [ url ] [ BibTeX ]
  • [PBG+10.tcsb]
    C Priami, R Breitling, DR Gilbert, M Heiner and AM Uhrmacher (eds.):
    Special Issue on Modeling Methodologies;
    volume 5945 of Transactions on Computational Systems Biology XII, LNCS/LNBI, Springer, February 2010. [ doi ] [ BibTeX ]
  • [CH10.bioppn]
    C Chaouiya and M Heiner (eds.):
    Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2010), satellite event of Petri Nets 2010;
    June 2010. [ pdf ] [ BibTeX ]
  • [BGHP09]
    R Breitling, DR Gilbert, M Heiner and C Priami (eds.):
    Formal Methods in Molecular Biology;
    volume 09091 of Dagstuhl Seminar Proceedings, May 2009. [ url ] [ BibTeX ]
  • [HU08.lncs]
    M Heiner and AM Uhrmacher (eds.):
    Computational Methods in Systems Biology; Proc. 6th International Conference CMSB 2008;
    volume 5307 of LNCS/LNBI, Springer, 2008. [ doi ] [ BibTeX ]
  • [KHW03.lncs]
    H König, M Heiner and A Wolisz (eds.):
    Formal Techniques for Networked and Distributed Systems; Proc. FORTE 2003, 23rd IFIP WG 6.1 Int. Conference;
    volume 2767 of LNCS, Springer, 2003. [ doi ] [ BibTeX ]

journal papers (peer reviewed)

  • [GHGC19]
    D Gilbert, M Heiner, L Ghanbar and J Chodak:
    Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking;
    BMC Bioinformatics, 20(supplement 4), 2019 (accepted for publication: July, 26 2018; published April 2019). [ doi ] [ BibTeX ]
  • [LHG19]
    F Liu, M Heiner and D Gilbert:
    Coloured Petri nets for multilevel, multiscale, and multidimensional modelling of biological systems;
    Briefings in Bioinformatics, 20(3):877-886, 2019 (Published: 03 November 2017). [ doi ] [ BibTeX ]
  • [BBB+17]
    Baldan, P, Bocci, M, Brigolin, D, Cocco, N , Heiner, M and Simeoni, M:
    Petri Nets for modelling and analysing Trophic Networks;
    Fundamenta Informaticae, 160(1-2):27-52, 2018 (accepted for publication: May, 18 2017). [ doi ] [ BibTeX ]
  • [HH17]
    Herajy, M and Heiner, M:
    Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation;
    Fundamenta Informaticae, 160(1-2):53-80, 2018 (accepted for publication: May, 18 2017). [ doi ] [ BibTeX ]
  • [HLH17]
    M Herajy, F Liu and M Heiner:
    Efficient Modelling of Yeast Cell Cycles Based on Multisite Phosphorylation Using Coloured Hybrid Petri Nets with Marking-dependent Arc Weights;
    J. Nonlinear Analysis: Hybrid Systems, 27(February):191-212, 2018 (online: October 10, 2017). [ doi ] [ BibTeX ]
  • [R17]
    Rohr, C:
    Discrete-Time Leap Method For Stochastic Simulation;
    Fundamenta Informaticae, 160(1-2):181-198, 2018 (accepted for publication: May, 16 2017). [ doi ] [ BibTeX ]
  • [BR17]
    MA Blätke and Rohr, C:
    BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models;
    Fundamenta Informaticae, 160(1-2):221-254, 2018 (accepted for publication: May, 16 2017). [ doi ] [ BibTeX ]
  • [CDG+18]
    R Colombo, C Damiani, D Gilbert, M Heiner, G Mauri and D Pescini:
    Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes;
    BMC Bioinformatics, 19(Suppl 7):251, 2018 (accepted for publication: February, 19 2018). [ doi ] [ BibTeX ]
  • [LHG18]
    F Liu, M Heiner and D Gilbert:
    Fuzzy Petri nets for modelling of uncertain biological systems;
    Briefings in Bioinformatics, 2018 (accepted for publication:16 November 2018, published: 27 December 2018). [ url ] [ doi ] [ BibTeX ]
  • [XCP+18]
    H Xu, TY Curtis, SJ Powers, S Raffan, R Gao, J Huang, M Heiner, DR Gilbert and NG Halford:
    Genomic, biochemical and modelling analyses of asparagine synthetases from wheat;
    Frontiers in Plant Science, section Plant Physiology, 2018 (accepted for publication: December, 20 2017). [ doi ] [ BibTeX ]
  • [HLRH18]
    M Herajy, F Liu, C Rohr and M Heiner:
    Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks;
    Computational Biology and Chemistry, 76:87-100, 2018. [ doi ] [ BibTeX ]
  • [GHR18]
    D Gilbert, M Heiner and Christian Rohr:
    Petri-net-based 2D Design of DNA Walker Circuits;
    Natural Computing, 17(1):161–182, 2018 (accepted for publication: November, 20 2017, online February, 28 2018). [ doi ] [ BibTeX ]
  • [LCHS18]
    F Liu, S Chen, M Heiner and H Song:
    Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets;
    BMC Systems Biology, 12(Suppl 4):42, 2018 (accepted for publication: January 2018). [ doi ] [ BibTeX ]
  • [GHJR17]
    D Gilbert, M Heiner, Y Jayaweera and C Rohr:
    Towards dynamic genome scale models;
    Briefings in Bioinformatics, 2017 (online: October 13, 2017). [ doi ] [ BibTeX ]
  • [HLRH17]
    M Herajy, F Liu, C Rohr and M Heiner:
    Snoopy's Hybrid Simulator: a Tool to Construct and Simulate Hybrid Biological Models;
    BMC Systems Biology, 2017 (published: July 28, 2017). [ url ] [ doi ] [ BibTeX ]
  • [BKH+16]
    LMF Bertens, J Kleijn, SC Hille, M Heiner, M Koutny and FJ Verbeek:
    Modeling biological gradient formation: combining partial differential equations and Petri nets;
    Natural Computing, 15(4):665-675, 2016 (First online: 31 October 2015). [ url ] [ doi ] [ BibTeX ]
  • [LHY16a]
    F Liu, M Heiner and M Yang:
    Representing Network Reconstruction Solutions with Colored Petri Nets;
    Neurocomputing, 174, Part A:483–493, January 2016 (accepted for publication: April 2015). [ url ] [ doi ] [ BibTeX ]
  • [HRST16]
    M Heiner, C Rohr, M Schwarick and A Tovchigrechko:
    MARCIE’s secrets of efficient model checking;
    Transactions on Petri Nets and Other Models of Concurrency (ToPNoC) XI, LNCS 9930, 2016 (accepted for publication: March 11, 2016). [ url ] [ doi ] [ BibTeX ]
  • [LHY16b]
    F Liu, M Heiner and M Yang:
    Fuzzy stochastic Petri nets for modeling biological systems with uncertain kinetic parameters;
    PLoS ONE, 11(2):e0149674, 2016 (accepted for publication: February 09, 2016). [ url ] [ doi ] [ BibTeX ]
  • [SPE+16]
    J Somekh, M Peleg, A Eran, I Koren, A Feiglin, A Demishtein, R Shiloh, M Heiner, SW Kong, Z Elazar and I Kohane:
    A Model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease;
    Biomedical Informatics, 63(366-378), 2016 (accepted for publication: August 08, 2016). [ doi ] [ BibTeX ]
  • [PGH+15]
    O Pârvu, D Gilbert, M Heiner, F Liu, N Saunders and S Shaw:
    Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes;
    ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2):25p., May 2015. [ url ] [ doi ] [ BibTeX ]
  • [HH15]
    Herajy, M and Heiner, M:
    Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets;
    Frontiers in Environmental Science, 3(53), 2015 (accepted for publication: 13 July 2015). [ url ] [ doi ] [ BibTeX ]
  • [BHHP15]
    B Barbot, S Haddad, M Heiner and C Picaronny:
    A Rare Event Method Applied to Signalling Cascades;
    International Journal on Advances in Systems and Measurements, 8(1-2):69-79, 2015 (improved version of [BHHP14]). [ pdf ] [ BibTeX ]
  • [LBHY14]
    F Liu, MA Blätke, M Heiner and M Yang:
    Modelling and simulating reaction–diffusion systems using coloured Petri nets;
    Computers in Biology and Medicine, 53:297–308, October 2014 (online July 2014). [ url ] [ doi ] [ BibTeX ]
  • [LHY14]
    F Liu, M Heiner and M Yang:
    Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development;
    WSPC Journal of Biological Systems, 22(3):463–493, online May 2014. [ doi ] [ BibTeX ]
  • [HH14a]
    M Herajy and M Heiner:
    Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks;
    Fundamenta Informaticae, 129(1-2):49-67, 2014. [ url ] [ doi ] [ BibTeX ]
  • [GGH+13]
    Q Gao, D Gilbert, M Heiner, F Liu, D Maccagnola and D Tree:
    Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing;
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(2):337-351, 2013 (online 01 August 2012). [ doi ] [ BibTeX ]
  • [BDR+13]
    MA Blätke, A Dittrich, C Rohr, M Heiner, F Schaper and W Marwan:
    JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology;
    Molecular BioSystems, 9(6):1290-1307, 2013. [ url ] [ doi ] [ BibTeX ]
  • [HG13]
    M Heiner and D Gilbert:
    BioModel Engineering for Multiscale Systems Biology;
    Progress in Biophysics and Molecular Biology, 111(2-3):119–128, April 2013 (online available 12-OCT-2012). [ url ] [ doi ] [ BibTeX ]
  • [LH13a]
    F Liu and M Heiner:
    Modeling membrane systems using colored stochastic Petri nets;
    Nat. Computing, 12(4):617 - 629, 2013. [ url ] [ doi ] [ BibTeX ]
  • [HSH13]
    M Herajy, M Schwarick and M Heiner:
    Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle;
    ToPNoC VIII, LNCS 8100, 2013. [ pdf ] [ doi ] [ BibTeX ]
  • [Rohr13]
    C Rohr:
    Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
    ToPNoC VIII, LNCS 8100, 2013. [ doi ] [ BibTeX ]
  • [LH13b]
    F Liu and M Heiner:
    Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets;
    IET Systems Biology, 7(4):106 - 113, August 2013. [ doi ] [ BibTeX ]
  • [HH12]
    M Herajy and M Heiner:
    Hybrid Representation and Simulation of Stiff Biochemical Networks;
    J. Nonlinear Analysis: Hybrid Systems, 6(4):942–959, November 2012. [ url ] [ doi ] [ BibTeX ]
  • [ST11]
    M Schwarick and A Tovchigrechko:
    IDD-based model validation of biochemical networks;
    Theoretical Computer Science, 412(26):2884–2908, 2011 (online July 2010). [ pdf ] [ doi ] [ BibTeX ]
  • [RMH10]
    C Rohr, W Marwan and M Heiner:
    Snoopy - a unifying Petri net framework to investigate biomolecular networks;
    Bioinformatics, 26(7):974–975, 2010 ((Advanced Access published February 7, 2010)). [ url ] [ doi ] [ BibTeX ]
  • [SH10b]
    S Soliman and M Heiner:
    A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
    PLoS ONE, 5(12):e14284, 2010. [ doi ] [ BibTeX ]
  • [HS10]
    M Heiner and K Sriram:
    Structural Analysis to Determine the Core of Hypoxia Response Network;
    PLoS ONE, 5(1):e8600, 2010. [ doi ] [ BibTeX ]
  • [BDGH10]
    R Breitling, RA Donaldson, DR Gilbert and M Heiner:
    Biomodel Engineering - From Structure to Behavior (position paper);
    Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies, 5945:1–12, 2010. [ pdf ] [ doi ] [ BibTeX ]
  • [HLGM09]
    M Heiner, S Lehrack, D Gilbert and W Marwan:
    Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments;
    Transactions on Computational Systems Biology XI, 5750:138–163, 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
  • [GSH+08]
    E Grafahrend-Belau, F Schreiber, M Heiner, A Sackmann, BH Junker, S Grunwald, A Speer, K Winder and I Koch:
    Modularization of biochemical networks based on classification of Petri net T-invariants;
    BMC Bioinformatics, 9:90, 2008. [ doi ] [ BibTeX ]
  • [BGHO08]
    R Breitling, D Gilbert, M Heiner and R Orton:
    A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
    Briefings in Bioinformatics, 9(5):404–421, September 2008. [ doi ] [ BibTeX ]
  • [SHK06]
    A Sackmann, M Heiner and I Koch:
    Application of Petri net based analysis techniques to signal transduction pathways;
    BMC Bioinformatics 2006, 7:482, 2006. [ url ] [ doi ] [ BibTeX ]
  • [PHK05]
    L Popova-Zeugmann, M Heiner and I Koch:
    Time Petri Nets for Modelling and Analysis of Biochemical Networks);
    Fundamenta Informaticae, 67:149–162, 2005. [ url ] [ pdf ] [ BibTeX ]
  • [KJH05]
    I Koch, BH Junker and M Heiner:
    Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber;
    Bioinformatics, April 2005, 21:1219 - 1226, 2005. [ doi ] [ BibTeX ]
  • [KSH04]
    I Koch, M Schüler and M Heiner:
    STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks;
    In Silico Biology, 5, 2004. [ url ] [ BibTeX ]
  • [HKW04]
    M Heiner, I Koch and J Will:
    Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
    BioSystems, 75/1-3:15-28, 2004. [ pdf ] [ doi ] [ BibTeX ]
  • [VHK03]
    K Voss, M Heiner and I Koch:
    Steady State Analysis of Metabolic Pathways Using Petri Nets;
    In Silico Biology, 3:367–387, 2003. [ url ] [ pdf ] [ BibTeX ]
  • [HVW94]
    M Heiner, G Ventre and D Wikarski:
    A Petri Net Based Methodology to Integrate Qaulitative and Quantitative Analysis;
    Information and Software Technology, 7(36):435–441, 1994. [ url ] [ pdf ] [ BibTeX ]

conference/workshop papers (peer reviewed)

  • [CH19]
    J Chodak and M Heiner:
    Spike – reproducible simulation experiments with configuration file branching;
    In Proc. CMSB 2019, Trento, Springer, LNCS/LNBI, September 2019. [ BibTeX ]
  • [AHL19]
    G Assaf, M Heiner and F Liu:
    Biochemical reaction networks with fuzzy kinetic parameters in Snoopy;
    In Proc. CMSB 2019, Trento, Springer, LNCS/LNBI, September 2019. [ 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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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. [ url ] [ pdf ] [ 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 ]
  • [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. [ url ] [ pdf ] [ BibTeX ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [Spra97]
    J Spranger:
    FUNlite - A Parallel Petri Net Simulator;
    In Proc. 42. IWK Ilmenau, September 1997), IWK Ilmenau, page 6, 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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]
  • [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 ]

book chapters

  • [H19]
    M Heiner:
    Petri Nets for BioModel Engineering: A Personal Perspective;
    In Carl Adam Petri: Ideas, Personality, Impact, (W Reisig and G Rozenberg, Eds.), Springer, Cham, pages 205–216, 2019 (first online 25 May 2019). [ url ] [ doi ] [ BibTeX ]
  • [IHH19]
    A Ismail, M Herajy and M Heiner:
    A Graphical Approach for the Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets;
    In Automated Reasoning for Systems Biology and Medicine, (P Zuliani and P Liò, Eds.), Springer, Cham, pages 349–367, 2019 (first online: 12. June 2019). [ url ] [ doi ] [ BibTeX ]
  • [BHM15]
    MA Blätke, M Heiner and W Marwan:
    BioModel Engineering with Petri Nets;
    In Algebraic and Discrete Mathematical Methods for Modern Biology, (R Robeva, Ed.), Elsevier Inc., pages 141–193, March 2015. [ url ] [ doi ] [ BibTeX ]
  • [LH14]
    F Liu and M Heiner:
    Petri Nets for Modeling and Analyzing Biochemical Reaction Networks;
    In Approaches in Integrative Bioinformatics, (M Chen and R Hofestädt, Eds.), Springer, pages 245–272, 2014. [ url ] [ pdf ] [ doi ] [ BibTeX ]
  • [BRHM14]
    MA Blätke, C Rohr, M Heiner and W Marwan:
    A Petri Net based Framework for Biomodel Engineering;
    In Large-Scale Networks in Engineering and Life Sciences, (Benner, P, Findeisen, R, Flockerzi, D, Reichl, U and Sundmacher, K, Eds.), Springer, Birkhäuser Mathematics, pages 317–366, December 2014. [ doi ] [ BibTeX ]
  • [MRH12]
    W Marwan, C Rohr and M Heiner:
    Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks;
    In Methods in Molecular Biology – Bacterial Molecular Networks, (Jv Helden, A Toussaint and D Thieffry, Eds.), Humana Press, pages 409–437, 2012. [ pdf ] [ doi ] [ BibTeX ]
  • [HG11]
    M Heiner and D Gilbert:
    How Might Petri Nets Enhance Your Systems Biology Toolkit;
    In Proc. PETRI NETS 2011, (Kristensen, LM and Petrucci, L, Eds.), Springer, pages 17–37, 2011. [ url ] [ pdf ] [ doi ] [ BibTeX ]
  • [VHK11]
    K Voss, M Heiner and I Koch:
    Petri Nets for Steady State Analysis of Metabolic Systems;
    In Biological Petri Nets, (E Wingender, Ed.) Pages 56–76, 2011 (reprint of [VHK03]). [ doi ] [ BibTeX ]
  • [HDG10]
    M Heiner, R Donaldson and D Gilbert:
    Petri Nets for Systems Biology;
    In Symbolic Systems Biology: Theory and Methods, (MS Iyengar, Ed.), Jones & Bartlett Learning, LCC, pages 61–97, 2010. [ url ] [ pdf ] [ BibTeX ]
  • [GHBO10]
    D Gilbert, M Heiner, R Breitling and R Orton:
    Computation modelling of kinase signalling cascades;
    In MAP Kinase Signaling Protocols, (R Seger, Ed.) Pages 369–384, 2010. [ url ] [ doi ] [ BibTeX ]
  • [H09]
    M Heiner:
    Understanding Network Behaviour by Structured Representations of Transition Invariants – A Petri Net Perspective on Systems and Synthetic Biology;
    In Algorithmic Bioprocesses, (A Condon, D Harel, JN Kok, A Salomaa and E Winfree, Eds.), Springer, pages 367–389, 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
  • [HGD08]
    M Heiner, D Gilbert and R Donaldson:
    Petri Nets for Systems and Synthetic Biology;
    In SFM 2008, (M Bernardo, P Degano and G Zavattaro, Eds.), Springer, pages 215–264, 2008. [ pdf ] [ doi ] [ BibTeX ]
  • [KH08]
    I Koch and M Heiner:
    Petri Nets;
    In Biological Network Analysis, (BH Junker and F Schreiber, Eds.), John Wiley & Sons, pages 139–179, 2008 (Series Eds. Yi Pan, Albert Y. Zomaya). [ url ] [ BibTeX ]

further papers (no or weak review process)

  • [CH18]
    J Chodak and M Heiner:
    Spike - a command line tool for continuous, stochastic & hybrid simulation of (coloured) Petri nets;
    In Proc. 21th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2018), University of Augsburg, pages 1-6, October 2018. [ url ] [ pdf ] [ BibTeX ]
  • [GHG17]
    D Gilbert, M Heiner and L Ghanbar:
    Personalised models for human – gut microbiota interaction;
    In Methods, tools & platforms for Personalised Medicine in the Big Data Era, NETTAB 2017 Workshop Collection, PeerJ, volume Preprints 5:e3267v1, pages 1-4, September 2017. [ url ] [ doi ] [ BibTeX ]
  • [H16]
    M Heiner:
    From Petri Nets to Partial Differential Equations: A Petri Net Perspective on Systems and Synthetic Biology;
    In Y Rondelez, D Woods (ed.): DNA Computing and Molecular Programming (DNA22), Springer, LNCS, volume 9818, September 2016. [ url ] [ pdf ] [ BibTeX ]
  • [H14-feature]
    Research Media:
    The power of Petri nets;
    In International Innovation, Special Focus - Women in Healthcare, Research Media, volume 137, pages 72-74, May 2014. [ url ] [ pdf ] [ BibTeX ]
  • [H14]
    M Heiner:
    Petri Nets Research at BTU in Cottbus, Germany;
    In Petri Net Newsletter, GI, Newsletter of the Special Interest Group on Petri Nets and Related System Models, ISSN 0391-1804, volume 83, pages 19-25, April 2014. [ pdf ] [ BibTeX ]
  • [HWW11]
    M Heiner, H Wimmel and K Wolf:
    Atomic Fragments of Petri Nets;
    In Proc. 18th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2011), Fernuniv. Hagen, September 2011. [ url ] [ pdf ] [ BibTeX ]
  • [HH10]
    M Herajy and M Heiner:
    Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions;
    In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 66–79, October 2010. [ pdf ] [ BibTeX ]
  • [LH10b]
    F Liu and M Heiner:
    Computation of Enabled Transition Instances for Colored Petri Nets;
    In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 51–65, October 2010. [ pdf ] [ BibTeX ]
  • [Schw10]
    M Schwarick:
    IDD-MC - a model checker for bounded stochastic Petri nets;
    In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 80–87, October 2010. [ pdf ] [ BibTeX ]
  • [Rohr10]
    C Rohr:
    Simulative CSL model checking of Stochastic Petri nets in IDD-MC;
    In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 88–93, October 2010. [ pdf ] [ BibTeX ]
  • [Schw08]
    M Schwarick:
    Transient Analysis of Stochastic Petri Nets With Interval Decision Diagrams;
    In Proc. 15th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2008), CEUR-WS.org, CEUR Workshop Proceedings, volume 380, pages 43–48, September 2008. [ pdf ] [ BibTeX ]
  • [HRRS08]
    M Heiner, R Richter, C Rohr and M Schwarick:
    Snoopy – A Tool to Design and Animate/Simulate Graph-Based Formalisms;
    In Petri Net Newsletter, GI, pages 8–22, April 2008 (This paper is an extended version of Proc. PNTAP 2008). [ pdf ] [ BibTeX ]
  • [HRS07]
    M Heiner, R Richter and M Schwarick:
    Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
    In Proc. AWPN Workshop, Koblenz, Sept. 2007, pages 8-13, 2007. [ url ] [ pdf ] [ BibTeX ]
  • [PHK04]
    L Popova-Zeugmann, M Heiner and I Koch:
    Modelling and Analysis of Biochemical Networks with Time Petri Nets;
    In Proc. Workshop Concurrency, Specification and Programming (CSP 2011), Humboldt University, Informatik-Berichte HUB, No 170, volume 1, pages 136-143, September 2004. [ pdf ] [ BibTeX ]

technical reports

  • [HLRH17.manual]
    M Herajy, F Liu, C Rohr and M Heiner:
    (Coloured Hybrid Petri Nets in Snoopy - User Manual;
    Technical report 01-17, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2017. [ url ] [ BibTeX ]
  • [H16.mcc]
    M Heiner:
    GPPP – Glycolysis and Pentose Phosphate Pathway, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2016. [ url ] [ pdf ] [ BibTeX ]
  • [SRH16]
    M Schwarick, C Rohr and M Heiner:
    MARCIE Manual;
    Technical report 02-16, Brandenburg University of Technology Cottbus, Department of Computer Science, December 2016. [ url ] [ pdf ] [ BibTeX ]
  • [A15]
    S Agarwal:
    Reengineering Snoopy’s GUI (Internship report);
    Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2015. [ pdf ] [ BibTeX ]
  • [S15]
    A Sharma:
    Snoopy Report Generator Snoopy2LATEX (Internship report);
    Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2015. [ pdf ] [ BibTeX ]
  • [H15.mcc]
    M Heiner:
    Phase variation in cell colony growth, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2015. [ url ] [ pdf ] [ BibTeX ]
  • [CS14]
    C Swapnil:
    Stochastic simulation efficiency;
    Technical report 02-14, Brandenburg University of Technology Cottbus-Senftenberg, Department of Computer Science, July 2014. [ url ] [ BibTeX ]
  • [H14a.mcc]
    M Heiner:
    Diffusion in 2D, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
  • [H14b.mcc]
    M Heiner:
    Parameterised Production Cell, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
  • [AS14]
    A Sinha:
    Comparison of stochastic simulation tools;
    Technical report 01-14, Brandenburg University of Technology Cottbus-Senftenberg, Department of Computer Science, June 2014. [ url ] [ BibTeX ]
  • [R14c.mcc]
    C Rohr:
    ERK signalling pathway, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
  • [H14c.mcc]
    M Heiner:
    Solitaire, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
  • [R14a.mcc]
    C Rohr:
    Angiogenesis, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
  • [R14b.mcc]
    C Rohr:
    Circadian Clock, a Petri net model;
    Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
  • [BKH+13]
    LMF Bertens, J Kleijn, SC Hille, M Koutny, M Heiner and FJ Verbeek:
    Modeling biological gradient formation: combining partial differential equations and Petri nets;
    Technical report CS-TR-1379, University of Newcastle upon Tyne, School of Computing Science, March 2013. [ url ] [ BibTeX ]
  • [HH13.manual]
    M Herajy and M Heiner:
    Snoopy Computational Steering Framework – User Manual Version 1.0;
    Technical report 02-13, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2013. [ pdf ] [ BibTeX ]
  • [LHR12.manual]
    F Liu, M Heiner and C Rohr:
    Manual for Colored Petri Nets in Snoopy;
    Technical report 02-12, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2012. [ pdf ] [ BibTeX ]
  • [BHM11]
    MA Blätke, M Heiner, and W Marwan:
    Tutorial - Petri Nets in Systems Biology;
    Technical report, Otto von Guericke University Magdeburg, Magdeburg Centre for Systems Biology, August 2011. [ pdf ] [ BibTeX ]
  • [HH11]
    M Herajy and M Heiner:
    Hybrid Representation and Simulation of Stiff Biochemical Networks through Generalised Hybrid Petri Nets;
    Technical report 02-11, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2011. [ pdf ] [ BibTeX ]
  • [LH11]
    F Liu and M Heiner:
    Manual for Colored Petri Nets in Snoopy;
    Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2011. [ pdf ] [ BibTeX ]
  • [Liu09.manual]
    F Liu:
    Manual for Snoopy2Prism Export;
    Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2009. [ pdf ] [ BibTeX ]
  • [GHL07a]
    D Gilbert, M Heiner and S Lehrack:
    A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
    Technical report I-02/2007, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2007. [ pdf ] [ BibTeX ]
  • [Lehr06]
    S Lehrack:
    Three Petri net approaches for Biochemical Network Analysis;
    Technical report I-01/2006, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2006. [ pdf ] [ BibTeX ]
  • [GH05]
    D Gilbert and M Heiner:
    From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis;
    Technical report I-04/2005, Brandenburg University of Technology Cottbus, Department of Computer Science, December 2005. [ pdf ] [ BibTeX ]
  • [Tovc04]
    A Tovchigrechko:
    Model Checking of Bounded Petri Nets Using Interval Diagrams;
    Technical report I-05/2004, Brandenburg University of Technology Cottbus, Department of Computer Science, November 2004. [ pdf ] [ BibTeX ]
  • [Runge04a]
    T Runge:
    Qualitative Path Analysis of Metabolic Pathways Using Petri Nets for Generic Modelling;
    Technical report I-03/2004, Brandenburg University of Technology Cottbus, Department of Computer Science, August 2004. [ pdf ] [ BibTeX ]
  • [WH02]
    J Will and M Heiner:
    Petri Nets in Biology, Chemistry, and Medicine - Bibliography;
    Technical report I-04/02, Brandenburg University of Technology Cottbus, Department of Computer Science, November 2002. [ pdf ] [ BibTeX ]
  • [HMD01]
    M Heiner, T Mertke and P Deussen:
    A Safety-Oriented Technical Language for the Requirement Specification in Control Engineering (in German, Eine Sicherheitsfachsprache zur Formulierung steuerungstechnischer Anforderungen), Mai 2001;
    Technical report, 2001. [ pdf ] [ BibTeX ]
  • [Deus99]
    P Deussen:
    Improvements of Concurrent Automata Generation;
    Technical report I-08/1999, Brandenburg University of Technology Cottbus, Department of Computer Science, July 1999. [ pdf ] [ BibTeX ]
  • [Deus98]
    P Deussen:
    Concurrent Automata;
    Technical report I-05/1998, Brandenburg University of Technology Cottbus, Department of Computer Science, August 1998. [ pdf ] [ BibTeX ]
  • [HM97]
    M Heiner and T Menzel:
    Petri-Netz-Semantik für die SPS-Anwenderprogrammiersprache Anweisungsliste;
    Technical report I-20/1997, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1997. [ pdf ] [ BibTeX ]
  • [HMMM97]
    M Heiner, M Meier, T Menzel and T Mertke:
    Petri-Netz basierte Methoden zur sicherheitsorientierten Zertifizierung von SPS Anwenderprogrammen;
    Technical report I-19/1997, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1997. [ pdf ] [ BibTeX ]
  • [HP96]
    M Heiner and L Popova-Zeugmann:
    Worst-case Analysis of Concurrent Systems with Duration Interval Petri Nets;
    Technical report I-02/1996, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1996. [ pdf ] [ BibTeX ]
  • [WH95]
    D Wikarski and M Heiner:
    On the Application of Markovian Object Nets to Integrated Qualitative and Software Analysis;
    Technical report 29/95, Fraunhofer ISST Berlin, October 1995. [ pdf ] [ BibTeX ]
  • [HD95]
    M Heiner, P Deussen:
    Petri Net Based Qualitative Analysis - A Case Study;
    Technical report I-08/1995, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1995. [ pdf ] [ BibTeX ]
  • [HW94]
    M Heiner and D Wikarski:
    An Approach to Petri Net Based Integration of Qualitative and Quantitative Analysis of Parallel Systems;
    Technical report I-09/1994, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1994. [ pdf ] [ BibTeX ]
  • [H92]
    M Heiner:
    Petri Net Based Software Validation - Prospects and Limitations;
    Technical report TR-92-022, ICSI Berkeley, March 1992. [ pdf ] [ BibTeX ]

talks

  • [HH18.sld]
    M Herajy and M Heiner:
    An improved simulation of hybrid biological models with many stochastic events and quasi-disjoint subnets;
    Talk, WSC 2018, Gothenburg, December 2018. [ pdf ] [ BibTeX ]
  • [H18.sld1]
    M Heiner:
    A Petri Net Framework for Spatial And Multiscale Modelling of Plant Biochemistry;
    Talk, Mathematical Modelling in Plants, Rothamsted Research, Harpenden, UK (invited talk), March 2018. [ url ] [ pdf ] [ BibTeX ]
  • [SGH18.sld]
    T Self, D Gilbert and M Heiner:
    Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models;
    Talk, Computational Methods in Systems Biology (CMSB2018), Brno/CZ, September 2018. [ pdf ] [ BibTeX ]
  • [CH18.sld]
    J Chodak and M Heiner:
    Spike - a command line tool for continuous, stochastic & hybrid simulation of (coloured) Petri nets;
    Talk, AWPN2018, University of Augsburg, October 2018. [ pdf ] [ BibTeX ]
  • [LCH17.sld]
    F Liu, S Chen and M Heiner:
    Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets;
    Talk, 11th International Conference on Computational Systems Biology (ISB 2017), Shenzhen, China, August 2017. [ url ] [ pdf ] [ BibTeX ]
  • [GHG17.sld]
    D Gilbert, M Heiner and L Ghanbar:
    Personalised models for human – gut microbiota interaction;
    Talk, Methods, tools & platforms for Personalised Medicine in the Big Data Era, NETTAB 2017 Workshop, Palermo/Italy, October 2017. [ url ] [ pdf ] [ BibTeX ]
  • [GH16.sld1]
    D Gilbert, M Heiner:
    Analysis and repair of whole genome bacterial metabolic models for synthetic biology;
    Talk, Brunel University London, Computer Science Seminar (invited talk), February 2016. [ url ] [ BibTeX ]
  • [HG16.sld1]
    M Heiner, D Gilbert:
    Analysis and repair of whole genome bacterial metabolic models for synthetic biology;
    Talk, Yamaguchi Workshop on Computational Network Biology (invited talk), March 2016. [ url ] [ pdf ] [ BibTeX ]
  • [H16.sld2]
    M Heiner:
    From Petri Nets to Partial Differential Equations;
    Talk, 22nd International Conference on DNA Computing and Molecular Programming (DNA22), Munich (invited talk), September 2016. [ url ] [ pdf ] [ BibTeX ]
  • [HG16.sld2]
    M Heiner, D Gilbert:
    Model-driven design for Synthetic Systems Biology;
    Talk, Bioinformaticsday@DAIS, Ca' Foscari University (invited talk), July 2016. [ url ] [ pdf ] [ BibTeX ]
  • [HH16.sld]
    M Herajy and M Heiner:
    Accelerated Simulation of Hybrid Biological Models with Quasi-disjoint Deterministic and Stochastic Subnets;
    Talk, 5th Int. Workshop on Hybrid Systems Biology (HSB 2016), October 2016. [ url ] [ pdf ] [ BibTeX ]
  • [H15.sld1]
    M Heiner:
    Petri Nets 4 Bacterial Bioengineering;
    Talk, Brunel University London, Centre for Systems and Synthetic Biology, March 2015. [ pdf ] [ BibTeX ]
  • [H15.sld2]
    M Heiner:
    Model-driven design for Synthetic Systems Biology;
    Talk, Brunel University London, Centre for Systems and Synthetic Biology, April 2015. [ pdf ] [ BibTeX ]
  • [H15.sld4]
    M Heiner:
    From Petri Nets to Partial Differential Equations;
    Talk, Leiden University, NL, Van Leeuwenhoek Lecture on BioScience (invited talk), November 2015. [ url ] [ pdf ] [ BibTeX ]
  • [HSW15.sld]
    M Heiner, M Schwarick and J Wegener:
    Charlie – an extensible Petri net analysis tool;
    Talk, PETRI NETS 2015, Brussels, June 2015. [ pdf ] [ BibTeX ]
  • [H15.sld5]
    M Heiner:
    From Petri Nets to Partial Differential Equations;
    Talk, International Conference for Mathematics and Applications (ICMS15), MSA University, Cairo (invited talk), December 2015. [ url ] [ pdf ] [ BibTeX ]
  • [H15.sld3]
    M Heiner:
    From Petri Nets to Partial Differential Equations – Spatial Modelling in Systems Biology;
    Talk, Sino-German Workshop, Beijing, Sino-German Center for Research Promotion, October 2015. [ url ] [ pdf ] [ BibTeX ]
  • [H14.sld1]
    M Heiner:
    BioModel Engineering - a Petri Net Perspective;
    Talk, Università Ca' Foscari Di Venezia (invited talk), March 2014. [ pdf ] [ BibTeX ]
  • [HH14.sld]
    M Herajy and M Heiner:
    A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
    Talk, PETRI NETS 2014, Tunis, June 2014. [ pdf ] [ BibTeX ]
  • [H14.sld2]
    M Heiner:
    From Petri Nets to Partial Differential Equations – Spatial Modelling in Systems Biology;
    Talk, Dagstuhl, November 2014. [ pdf ] [ BibTeX ]
  • [GHLS13.sld]
    D Gilbert, M Heiner, F Liu and N Saunders:
    Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology;
    Talk, PETRI NETS 2013, Milano, June 2013. [ pdf ] [ BibTeX ]
  • [HRS13.sld]
    M Heiner, C Rohr and M Schwarick:
    MARCIE - Model checking And Reachability analysis done effiCIEntly;
    Talk, PETRI NETS 2013, Milano, June 2013. [ pdf ] [ BibTeX ]
  • [H13.sld1]
    M Heiner:
    BioModel Engineering - a Petri Net Perspective;
    Talk, Workshop: Teaching Discrete and Algebraic Mathematical Biology to Undergraduates, MBI, Ohio State University (invited talk), July 2013. [ url ] [ pdf ] [ BibTeX ]
  • [H13.sld5]
    M Heiner:
    Time Petri Nets for Modelling and Analysis of Biochemical Networks – On the Influence of Time;
    Talk, KOSMOS workshop, Humboldt University, Berlin, November 2013. [ pdf ] [ BibTeX ]
  • [H13.sld2]
    M Heiner:
    BioModel Engineering - a Petri Net Perspective;
    Talk, Laboratoire Spécification et Vérification, Cachan/Paris (invited talk), October 2013. [ url ] [ pdf ] [ BibTeX ]
  • [H13.sld4]
    M Heiner:
    Modular Modelling with Petri Nets;
    Talk, ENS, Département de Biologie/Paris, October 2013. [ pdf ] [ BibTeX ]
  • [H13.sld3]
    M Heiner:
    From Petri Nets to Partial Differential Equations;
    Talk, Seminaire MeFoSyLoMa (Formal Methods for Hardware and Software Systems), LIPN/Paris (invited talk), October 2013. [ url ] [ pdf ] [ BibTeX ]
  • [HG12.sld]
    M Heiner and D Gilbert:
    From Petri Nets to Partial Differential Equations and beyond;
    Talk, Workshop on Conceptional Foundations of Systems Biology, Balliol College Oxford (invited talk), March 2012. [ pdf ] [ BibTeX ]
  • [H12.sld1]
    M Heiner:
    BioModel Engineering - a Petri Net Perspective;
    Talk, Jena Centre of Bioinformatics (invited talk), March 2012. [ BibTeX ]
  • [H12.sld2]
    M Heiner:
    Coloured Petri Nets for Multiscale Systems Biology;
    Talk, Workshop 6: Algebraic Methods in Systems and Evolutionary Biology, MBI, Ohio State University (invited talk), May 2012. [ url ] [ BibTeX ]
  • [HS12.sld1]
    M Herajy and M Schwarick:
    A Hybrid Petri Net Model of the Eukaryotic Cell Cycle;
    Talk, 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
  • [HS12.sld2]
    M Heiner and M Schwarick:
    Markov Chains & Functional Safety;
    Talk, Philotech Academy, Berlin, October 2012. [ pdf ] [ BibTeX ]
  • [HH12+.sld]
    M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
    Snoopy – a unifying Petri net tool;
    Talk, PETRI NETS 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
  • [Rohr12.sld]
    C Rohr:
    Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
    Talk, 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
  • [HH11.sld]
    M. Herajy and M. Heiner:
    Generalized Hybrid Petri Nets;
    Talk, Formal Methods in Molecular Biology, Dagstuhl seminar, April 2011. [ pdf ] [ BibTeX ]
  • [H11.sld2]
    M Heiner:
    Biochemical Networks - a Petri Net Perspective;
    Talk, Universtita Torino, PhD School (invited talk), March 2011. [ pdf ] [ BibTeX ]
  • [H11.sld1]
    M Heiner:
    Biochemically Interpreted Petri Nets, Some Open Problems;
    Talk, Universtita Torino, research group Prof. G Balbo (invited talk), March 2011. [ pdf ] [ BibTeX ]
  • [Liu11]
    F. Liu:
    Colored Petri Nets for Modeling and Analyzing Biological Systems;
    Talk, Formal Methods in Molecular Biology, Dagstuhl seminar, April 2011. [ pdf ] [ BibTeX ]
  • [H11.sld5]
    M Heiner:
    Petri Nets for Multiscale Systems Biology;
    Talk, Brunel University, DISC seminar, September 2011. [ pdf ] [ BibTeX ]
  • [H11.sld3]
    M Heiner:
    BioModel Engineering - a Petri Net Perspective;
    Talk, Brunel University, DISC seminar, May 2011. [ pdf ] [ BibTeX ]
  • [WSH11.sld]
    J Wegener, M Schwarick and M Heiner:
    A Plugin System for Charlie;
    Talk, International Workshop on Concurrency, Specification, and Programming (CSP 2011), September 2011. [ pdf ] [ BibTeX ]
  • [SRH11.sld]
    M Schwarick, C Rohr and M Heiner:
    MARCIE - Model checking And Reachability analysis done effiCIEntly;
    Talk, QEST 2011, Aachen, September 2011. [ pdf ] [ BibTeX ]
  • [H11.sld4]
    M Heiner:
    How Might Petri Nets Enhance Your Systems Biology Toolkit;
    Talk, PETRI NET 2011, Newcastle (invited talk), June 2011. [ pdf ] [ BibTeX ]
  • [LH10.sld2]
    F Liu and M Heiner:
    Colored Petri nets to model and simulate biological systems;
    Talk, Workshop on Biological Processes & Petri Nets (BioPPN), Braga, June 2010. [ pdf ] [ BibTeX ]
  • [H10.sld4]
    M Heiner:
    Biochemical Networks - a Petri Net Perspective;
    Talk, Virginia Bioinformatics Institute at Virginia Tech, Blacksburg (invited talk), August 2010. [ pdf ] [ BibTeX ]
  • [HMS10.sld]
    M Heiner, C Mahulea and M Silva:
    On the Importance of the Deadlock Trap Property for Monotonic Liveness;
    Talk, Workshop on Biological Processes & Petri Nets (BioPPN), Braga, June 2010. [ pdf ] [ BibTeX ]
  • [H10.sld5]
    M Heiner:
    Biochemical Networks - a Petri Net Perspective;
    Talk, College of William and Mary, Dep. of Computer Science, Williamsburg (invited talk), August 2010. [ pdf ] [ BibTeX ]
  • [H10.sld3]
    M Heiner:
    Schaltkreise des Lebens - wie die Informatik beim Lösen der Rätsel hilft, die uns die Evolution aufgibt;
    Talk, BTU Cottbus, Seniorenkolleg, June 2010. [ pdf ] [ BibTeX ]
  • [LH10.sld1]
    F Liu and M Heiner:
    A colored Petri nets-based framework for modeling and simulating biological systems;
    Talk, Summer School on Integrative Biological Pathway Analysis and Simulation (IB-PAS 2010), Bielefeld, May 2010. [ pdf ] [ BibTeX ]
  • [H10.sld2]
    M Heiner:
    Modularization and hierarchical representation of biomolecular networks with Petri nets transition invariants;
    Talk, Workshop on Integrative Biological Pathway Analysis and Simulation (IB-PAS), Bielefeld, May 2010. [ pdf ] [ BibTeX ]
  • [H10.sld1]
    M Heiner:
    Snoopy - a unifying Petri net framework to investigate biomolecular networks;
    Talk, Summer School on Integrative Biological Pathway Analysis and Simulation (IB-PAS 2010), Bielefeld (invited talk), May 2010. [ pdf ] [ BibTeX ]
  • [H09.sld1]
    M Heiner:
    A Petri Net Perspective on Systems and Synthetic Biology;
    Talk, Brunel University London (invited talk), June 2009. [ pdf ] [ BibTeX ]
  • [HST09.sld]
    M Heiner, M Schwarick and A Tovchigrechko:
    DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets;
    Talk, PETRI NETS 2009 Paris, June 2009. [ pdf ] [ BibTeX ]
  • [SH09.sld]
    M Schwarick and M Heiner:
    CSL model checking of biochemical networks with Interval Decision Diagrams;
    Talk, CMSB 2009, Bologna, September 2009. [ pdf ] [ BibTeX ]
  • [HGD08.sld1]
    M Heiner, D Gilbert and R Donaldson:
    Petri Nets for Systems and Synthetic Biology;Workshop on Computational Models for Cell Processes;
    Talk, Satellite event to Formal Methods 2008, Turku, May 2008. [ pdf ] [ BibTeX ]
  • [H08.sld1]
    M Heiner:
    Modularization of Biochemical Networks by T-invariants;
    Talk, MPI Martinsried, January 2008 (for improved version see: talk given at IB-PAS 2010). [ BibTeX ]
  • [HGD08.sld2]
    M Heiner, D Gilbert and R Donaldson:
    Petri Nets for Systems and Synthetic Biology;
    Talk, Bertinoro (invited talk), June 2008. [ pdf ] [ BibTeX ]
  • [H08.sld2]
    M Heiner:
    Time Petri nets for modelling and analysis of biochemical networks - on the influence of time;
    Talk, MaReBio, Marseille (invited talk), November 2008. [ pdf ] [ BibTeX ]
  • [H07.sld1]
    M Heiner:
    Mathematical Modelling of Biochemical Networks with Petri Nets;
    Talk, FMP Berlin, February 2007. [ pdf ] [ BibTeX ]
  • [H07.sld2]
    M Heiner:
    Biochemically Interpreted Petri Nets - Two Open Problems (invited talk);
    Talk, Seminaire MeFoSyLoMa (Formal Methods for Hardware and Software Systems), Université Paris 13 (invited talk), June 2007. [ pdf ] [ BibTeX ]
  • [H07.sld3]
    M Heiner:
    Modularization by T-invariants;
    Talk, 4ème réunion de l'ARC MOCA, Paris, June 2007 (for improved version see: talk given at MPI Martinsried, January 2008). [ BibTeX ]
  • [H07.sld4]
    M Heiner:
    Modularization of Biochemical Networks by T-invariants;
    Talk, Univ. Rostock, CS Dep (invited talk), November 2007 (for improved version see: talk given at IB-PAS 2010). [ BibTeX ]
  • [GHL07.sld]
    D Gilbert, M Heiner and S Lehrack:
    A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
    Talk, CMSB 2007, Edinburgh, September 2007. [ pdf ] [ BibTeX ]
  • [W06.sld]
    K Winder:
    Strukturelle Charakterisierung der Invarianten eines Petrinetzes;
    Talk, FU Berlin, DFG-Research Center Matheon, May 2006. [ pdf ] [ BibTeX ]
  • [H06.sld2]
    M Heiner:
    Systems Biology - A Petri Net Perspective;
    Talk, TU Ilmenau, Fakultätskolloquium zum Informatikjahr (invited talk), July 2006. [ pdf ] [ BibTeX ]
  • [H06.sld1]
    M Heiner:
    Pathway Analysis of Biochemical Networks with Petri Nets: animated version / printable;
    Talk, FU Berlin, DFG-Research Center Matheon, May 2006. [ pdf ] [ BibTeX ]
  • [H05.sld2]
    M Heiner:
    Qualitative Modelling and Analysis Concurrent Systems with Petri Nets – Tutorial;
    Talk, Glasgow University, Bioinformatics Research Centre (invited talk), March 2005. [ pdf ] [ BibTeX ]
  • [H05.sld3]
    M Heiner:
    Modelling of Biochemical Networks with Time Petri Nets;
    Talk, HU Berlin, CS Dep., Seminar "Logic in Computer Science", April 2005. [ pdf ] [ BibTeX ]
  • [H05.sld1]
    M Heiner:
    From Petri Nets to Differential Equations (ODEs);
    Talk, Glasgow University, Bioinformatics Research Centre (invited talk), March 2005. [ pdf ] [ BibTeX ]
  • [H05.sld4]
    M Heiner:
    From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis;
    Talk, Munich Systems Biology Forum, Munich (invited talk), May 2005. [ pdf ] [ BibTeX ]
  • [H05.sld7]
    M Heiner:
    Modelling Biochemical Networks with Time Petri Nets;
    Talk, Glasgow University, Bioinformatics Research Centre (invited talk), September 2005. [ pdf ] [ BibTeX ]
  • [H05.sld6]
    M Heiner:
    Petri Nets as Partial Order Semantics for Biochemical Networks;
    Talk, European Conference on Mathematical and Theoretical Biology (ECMTB '05), Mini-Symposium on Qualitative and Structual Analysis of Biological Regulatory Networks, Dresden, July 2005. [ pdf ] [ BibTeX ]
  • [H05.sld5]
    M Heiner:
    An Integrative Approach for Qualitative and Quantitative Analysis of Biochemical Networks Using Petri Nets;
    Talk, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg (invited talk), June 2005. [ pdf ] [ BibTeX ]
  • [KH04.sld2]
    I Koch and M Heiner:
    Possibilities of Petri net Theory to Validate Metabolic Pathways;
    Talk, 2nd BCB 2004, Bertinoro, June 2004. [ pdf ] [ BibTeX ]
  • [H04.sld1]
    M Heiner:
    Dependable Software for Embedded Systems;
    Talk, VW Wolfsburg (invited talk), February 2004. [ pdf ] [ BibTeX ]
  • [KH04.sld1]
    I Koch and M Heiner:
    Qualitative Biochemical Pathway Analysis Using Petri Nets;
    Talk, CNRS, Structural & Genomic Information Lab., Marseille (invited talk), February 2004. [ pdf ] [ BibTeX ]
  • [HK04.sld1]
    M Heiner and I Koch:
    Petri Net Based Model Validation in Systems Biology;
    Talk, ICATPN 2004, Bologna, June 2004. [ pdf ] [ BibTeX ]
  • [KH04.sld4]
    I Koch and M Heiner:
    Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets;
    Talk, Tutorial Notes, 5th Int. Conference on Systems Biology - ICSB 2004, Heidelberg/Germany, October 2004. [ pdf ] [ BibTeX ]
  • [H04.sld2]
    M Heiner:
    Modelchecking in der Automatisierungstechnik; Wie formal müssen formale Methoden sein?
    Talk, Software Forum Berlin-Brandenburg (invited talk), September 2004. [ pdf ] [ BibTeX ]
  • [HK04.sld2]
    M Heiner and I Koch:
    Model Checking of Biological Networks Using Petri Nets - Three Styles of Environment Models;
    Talk, Schloss Dagstuhl, Workshop Integrative Bioinformatics, July 2004. [ pdf ] [ BibTeX ]
  • [PHK04.sld]
    I Popova-Zeugmann, M Heiner and I Koch:
    Modelling and Analysis of Biochemical Networks with Time Peri Nets;
    Talk, CS&P 2004, Caputh, September 2004. [ pdf ] [ BibTeX ]
  • [HK04.sld3]
    M Heiner and I Koch:
    Model Checking of Biological Networks Using Petri Nets;
    Talk, IPK Gatersleben, August 2004. [ pdf ] [ BibTeX ]
  • [KH04.sld3]
    I Koch and M Heiner:
    The Petri Net Model of the Sucrose-to-Starch Breakdown in the Potato Tuber;
    Talk, IPK Gatersleben, August 2004. [ pdf ] [ BibTeX ]
  • [H03.sld]
    M Heiner:
    About some Applications of Petri Net Theory - My Petri Net Picture Book;
    Talk, Adventmatik 2003, Paderborn, December 2003. [ pdf ] [ BibTeX ]
  • [HK02.sld]
    M Heiner and I Koch:
    Biopathways & Petri Nets - Demonstrated for Apoptosis;
    Talk, Charité Berlin, September 2002. [ pdf ] [ BibTeX ]
  • [H02.sld1]
    M Heiner:
    Concurrency Patterns - A Petri Net Perspective;
    Talk, Workshop Dependable Components, Schloss Dagstuhl, November 2002. [ pdf ] [ BibTeX ]
  • [H02.sld2]
    M Heiner:
    Increased Safety by Fault Tolerant Software - Just another Way to Waste Money?
    Talk, Bosch-Zuverlässigkeits-Workshop, Böblingen (invited talk), October 2002. [ pdf ] [ BibTeX ]
  • [H00.sld1]
    M Heiner:
    Dependable Software - an Unrealistic Dream or Just a Reality Far Away ?
    Talk, Bosch-Zuverlässigkeits-Workshop, Böblingen (invited talk), April 2000. [ pdf ] [ BibTeX ]
  • [H00.sld2]
    M Heiner:
    Time-related Modelling of PLC systems with Time-less Petri Nets;
    Talk, WODES 2000, Gent, August 2000. [ pdf ] [ BibTeX ]
  • [HH00.sld]
    M Heiner and R Heinrich:
    Metabolic Petri Nets;
    Talk, Schloss Hohenkammer, DFG-Kolloquium, October 2000. [ pdf ] [ BibTeX ]
  • [H99.sld]
    M Heiner:
    Software Testing - State of the Art, Methods, and Limitations;
    Talk, March 1999. [ pdf ] [ BibTeX ]
  • [H98.sld]
    M Heiner:
    Application of Petri Nets to Metabolic Networks (in German);
    Talk, HU Berlin, August 1998. [ pdf ] [ BibTeX ]
  • [S97.sld1]
    J Spranger:
    FUNlite - A Parallel Petri Net Simulator;
    Talk, 42. IWK Ilmenau, September 1997. [ pdf ] [ BibTeX ]
  • [S97.sld2]
    J Spranger:
    Symbolic Petri Net Analysis Using Polynomials;
    Talk, AWPN97, October 1997. [ pdf ] [ BibTeX ]
  • [HDS96.sld]
    M Heiner, P Deussen and J Spranger:
    Production Cell I, A Case Study in Petri Net Based Design and Analysis;
    Talk, August 1996. [ pdf ] [ BibTeX ]
  • [H96.sld1]
    M Heiner:
    Safety-related Certification of PLC Application Programs with Petri Nets;
    Talk, December 1996. [ pdf ] [ BibTeX ]

posters

  • [GHG.poster]
    D Gilbert, M Heiner and L Ghanbar:
    Spatial Quorum Sensing Modelling Using Coloured Petri Nets and Simulative Model Checking, CMSB 2018, Brno/CZ, September 2018;
    Poster, September 2018 (1 MB). [ pdf ] [ BibTeX ]
  • [CH18.poster]
    J Chodak and M Heiner:
    Spike - A tool for efficient simulation of Petri nets;
    Poster, May 2018 (804 KB). [ pdf ] [ BibTeX ]
  • [HC18.poster]
    M Heiner and J Chodak:
    Petri Nets for Multilevel Systems Biology;
    Poster, May 2018 (7.8 MB). [ pdf ] [ BibTeX ]
  • [GH+16]
    D Gilbert, M Heiner, Y Jayaweere, B Suleiman, A Pandini, A Khan and N Saunders:
    Network-based Computational Design of Bacterial Genome Scale Metabolic Systems;
    Poster, 2016. [ pdf ] [ BibTeX ]
  • [HRS13.poster]
    M Heiner, C Rohr and M Schwarick:
    Petri net based system analysis;
    Poster, 2013. [ pdf ] [ BibTeX ]
  • [PG+13]
    O Pârvu, D Gilbert, M Heiner, F Liu and N Saunders:
    A systems biology approach to modelling growth and phase variation in bacterial colonies;
    Poster, 2013. [ pdf ] [ BibTeX ]
  • [HH12.poster]
    M Herajy and M Heiner:
    Distributed Collaborative and Interactive Simulationof Large Scale Biochemical Networks; BioPPN 12, June 2012;
    Poster, 2012. [ pdf ] [ BibTeX ]
  • [Rohr12.poster]
    C Rohr:
    Simulative  Model  Checking  of Colored  Stochastic  Petri  Nets; IGS/ZUSYS, 2012;
    Poster, 2012. [ pdf ] [ BibTeX ]
  • [HRS12]
    M Heiner, C Rohr and M Schwarick:
    Petri net based system analysis;
    Poster, 2012. [ pdf ] [ BibTeX ]
  • [RMH11]
    C Rohr, M Heiner and W Marwan:
    Stochastic Modelling and Simulation of Biochemical Networks; IMPRS evaluation, November 2011;
    Poster, 2011. [ pdf ] [ BibTeX ]
  • [HRS11]
    M Heiner, C Rohr and M Schwarick:
    Petri net based system analysis;
    Poster, 2011. [ pdf ] [ BibTeX ]
  • [GHDB08b]
    D Gilbert, M Heiner, R Donaldson and R Breitling:
    A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets, FORSYS Meeting, Berlin, June 2008;
    Poster, 2008. [ pdf ] [ BibTeX ]
  • [GHDB08a]
    D Gilbert, M Heiner, R Donaldson and R Breitling:
    A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets,ESF-UB Conference in Biomedicine, Systems Biology, April 2008;
    Poster, 2008. [ BibTeX ]
  • [BGH08]
    R Breitling, D Gilbert and M Heiner:
    BioModel Engineering - from Structure to Behaviour, CMSB 2008, Rostock, October 2008;
    Poster, 2008. [ pdf ] [ BibTeX ]
  • [GXKF07]
    D Gilbert, Xu Gu, R Khanin, D Forehand, S Rosser, E Travis, G Gray, D Leader, G Kalna, T Friend, R Fulton, C Harkness, M-B Jensen, K Kidykas, M Marbà, L McLeay, C Merrick, M Paakkunainen, S Ramsay, M Trybilo, M Heiner:
    Modelling techniques and tools to support the design and construction process in Synthetic Biology – a practical comparative analysis, European Conference on Synthetic Biology (ECSB '07): Design, Programming and Optimisation of Biological Systems, Sant Feliu de Guixols/Spain, November 2007;
    Poster, 2007. [ pdf ] [ BibTeX ]
  • [HRT06b]
    M Heiner, R Richter and A Tovchigrechko:
    Petri Net Based System Analysis, Overview on the research activities of our working group, May 2006;
    Poster, 2006. [ pdf ] [ BibTeX ]
  • [HRT06a]
    M Heiner, R Richter and A Tovchigrechko:
    Snoopy - a Tool to Design and Animate / Simulate Graphs;
    Poster, 2006. [ pdf ] [ BibTeX ]
  • [SHK05]
    A Sackmann, M Heiner and I Koch:
    Modelling signal transduction pathways of yeast with Petri nets, European Conference on Mathematical and Theoretical Biology (ECMTB 2005), Dresden/Germany, July 2005;
    Poster, 2005. [ pdf ] [ BibTeX ]
  • [KJH04]
    I Koch, BH Junker and M Heiner:
    A Petri Net Based Model Validation Technique for the Central Carbon Metabolism of Solanum Tuberosum Tubers, 5th Int. Conference on Systems Biology (ICSB 2004), Heidelberg/Germany, October 2004;
    Poster, 2004. [ pdf ] [ BibTeX ]
  • [GHK04]
    A Gevorgyan, M Heiner and I Koch:
    Japet: an Integrated Tool for Recreating KEGG Data into Hierarchical and Petri Net Analysis, 5th Int. Conference on Systems Biology (ICSB 2004), Heidelberg/Germany, October 2004;
    Poster, 2004. [ pdf ] [ BibTeX ]

PhD theses

  • [Rohr17]
    Christian Rohr:
    Simulative analysis of coloured extended stochastic Petri nets;
    PhD thesis, BTU Cottbus, Dep. of CS, January 2017. [ pdf ] [ BibTeX ]
  • [Schwarick14]
    Martin Schwarick:
    Symbolic on-the-fly analysis of stochastic Petri nets;
    PhD thesis, BTU Cottbus, Dep. of CS, June 2014. [ pdf ] [ BibTeX ]
  • [Herajy13]
    Mostafa Herajy:
    Computational Steering of Multi-Scale Biochemical Networks;
    PhD thesis, BTU Cottbus, Dep. of CS, January 2013. [ pdf ] [ BibTeX ]
  • [Liu12]
    Fei Liu:
    Colored Petri Nets for Systems Biology;
    PhD thesis, BTU Cottbus, Dep. of CS, January 2012. [ pdf ] [ BibTeX ]
  • [Tovchig08]
    Alexey Tovchigrechko:
    Efficient symbolic analysis of bounded Petri nets using Interval Decision Diagrams;
    PhD thesis, BTU Cottbus, Dep. of CS, October 2008. [ pdf ] [ BibTeX ]
  • [Mertke03]
    Thomas Mertke:
    A Technical Language for Formal Safety Specification of Reactive Systems;
    PhD thesis, BTU Cottbus, Dep. of CS, October 2003. [ pdf ] [ BibTeX ]
  • [Spranger01]
    Jochen Spranger:
    Symbolic LTL verification of Petri nets;
    PhD thesis, BTU Cottbus, Dep. of CS, December 2001. [ BibTeX ]
  • [Deussen01]
    Peter Deussen:
    Analysis of concurrent systems by Process Automata;
    PhD thesis, BTU Cottbus, Dep. of CS, December 2001. [ BibTeX ]

selected students' theses

  • [Schw09]
    Marcel Schwarze:
    Web-based Petri net animation (in German);
    Diploma thesis, FH Lausitz, Dep. of CS, November 2009. [ BibTeX ]
  • [Fisc09]
    Ansgar Fischer:
    Reachability graph based analysis of time-dependent Petri nets (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, October 2009. [ BibTeX ]
  • [Fran09]
    Andreas Franzke:
    Charlie 2.0 – a multi-threaded Petri net analyzer;
    Diploma thesis, BTU Cottbus, Dep. of CS, December 2009. [ pdf ] [ BibTeX ]
  • [Bayer08]
    Denny Bayer:
    Testing with Music (in German);
    Bachelor thesis, BTU Cottbus, Dep. of CS, September 2008. [ pdf ] [ BibTeX ]
  • [Schu08]
    Krispin Schulz:
    An Extension of the Snoopy Software to Process and Manage Petri Net Animations (in German);
    Bachelor thesis, BTU Cottbus, Dep. of CS, November 2008. [ pdf ] [ BibTeX ]
  • [Dube07]
    Matthias Dube:
    Development and Realisation of a General Concept for Interactions between two Net Classes in Snoopy (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, February 2007. [ BibTeX ]
  • [Lehr07]
    Sebastian Lehrack:
    A Modelling and Simulation Tool for Stochastic Petri Nets Models of Biochemical Networks (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, November 2007. [ pdf ] [ BibTeX ]
  • [Kurth07]
    Anja Kurth:
    Fault trees in Snoopy (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, January 2007. [ BibTeX ]
  • [Dier07]
    Stefan Dieringer:
    Design and Development of a System for Distributed Petri Net Analyses (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, November 2007. [ pdf ] [ BibTeX ]
  • [Schw06]
    Martin Schwarick:
    A Tool to Analyse Petri Net Models (in German);
    Master thesis, BTU Cottbus, Dep. of CS, September 2006. [ BibTeX ]
  • [Wind06]
    Katja Winder:
    Invariant-supported Petri Net Structuring (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, January 2006. [ pdf ] [ BibTeX ]
  • [Sche06]
    Daniel Scheibler:
    A Tool to Design and Simulate continuous Petri Nets (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, January 2006. [ pdf ] [ BibTeX ]
  • [Dube05]
    Matthias Dube:
    Signing and Verifying SNOOPY-files;
    Student thesis, BTU Cottbus, Dep. of CS, March 2005. [ pdf ] [ BibTeX ]
  • [Fieb04]
    Markus Fieber:
    Entwurf und Implementierung eines generischen, adaptiven Werkzeugs zur Arbeit mit Graphen (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, July 2004. [ pdf ] [ BibTeX ]
  • [Schw04]
    Martin Schwarick:
    Extension of a BDD-based LTL Model Checker (in German);
    Bachelor thesis, BTU Cottbus, Dep. of CS, April 2004. [ pdf ] [ BibTeX ]
  • [Neum04]
    Gerry Neumann:
    Modelling of Biochemical Processes with Petri Nets; Hemostasis vs. Fibrinolysis vs. Inhibitors (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, July 2004. [ pdf ] [ BibTeX ]
  • [Rung04]
    Thomas Runge:
    Methodology to Model and Validate Biochemichal Networks Using Coloured Petri Nets, Described by the Example Glycolysis (in German);
    Diploma thesis, BTU Cottbus, Dep. of CS, November 2004. [ pdf ] [ BibTeX ]
  • [Fieb03]
    Markus Fieber:
    Snoopy: Ein generisches, adaptives Werkzeug für Graphen (in German);
    Study thesis, BTU Cottbus, Dep. of CS, January 2003. [ pdf ] [ BibTeX ]
  • [Noac99]
    Andreas Noack:
    Ein ZBDD-Paket für effizientes Model Checking von Petrinetzen;
    Study thesis, BTU Cottbus, Dep. of CS, June 1999. [ BibTeX ]

… the end …

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