data structures and software dependability

• home

• contact

• members

• teaching

• research

• publications

• software

• events

Selected references

Sort by: date, category, title

---

369 publications:

A B C D E F G-H I J-L M N-O P Q-R S T U-Z

A

• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [IHAH20]
  A Ismail, M Herajy, ES Atlam and M Heiner:
  A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-models via Coloured Hybrid Petri Nets;
  Modelling and Simulation in Engineering, 2020, 2020 (Article ID 4715172, 14 pages). [ 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 ]
• [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 ]
• [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 ]
• [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: August 08, 2016). [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [H09.sld1]
  M Heiner:
  A Petri Net Perspective on Systems and Synthetic Biology;
  Talk, Brunel University London (invited talk), June 2009. [ 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 ]
• [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 ]
• [LAC+21]
  F Liu, G Assaf, M Chen and M Heiner:
  A Petri nets-based framework for whole-cell modeling;
  BioSystems, 210:104533, 2021 (accepted: 06 September 2021). [ url ] [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [Mertke03]
  Thomas Mertke:
  A Technical Language for Formal Safety Specification of Reactive Systems;
  PhD thesis, BTU Cottbus, Dep. of CS, October 2003. [ pdf ] [ BibTeX ]
• [Schw06]
  Martin Schwarick:
  A Tool to Analyse Petri Net Models (in German);
  Master thesis, BTU Cottbus, Dep. of CS, September 2006. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [SH10b]
  S Soliman and M Heiner:
  A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
  PLoS ONE, 5(12):e14284, 2010. [ doi ] [ BibTeX ]
• [HLH24b]
  M Herajy, F Liu and M Heiner:
  A Workflow for the hybrid modelling and simulation of multi-timescale biological systems;
  BioSystems, 2024 (accepted: 10 November 2024). [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [H03.sld]
  M Heiner:
  About some Applications of Petri Net Theory - My Petri Net Picture Book;
  Talk, Adventmatik 2003, Paderborn, December 2003. [ pdf ] [ 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 ]
• [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 ]
• [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: May 18, 2017). [ doi ] [ BibTeX ]
• [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 ]
• [NGH+19]
  N Nickaeen, J Ghaisari, M Heiner, S Moein and Y Gheisari:
  Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution;
  Scientific Reports, 9:Article number: 12764, 2019 (accepted: August 14, 2019, published: September 04, 2019). [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [Deussen01]
  Peter Deussen:
  Analysis of concurrent systems by Process Automata;
  PhD thesis, BTU Cottbus, Dep. of CS, December 2001. [ pdf ] [ BibTeX ]
• [R14a.mcc]
  C Rohr:
  Angiogenesis, a Petri net model;
  Technical report, Model Checking Contest @ Petri nets, June 2014. [ 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 ]
• [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 ]
• [H98.sld]
  M Heiner:
  Application of Petri Nets to Metabolic Networks (in German);
  Talk, HU Berlin, August 1998. [ pdf ] [ 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 ]
• [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 ]

B

• [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 ]
• [H12.sld1]
  M Heiner:
  BioModel Engineering - a Petri Net Perspective;
  Talk, Jena Centre of Bioinformatics (invited talk), March 2012. [ BibTeX ]
• [H11.sld3]
  M Heiner:
  BioModel Engineering - a Petri Net Perspective;
  Talk, Brunel University, DISC seminar, May 2011. [ pdf ] [ BibTeX ]
• [H14.sld1]
  M Heiner:
  BioModel Engineering - a Petri Net Perspective;
  Talk, Università Ca' Foscari Di Venezia (invited talk), March 2014. [ 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 ]
• [BGH08]
  R Breitling, D Gilbert and M Heiner:
  BioModel Engineering - from Structure to Behaviour, CMSB 2008, Rostock, October 2008;
  Poster, 2008. [ pdf ] [ 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: October 12, 2012). [ 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 ]
• [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: May 16, 2017). [ doi ] [ 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 ]
• [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 ]
• [H11.sld2]
  M Heiner:
  Biochemical Networks - a Petri Net Perspective;
  Talk, Universtita Torino, PhD School (invited talk), March 2011. [ pdf ] [ BibTeX ]
• [AHL19.sld]
  G Assaf, M Heiner and F Liu:
  Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy;
  Talk, Trento, September 2019. [ pdf ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [HK02.sld]
  M Heiner and I Koch:
  Biopathways & Petri Nets - Demonstrated for Apoptosis;
  Talk, Charité Berlin, September 2002. [ pdf ] [ BibTeX ]

C

• [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 ]
• [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 ]
• [Fran09]
  Andreas Franzke:
  Charlie 2.0 – a multi-threaded Petri net analyzer;
  Diploma thesis, BTU Cottbus, Dep. of CS, December 2009. [ 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 ]
• [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 ]
• [R14b.mcc]
  C Rohr:
  Circadian Clock, a Petri net model;
  Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ 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 ]
• [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 ]
• [Liu12]
  Fei Liu:
  Colored Petri Nets for Systems Biology;
  PhD thesis, BTU Cottbus, Dep. of CS, January 2012. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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: November 03, 2017). [ doi ] [ BibTeX ]
• [AHL22]
  G Assaf, M Heiner and F Liu:
  Coloured fuzzy Petri nets for modelling and analysing membrane systems;
  Biosystems, 2022. [ 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 ]
• [AHL21]
  G Assaf, M Heiner and F Liu:
  Colouring Fuzziness for Systems Biology;
  Theoretical Computer Science, 875(0304-3975):52-64, 2021 (accepted: 11 April 2021, online: 19 April 2021). [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [Herajy13]
  Mostafa Herajy:
  Computational Steering of Multi-Scale Biochemical Networks;
  PhD thesis, BTU Cottbus, Dep. of CS, January 2013. [ pdf ] [ BibTeX ]
• [H02.sld1]
  M Heiner:
  Concurrency Patterns - A Petri Net Perspective;
  Talk, Workshop Dependable Components, Schloss Dagstuhl, November 2002. [ 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 ]

D

• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [H04.sld1]
  M Heiner:
  Dependable Software for Embedded Systems;
  Talk, VW Wolfsburg (invited talk), February 2004. [ 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 ]
• [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 ]
• [HLH24a]
  M Herajy, F Liu and M Heiner:
  Design Patterns for the Construction of Computational Biological Models;
  Briefings in Bioinformatics, 25, 2024 (accepted: 10 June 2024). [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [H14a.mcc]
  M Heiner:
  Diffusion in 2D, a Petri net model;
  Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ 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 ]
• [R17]
  Rohr, C:
  Discrete-Time Leap Method For Stochastic Simulation;
  Fundamenta Informaticae, 160(1-2):181-198, 2018 (accepted: May 16, 2017). [ doi ] [ 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 ]
• [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 ]

E

• [R14c.mcc]
  C Rohr:
  ERK signalling pathway, a Petri net model;
  Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ 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 ]
• [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 ]
• [SRL+20a.sld]
  M Schwarick, C Rohr, F Liu, G Assaf, J Chodak and M Heiner:
  Efficient Unfolding of Coloured Petri Nets using Interval Decision Diagrams;
  Talk, PETRI NETS 2020, Paris, June 2020. [ pdf ] [ BibTeX ]
• [SRL+20b.sld]
  M Schwarick, C Rohr, F Liu, G Assaf, J Chodak and M Heiner:
  Efficient Unfolding of Coloured Petri Nets using Interval Decision Diagrams - Teaser;
  Talk, PETRI NETS 2020, Paris, June 2020. [ 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 ]
• [Noac99]
  Andreas Noack:
  Ein ZBDD-Paket für effizientes Model Checking von Petrinetzen;
  Study thesis, BTU Cottbus, Dep. of CS, June 1999. [ 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 ]
• [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: February 19, 2018). [ doi ] [ 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 ]
• [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 ]
• [Schw04]
  Martin Schwarick:
  Extension of a BDD-based LTL Model Checker (in German);
  Bachelor thesis, BTU Cottbus, Dep. of CS, April 2004. [ pdf ] [ BibTeX ]

F

• [Spra97]
  J Spranger:
  FUNlite - A Parallel Petri Net Simulator;
  In Proc. 42. IWK Ilmenau, September 1997), IWK Ilmenau, page 6, 1997. [ pdf ] [ BibTeX ]
• [S97.sld1]
  J Spranger:
  FUNlite - A Parallel Petri Net Simulator;
  Talk, 42. IWK Ilmenau, September 1997. [ pdf ] [ BibTeX ]
• [Kurth07]
  Anja Kurth:
  Fault trees in Snoopy (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, January 2007. [ 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 ]
• [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 ]
• [CGH21]
  S Connolly, D Gilbert and M Heiner:
  From Epidemic to Pandemic Modelling;
  Technical report arXiv preprint, Brunel University London and Brandenburg University of Technology Cottbus, March 2021. [ url ] [ pdf ] [ BibTeX ]
• [CGH22]
  S Connolly, D Gilbert and M Heiner:
  From Epidemic to Pandemic Modelling;
  Frontiers in Systems Biology, March 2022 (accepted: 14 March 2022, published: 14 July 2022). [ url ] [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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.sld2]
  M Heiner:
  From Petri Nets to Partial Differential Equations – Spatial Modelling in Systems Biology;
  Talk, Dagstuhl, November 2014. [ 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 ]
• [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 ]
• [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 ]
• [AHL21.manual]
  G Assaf, M Heiner and F Liu:
  Fuzzy Petri Nets in Snoopy - User Manual;
  Technical report 01-34, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2021. [ url ] [ pdf ] [ BibTeX ]
• [LHG20]
  F Liu, M Heiner and D Gilbert:
  Fuzzy Petri nets for modelling of uncertain biological systems;
  Briefings in Bioinformatics, 21(1):198-210, 2020 (accepted: November 16, 2018; published: December 27, 2018). [ url ] [ doi ] [ BibTeX ]
• [Assaf21]
  George Assaf:
  Fuzzy coloured Petri nets for modelling biological systems with uncertain kinetic parameters;
  PhD thesis, BTU Cottbus, Dep. of CS, December 2022. [ 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: February 09, 2016). [ url ] [ doi ] [ BibTeX ]

G

• [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 ]
• [HH11.sld]
  M. Herajy and M. Heiner:
  Generalized Hybrid Petri Nets;
  Talk, Formal Methods in Molecular Biology, Dagstuhl seminar, April 2011. [ pdf ] [ 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: December 20, 2017). [ doi ] [ BibTeX ]

H

• [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 ]
• [H11.sld4]
  M Heiner:
  How Might Petri Nets Enhance Your Systems Biology Toolkit;
  Talk, PETRI NET 2011, Newcastle (invited talk), June 2011. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [LSHG19]
  F Liu, W Sun, M Heiner and D Gilbert:
  Hybrid modelling of biological systems using fuzzy continuous Petri nets;
  Briefings in Bioinformatics, 12 2019. [ url ] [ doi ] [ BibTeX ]
• [FHG22]
  F Liu, M Heiner and D Gilbert:
  Hybrid modelling of biological systems: current progress and future prospects;
  Briefings in Bioinformatics, 2022 (accepted: 16 February 2022, published: 30 March 2022). [ doi ] [ BibTeX ]

I

• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [Wind06]
  Katja Winder:
  Invariant-supported Petri Net Structuring (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, January 2006. [ pdf ] [ BibTeX ]

J

• [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 ]
• [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 ]
• [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 ]

K

L

M

• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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: March 11, 2016). [ url ] [ doi ] [ 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 ]
• [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 ]
• [Liu09.manual]
  F Liu:
  Manual for Snoopy2Prism Export;
  Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2009. [ pdf ] [ BibTeX ]
• [HS12.sld2]
  M Heiner and M Schwarick:
  Markov Chains & Functional Safety;
  Talk, Philotech Academy, Berlin, October 2012. [ pdf ] [ BibTeX ]
• [H07.sld1]
  M Heiner:
  Mathematical Modelling of Biochemical Networks with Petri Nets;
  Talk, FMP Berlin, February 2007. [ pdf ] [ BibTeX ]
• [HH00.sld]
  M Heiner and R Heinrich:
  Metabolic Petri Nets;
  Talk, Schloss Hohenkammer, DFG-Kolloquium, October 2000. [ 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 ]
• [HK04.sld3]
  M Heiner and I Koch:
  Model Checking of Biological Networks Using Petri Nets;
  Talk, IPK Gatersleben, August 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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: January 2018). [ doi ] [ 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 ]
• [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: July 13, 2015). [ 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 ]
• [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: October 31, 2015). [ url ] [ doi ] [ 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 ]
• [LH13a]
  F Liu and M Heiner:
  Modeling membrane systems using colored stochastic Petri nets;
  Nat. Computing, 12(4):617 - 629, 2013. [ url ] [ doi ] [ 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 ]
• [H05.sld7]
  M Heiner:
  Modelling Biochemical Networks with Time Petri Nets;
  Talk, Glasgow University, Bioinformatics Research Centre (invited talk), September 2005. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [H13.sld4]
  M Heiner:
  Modular Modelling with Petri Nets;
  Talk, ENS, Département de Biologie/Paris, October 2013. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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: August 01, 2012). [ 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 ]
• [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 ]

N

• [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 ]

O

• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]

P

• [H14b.mcc]
  M Heiner:
  Parameterised Production Cell, a Petri net model;
  Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [HK04.sld1]
  M Heiner and I Koch:
  Petri Net Based Model Validation in Systems Biology;
  Talk, ICATPN 2004, Bologna, June 2004. [ 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 ]
• [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 ]
• [H92]
  M Heiner:
  Petri Net Based Software Validation - Prospects and Limitations;
  Technical report TR-92-022, ICSI Berkeley, March 1992. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [H15.sld1]
  M Heiner:
  Petri Nets 4 Bacterial Bioengineering;
  Talk, Brunel University London, Centre for Systems and Synthetic Biology, March 2015. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [HC18.poster]
  M Heiner and J Chodak:
  Petri Nets for Multilevel Systems Biology;
  Poster, May 2018 (7.8 MB). [ pdf ] [ BibTeX ]
• [H11.sld5]
  M Heiner:
  Petri Nets for Multiscale Systems Biology;
  Talk, Brunel University, DISC seminar, September 2011. [ pdf ] [ 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 ]
• [LMH22]
  F Liu, H Matsuno, M Heiner:
  Petri Nets for Systems Biology Modelling and Analysis;
  In Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools, (Elisabetta De Maria, Ed.), John Wiley & Sons, Inc., pages 15-34, 2022. [ 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 ]
• [HGD08.sld2]
  M Heiner, D Gilbert and R Donaldson:
  Petri Nets for Systems and Synthetic Biology;
  Talk, Bertinoro (invited talk), June 2008. [ 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 ]
• [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: May 18, 2017). [ doi ] [ 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 ]
• [HRS11]
  M Heiner, C Rohr and M Schwarick:
  Petri net based system analysis;
  Poster, 2011. [ pdf ] [ BibTeX ]
• [HRS13.poster]
  M Heiner, C Rohr and M Schwarick:
  Petri net based system analysis;
  Poster, 2013. [ pdf ] [ BibTeX ]
• [HRS12]
  M Heiner, C Rohr and M Schwarick:
  Petri net based system analysis;
  Poster, 2012. [ pdf ] [ 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 ]
• [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 ]
• [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 ]
• [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: November 20, 2017; online February 28, 2018). [ doi ] [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [LHG23]
  F Liu, M Heiner and D Gilbert:
  Protocol for biomodel engineering of unilevel to multilevel biological models using colored Petri nets;
  STAR Protocols, 4(4):102651, 2023 (accepted: September 2023). [ doi ] [ BibTeX ]

Q

• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]

R

• [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 ]
• [Fisc09]
  Ansgar Fischer:
  Reachability graph based analysis of time-dependent Petri nets (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, October 2009. [ 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 ]
• [PPH+21]
  A Pretschner, S Pabel, M Haas, M Heiner and W Marwan:
  Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells;
  Frontiers in Genetics, section Systems Biology, 2021 (accepted: 07 December 2020; published: 08 January 2021). [ 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: April 2015). [ url ] [ doi ] [ BibTeX ]

S

• [CH19b]
  J Chodak and M Heiner:
  SPIKE – as a Supporting Tool for a Model Parameters Optimization via Branched Simulations;
  In Proc. 23th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2019), University of Hagen, pages 18-23, October 2019. [ url ] [ pdf ] [ BibTeX ]
• [CH19b.sld]
  J Chodak and M Heiner:
  SPIKE – as a Supporting Tool for a Model Parameters Optimization via Branched Simulations;
  Talk, AWPN2019, University of Hagen, October 2019. [ pdf ] [ 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 ]
• [H96.sld1]
  M Heiner:
  Safety-related Certification of PLC Application Programs with Petri Nets;
  Talk, December 1996. [ 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 ]
• [Dube05]
  Matthias Dube:
  Signing and Verifying SNOOPY-files;
  Student thesis, BTU Cottbus, Dep. of CS, March 2005. [ 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 ]
• [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 ]
• [Rohr13]
  C Rohr:
  Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
  ToPNoC VIII, LNCS 8100, 2013. [ 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 ]
• [Rohr17]
  Christian Rohr:
  Simulative analysis of coloured extended stochastic Petri nets;
  PhD thesis, BTU Cottbus, Dep. of CS, January 2017. [ pdf ] [ BibTeX ]
• [Rohr12.poster]
  C Rohr:
  Simulative  Model  Checking  of Colored  Stochastic  Petri  Nets; IGS/ZUSYS, 2012;
  Poster, 2012. [ 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 ]
• [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 ]
• [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 ]
• [HRT06a]
  M Heiner, R Richter and A Tovchigrechko:
  Snoopy - a Tool to Design and Animate / Simulate Graphs;
  Poster, 2006. [ 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 ]
• [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: February 7, 2010)). [ url ] [ doi ] [ 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 ]
• [S15]
  A Sharma:
  Snoopy Report Generator Snoopy2LATEX (Internship report);
  Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2015. [ 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 ]
• [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 ]
• [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 ]
• [Fieb03]
  Markus Fieber:
  Snoopy: Ein generisches, adaptives Werkzeug für Graphen (in German);
  Study thesis, BTU Cottbus, Dep. of CS, January 2003. [ pdf ] [ BibTeX ]
• [H99.sld]
  M Heiner:
  Software Testing - State of the Art, Methods, and Limitations;
  Talk, March 1999. [ pdf ] [ BibTeX ]
• [H14c.mcc]
  M Heiner:
  Solitaire, a Petri net model;
  Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
• [AH19.sld]
  G Assaf and M Heiner:
  Spatial Encoding of Systems Using Coloured Petri Nets;
  Talk, AWPN2019, University of Hagen, October 2019. [ pdf ] [ BibTeX ]
• [AH19]
  G Assaf and M Heiner:
  Spatial Encoding of Systems Using Coloured Petri Nets;
  In Proc. 22th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2019), University of Hagen, pages 38-44, October 2019. [ url ] [ pdf ] [ BibTeX ]
• [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 ]
• [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: July, 26 2018; published: April 2019). [ 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 ]
• [GH15.tcs]
  D Gilbert and M Heiner (eds.):
  Special Issue 'Advances in CMSB';
  volume 599 of J. Theoretical Computer Science, Elsevier, 2015. [ 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 ]
• [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 ]
• [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 ]
• [Chodak21]
  Jacek Chodak:
  Spike – a tool for reproducible simulation experiments;
  PhD thesis, BTU Cottbus, Dep. of CS, December 2022. [ doi ] [ BibTeX ]
• [CH18.poster]
  J Chodak and M Heiner:
  Spike - A tool for efficient simulation of Petri nets;
  Poster, May 2018 (804 KB). [ 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 ]
• [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 ]
• [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 ]
• [CH19a.sld]
  J Chodak and M Heiner:
  Spike – reproducible simulation experiments with configuration file branching;
  Talk, Trento, September 2019. [ pdf ] [ 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 ]
• [RMH11]
  C Rohr, M Heiner and W Marwan:
  Stochastic Modelling and Simulation of Biochemical Networks; IMPRS evaluation, November 2011;
  Poster, 2011. [ 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 ]
• [HS10]
  M Heiner and K Sriram:
  Structural Analysis to Determine the Core of Hypoxia Response Network;
  PLoS ONE, 5(1):e8600, 2010. [ doi ] [ BibTeX ]
• [W06.sld]
  K Winder:
  Strukturelle Charakterisierung der Invarianten eines Petrinetzes;
  Talk, FU Berlin, DFG-Research Center Matheon, May 2006. [ pdf ] [ BibTeX ]
• [Spranger01]
  Jochen Spranger:
  Symbolic LTL verification of Petri nets;
  PhD thesis, BTU Cottbus, Dep. of CS, December 2001. [ pdf ] [ BibTeX ]
• [S97.sld2]
  J Spranger:
  Symbolic Petri Net Analysis Using Polynomials;
  Talk, AWPN97, October 1997. [ pdf ] [ 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 ]
• [Schwarick14]
  Martin Schwarick:
  Symbolic on-the-fly analysis of stochastic Petri nets;
  PhD thesis, BTU Cottbus, Dep. of CS, June 2014. [ pdf ] [ BibTeX ]
• [H06.sld2]
  M Heiner:
  Systems Biology - A Petri Net Perspective;
  Talk, TU Ilmenau, Fakultätskolloquium zum Informatikjahr (invited talk), July 2006. [ pdf ] [ BibTeX ]

T

• [Bayer08]
  Denny Bayer:
  Testing with Music (in German);
  Bachelor thesis, BTU Cottbus, Dep. of CS, September 2008. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [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 ]
• [H00.sld2]
  M Heiner:
  Time-related Modelling of PLC systems with Time-less Petri Nets;
  Talk, WODES 2000, Gent, August 2000. [ 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 ]
• [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 ]
• [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 ]
• [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 ]
• [SAH23]
  NH Sweilam, S Ahmed and M Heiner:
  Two different parallel approaches for a hybrid fractional order Coronavirus model;
  Egyptian Informatics Journal, 24(4):100408, December 2023 (accepted: 28 September 2023, available online 12 October 2023). [ doi ] [ BibTeX ]

U

• [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 ]
• [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 ]

V

• [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 ]

W

• [Schw09]
  Marcel Schwarze:
  Web-based Petri net animation (in German);
  Diploma thesis, FH Lausitz, Dep. of CS, November 2009. [ 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 ]
• [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 ]

X

Y

Z