Selected references

368 publications:

editorships · journal papers · conference papers · book chapters · technical reports · further reports · tutorials · 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)

[HLH24]
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 ]
[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 ]
[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 ]
[AHL22]
G Assaf, M Heiner and F Liu:
Coloured fuzzy Petri nets for modelling and analysing membrane systems;
Biosystems, 2022. [ 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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[R17]
Rohr, C:
Discrete-Time Leap Method For Stochastic Simulation;
Fundamenta Informaticae, 160(1-2):181-198, 2018 (accepted: 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: May 16, 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: May 18, 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: February 19, 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: 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: January 2018). [ 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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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: July 13, 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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[SH10b]
S Soliman and M Heiner:
A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
PLoS ONE, 5(12):e14284, 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 ]
[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 ]
[HS10]
M Heiner and K Sriram:
Structural Analysis to Determine the Core of Hypoxia Response Network;
PLoS ONE, 5(1):e8600, 2010. [ 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)

[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 ]
[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 ]
[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 ]
[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 ]
[BHAH18]
A Badawy, M Herajy, W Awad and M Heiner:
Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets;
In 13th International Conference on Computer Engineering and Systems (ICCES), IEEE, pages 268–272, 2018. [ doi ] [ BibTeX ]
[HH18]
M Herajy and M Heiner:
An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets;
In Proceedings of the 2018 Winter Simulation Conference (WSC 2018), Gothenburg, Sweden, IEEE, 978-1-5386-6572-5/18, pages 1346-1357, December 2018. [ url ] [ pdf ] [ doi ] [ BibTeX ]
[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 ]
[BHHP14]
B Barbot, S Haddad, M Heiner and C Picaronny:
Rare Event Handling in Signalling Cascades;
In Proc. SIMUL 2014, The Sixth International Conference on Advances in System Simulation, Nice, France, ThinkMind Digital Library, pages 126–131, October 2014. [ url ] [ pdf ] [ BibTeX ]
[HLR14]
M Herajy, F Liu and C Rohr:
Coloured hybrid Petri nets for systems biology;
In Proc. of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 60-76, June 2014. [ url ] [ pdf ] [ BibTeX ]
[GHLS13]
D Gilbert, M Heiner, F Liu and N Saunders:
Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology;
In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 230–249, June 2013. [ url ] [ doi ] [ BibTeX ]
[HRS13]
M Heiner, C Rohr and M Schwarick:
MARCIE - Model checking And Reachability analysis done effiCIEntly;
In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 389–399, June 2013. [ url ] [ pdf ] [ doi ] [ BibTeX ]
[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 ]
[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 ]
[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. [ pdf ] [ doi ] [ BibTeX ]
[Runge04b]
T Runge:
Application of Coloured Petri Nets in Systems Biology;
In Proc. 5th Workshop CPN, Univ. of Aarhus, October 2004, pages 77-95, 2004. [ pdf ] [ BibTeX ]
[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 ]
[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

[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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)

[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 ]
[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 ]
[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]
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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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

[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 ]
[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 ]
[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 ]
[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 ]
[A15]
S Agarwal:
Reengineering Snoopy’s GUI (Internship report);
Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2015. [ 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 ]
[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 ]
[R14b.mcc]
C Rohr:
Circadian Clock, a Petri net model;
Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ BibTeX ]
[R14c.mcc]
C Rohr:
ERK signalling pathway, a Petri net model;
Technical report, Model Checking Contest @ Petri nets, June 2014. [ url ] [ pdf ] [ 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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]

tutorials

talks

[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 ]
[AHL19.sld]
G Assaf, M Heiner and F Liu:
Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy;
Talk, Trento, September 2019. [ pdf ] [ BibTeX ]
[CH19a.sld]
J Chodak and M Heiner:
Spike – reproducible simulation experiments with configuration file branching;
Talk, Trento, September 2019. [ 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 ]
[AH19.sld]
G Assaf and M Heiner:
Spatial Encoding of Systems Using Coloured Petri Nets;
Talk, AWPN2019, University of Hagen, October 2019. [ 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 ]
[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 ]
[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 ]
[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 ]
[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.sld2]
M Heiner:
Model-driven design for Synthetic Systems Biology;
Talk, Brunel University London, Centre for Systems and Synthetic Biology, April 2015. [ 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.sld1]
M Heiner:
Petri Nets 4 Bacterial Bioengineering;
Talk, Brunel University London, Centre for Systems and Synthetic Biology, March 2015. [ 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 ]
[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.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 ]
[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.sld4]
M Heiner:
Modular Modelling with Petri Nets;
Talk, ENS, Département de Biologie/Paris, October 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.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.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 ]
[H12.sld1]
M Heiner:
BioModel Engineering - a Petri Net Perspective;
Talk, Jena Centre of Bioinformatics (invited talk), March 2012. [ 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 ]
[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 ]
[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 ]
[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.sld1]
M Heiner:
Biochemically Interpreted Petri Nets, Some Open Problems;
Talk, Universtita Torino, research group Prof. G Balbo (invited talk), March 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.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 ]
[H11.sld5]
M Heiner:
Petri Nets for Multiscale Systems Biology;
Talk, Brunel University, DISC seminar, 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 ]
[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.sld4]
M Heiner:
Biochemical Networks - a Petri Net Perspective;
Talk, Virginia Bioinformatics Institute at Virginia Tech, Blacksburg (invited talk), August 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 ]
[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.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 ]
[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 ]
[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.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 ]
[H09.sld1]
M Heiner:
A Petri Net Perspective on Systems and Synthetic Biology;
Talk, Brunel University London (invited talk), 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 ]
[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 ]
[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.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.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.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 ]
[HK04.sld1]
M Heiner and I Koch:
Petri Net Based Model Validation in Systems Biology;
Talk, ICATPN 2004, Bologna, June 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 ]
[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.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 ]
[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 ]
[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 ]
[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 ]
[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.sld3]
M Heiner and I Koch:
Model Checking of Biological Networks Using Petri Nets;
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 ]
[H02.sld1]
M Heiner:
Concurrency Patterns - A Petri Net Perspective;
Talk, Workshop Dependable Components, Schloss Dagstuhl, November 2002. [ pdf ] [ BibTeX ]
[HK02.sld]
M Heiner and I Koch:
Biopathways & Petri Nets - Demonstrated for Apoptosis;
Talk, Charité Berlin, September 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.sld2]
J Spranger:
Symbolic Petri Net Analysis Using Polynomials;
Talk, AWPN97, October 1997. [ pdf ] [ BibTeX ]
[S97.sld1]
J Spranger:
FUNlite - A Parallel Petri Net Simulator;
Talk, 42. IWK Ilmenau, September 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

[Chodak21]
Jacek Chodak:
Spike – a tool for reproducible simulation experiments;
PhD thesis, BTU Cottbus, Dep. of CS, December 2022. [ 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 ]
[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 ]
[Deussen01]
Peter Deussen:
Analysis of concurrent systems by Process Automata;
PhD thesis, BTU Cottbus, Dep. of CS, December 2001. [ pdf ] [ BibTeX ]
[Spranger01]
Jochen Spranger:
Symbolic LTL verification of Petri nets;
PhD thesis, BTU Cottbus, Dep. of CS, December 2001. [ pdf ] [ 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 …

Any comments or questions are welcome. Please direct them to monika [period] heiner [snail] b-tu [period] de Privacy Policy

data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

Selected references

editorships

journal papers (peer reviewed)

conference/workshop papers (peer reviewed)

book chapters

further papers (no or weak review process)

technical reports

tutorials

talks

posters

PhD theses

selected students' theses

… the end …