Selected references

368 entries sort by: date, category, title

2024 - 2023 - 2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 -2005 - 2004 - 2003 - 2002 - 2001 - 2000 - 1999 - 1998 - 1997 - 1996 - 1995 - 1994 - 1992

2024

[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 ]

2023

[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 ]
[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 ]

2022

[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 ]
[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 ]
[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 ]
[AHL22]
G Assaf, M Heiner and F Liu:
Coloured fuzzy Petri nets for modelling and analysing membrane systems;
Biosystems, 2022. [ url ] [ doi ] [ BibTeX ]
[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 ]

2021

[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 ]
[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 ]
[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 ]
[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 ]

2020

[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 ]
[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 ]
[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 ]

2019

[H19]
M Heiner:
Petri Nets for BioModel Engineering: A Personal Perspective;
In Carl Adam Petri: Ideas, Personality, Impact, (W Reisig and G Rozenberg, Eds.), Springer, Cham, pages 205–216, 2019 (first online 25 May 2019). [ url ] [ doi ] [ BibTeX ]
[IHH19]
A Ismail, M Herajy and M Heiner:
A Graphical Approach for the Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets;
In Automated Reasoning for Systems Biology and Medicine, (P Zuliani and P Liò, Eds.), Springer, Cham, pages 349–367, 2019 (first online: 12. June 2019). [ url ] [ doi ] [ BibTeX ]
[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 ]
[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 ]
[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 ]
[CH19a]
J Chodak and M Heiner:
Spike – reproducible simulation experiments with configuration file branching;
In Proc. CMSB 2019, Trento, Springer, LNCS/LNBI, volume 11773, pages 315-321, September 2019. [ doi ] [ BibTeX ]
[AHL19]
G Assaf, M Heiner and F Liu:
Biochemical reaction networks with fuzzy kinetic parameters in Snoopy;
In Proc. CMSB 2019, Trieste, Springer, LNCS/LNBI, volume 11773, pages 302-307, September 2019. [ doi ] [ BibTeX ]
[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 ]
[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 ]
[CH19a.sld]
J Chodak and M Heiner:
Spike – reproducible simulation experiments with configuration file branching;
Talk, Trento, September 2019. [ 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 ]

2018

[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[R17]
Rohr, C:
Discrete-Time Leap Method For Stochastic Simulation;
Fundamenta Informaticae, 160(1-2):181-198, 2018 (accepted: May 16, 2017). [ 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 ]
[BHAH18]
A Badawy, M Herajy, W Awad and M Heiner:
Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets;
In 13th International Conference on Computer Engineering and Systems (ICCES), IEEE, pages 268–272, 2018. [ doi ] [ BibTeX ]
[HH18]
M Herajy and M Heiner:
An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets;
In Proceedings of the 2018 Winter Simulation Conference (WSC 2018), Gothenburg, Sweden, IEEE, 978-1-5386-6572-5/18, pages 1346-1357, December 2018. [ url ] [ pdf ] [ doi ] [ BibTeX ]
[SGH18]
T Self, D Gilbert and M Heiner:
Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models;
In Proc. CMSB 2018, Brno, Springer, LNCS/LNBI, volume 11095, pages 39-58, September 2018. [ doi ] [ BibTeX ]
[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 ]
[HC18.poster]
M Heiner and J Chodak:
Petri Nets for Multilevel Systems Biology;
Poster, May 2018 (7.8 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 ]
[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 ]
[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 ]
[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 ]
[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 ]

2017

[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 ]
[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 ]
[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 ]
[Rohr17]
Christian Rohr:
Simulative analysis of coloured extended stochastic Petri nets;
PhD thesis, BTU Cottbus, Dep. of CS, January 2017. [ 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 ]
[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 ]

2016

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

2015

[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 ]
[GH15.tcs]
D Gilbert and M Heiner (eds.):
Special Issue 'Advances in CMSB';
volume 599 of J. Theoretical Computer Science, Elsevier, 2015. [ 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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[HSW15]
M Heiner, M Schwarick and J Wegener:
Charlie – an extensible Petri net analysis tool;
In Proc. PETRI NETS 2015, Brussels, Springer, LNCS, volume 9115, pages 200–211, June 2015. [ url ] [ doi ] [ BibTeX ]
[BR15]
MA Blätke, C Rohr:
A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit;
In Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2015), CEUR-WS.org, CEUR Workshop Proceedings, volume 1373, pages 37–54, June 2015. [ url ] [ pdf ] [ BibTeX ]
[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 ]
[S15]
A Sharma:
Snoopy Report Generator Snoopy2LATEX (Internship report);
Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2015. [ 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 ]
[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 ]
[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 ]
[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.sld2]
M Heiner:
Model-driven design for Synthetic Systems Biology;
Talk, Brunel University London, Centre for Systems and Synthetic Biology, April 2015. [ pdf ] [ BibTeX ]
[H15.sld1]
M Heiner:
Petri Nets 4 Bacterial Bioengineering;
Talk, Brunel University London, Centre for Systems and Synthetic Biology, March 2015. [ pdf ] [ BibTeX ]

2014

[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 ]
[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 ]
[LBHY14]
F Liu, MA Blätke, M Heiner and M Yang:
Modelling and simulating reaction–diffusion systems using coloured Petri nets;
Computers in Biology and Medicine, 53:297–308, October 2014 (online July 2014). [ url ] [ doi ] [ BibTeX ]
[LHY14]
F Liu, M Heiner and M Yang:
Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development;
WSPC Journal of Biological Systems, 22(3):463–493, online May 2014. [ doi ] [ BibTeX ]
[HH14a]
M Herajy and M Heiner:
Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks;
Fundamenta Informaticae, 129(1-2):49-67, 2014. [ url ] [ doi ] [ BibTeX ]
[BHHP14]
B Barbot, S Haddad, M Heiner and C Picaronny:
Rare Event Handling in Signalling Cascades;
In Proc. SIMUL 2014, The Sixth International Conference on Advances in System Simulation, Nice, France, ThinkMind Digital Library, pages 126–131, October 2014. [ url ] [ pdf ] [ BibTeX ]
[HLR14]
M Herajy, F Liu and C Rohr:
Coloured hybrid Petri nets for systems biology;
In Proc. of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 60-76, June 2014. [ url ] [ pdf ] [ BibTeX ]
[HH14b]
M Herajy and M Heiner:
A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
In Proc. PETRI NETS 2014, Tunis, Springer, LNCS, volume 8489, pages 374–384, June 2014. [ url ] [ doi ] [ BibTeX ]
[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 ]
[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 ]
[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 ]
[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 ]
[CS14]
C Swapnil:
Stochastic simulation efficiency;
Technical report 02-14, Brandenburg University of Technology Cottbus-Senftenberg, Department of Computer Science, July 2014. [ url ] [ BibTeX ]
[Schwarick14]
Martin Schwarick:
Symbolic on-the-fly analysis of stochastic Petri nets;
PhD thesis, BTU Cottbus, Dep. of CS, 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 ]
[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.sld1]
M Heiner:
BioModel Engineering - a Petri Net Perspective;
Talk, Università Ca' Foscari Di Venezia (invited talk), March 2014. [ pdf ] [ BibTeX ]

2013

[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 ]
[Rohr13]
C Rohr:
Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
ToPNoC VIII, LNCS 8100, 2013. [ 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 ]
[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 ]
[BDR+13]
MA Blätke, A Dittrich, C Rohr, M Heiner, F Schaper and W Marwan:
JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology;
Molecular BioSystems, 9(6):1290-1307, 2013. [ url ] [ doi ] [ BibTeX ]
[HG13]
M Heiner and D Gilbert:
BioModel Engineering for Multiscale Systems Biology;
Progress in Biophysics and Molecular Biology, 111(2-3):119–128, April 2013 (online: 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 ]
[PGH+13]
O Parvu, D Gilbert, M Heiner, F Liu and N Saunders:
Modelling and Analysis of Phase Variation in Bacterial Colony Growth;
In Proc. CMSB 2013, Vienna, Springer, LNCS/LNBI, volume 8130, pages 78–-91, September 2013. [ doi ] [ BibTeX ]
[LHY13]
F Liu, M Heiner and M Yang:
Colored Petri Nets for Multiscale Systems Biology – Current Modeling and Analysis Capabilities in Snoopy;
In Proc. 7th International Conference on Systems Biology (ISB 2013), Huangshan/China, IEEE, pages 24 - 30, August 2013. [ url ] [ doi ] [ BibTeX ]
[GHLS13]
D Gilbert, M Heiner, F Liu and N Saunders:
Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology;
In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 230–249, June 2013. [ url ] [ doi ] [ BibTeX ]
[HRS13]
M Heiner, C Rohr and M Schwarick:
MARCIE - Model checking And Reachability analysis done effiCIEntly;
In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 389–399, June 2013. [ url ] [ pdf ] [ doi ] [ BibTeX ]
[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 ]
[HRS13.poster]
M Heiner, C Rohr and M Schwarick:
Petri net based system analysis;
Poster, 2013. [ 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 ]
[Herajy13]
Mostafa Herajy:
Computational Steering of Multi-Scale Biochemical Networks;
PhD thesis, BTU Cottbus, Dep. of CS, January 2013. [ 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.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 ]
[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.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 ]
[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 ]

2012

[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 ]
[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 ]
[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 ]
[LHY12]
F Liu, M Heiner and M Yang:
An efficient method for unfolding colored Petri nets;
In Proceedings of the 2012 Winter Simulation Conference (WSC 2012), Berlin, IEEE, 978-1-4673-4781-5/12, 2012. [ url ] [ pdf ] [ BibTeX ]
[BDH+12]
MA Blätke, A Dittrich, M Heiner, F Schaper and W Marwan:
JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept;
In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI, volume 7605, pages 362–365, 2012. [ url ] [ doi ] [ BibTeX ]
[BHM12]
MA Blätke, M Heiner and W Marwan:
Predicting Phenotype from Genotype Through Automatically Composed Petri Nets;
In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI, volume 7605, pages 87–106, 2012. [ url ] [ doi ] [ BibTeX ]
[Schw12]
M Schwarick:
Symbolic model checking of stochastic reward nets;
In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2012), CEUR-WS.org, CEUR Workshop Proceedings, volume 928, pages 343–357, September 2012. [ url ] [ pdf ] [ BibTeX ]
[HH12.csp]
M Herajy and M Heiner:
Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks;
In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2012), CEUR-WS.org, CEUR Workshop Proceedings, volume 928, pages 147–159, September 2012. [ url ] [ pdf ] [ BibTeX ]
[HH+12]
M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
Snoopy – a unifying Petri net tool;
In Proc. PETRI NETS 2012, Hamburg, Springer, LNCS, volume 7347, 398–407, June 2012. [ url ] [ doi ] [ BibTeX ]
[HS12]
M Herajy and M Schwarick:
A Hybrid Petri Net Model of the Eukaryotic Cell Cycle;
In Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2012, CEUR-WS.org, CEUR Workshop Proceedings, volume 852, pages 29-43, June 2012. [ url ] [ pdf ] [ BibTeX ]
[Rohr12]
C Rohr:
Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
In Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2012, CEUR-WS.org, CEUR Workshop Proceedings, volume 852, pages 62-75, June 2012. [ url ] [ pdf ] [ BibTeX ]
[HRS12]
M Heiner, C Rohr and M Schwarick:
Petri net based system analysis;
Poster, 2012. [ pdf ] [ BibTeX ]
[Rohr12.poster]
C Rohr:
Simulative Model Checking of Colored Stochastic Petri Nets; IGS/ZUSYS, 2012;
Poster, 2012. [ 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 ]
[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 ]
[Liu12]
Fei Liu:
Colored Petri Nets for Systems Biology;
PhD thesis, BTU Cottbus, Dep. of CS, January 2012. [ pdf ] [ BibTeX ]
[HS12.sld2]
M Heiner and M Schwarick:
Markov Chains & Functional Safety;
Talk, Philotech Academy, Berlin, October 2012. [ pdf ] [ BibTeX ]
[HH12+.sld]
M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
Snoopy – a unifying Petri net tool;
Talk, PETRI NETS 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
[Rohr12.sld]
C Rohr:
Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
Talk, 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
[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 ]
[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 ]
[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 ]

2011

[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[GLT+11]
Q Gao, F Liu, D Tree and D Gilbert:
Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity;
In Proc. of the 2nd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 135–150, June 2011. [ pdf ] [ BibTeX ]
[GLG+11]
Q Gao, F Liu, D Gilbert, M Heiner and D Tree:
A Multiscale Approach to Modelling Planar Cell Polarity in Drosophila Wing using Hierarchically Coloured Petri Nets;
In Proc. 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, ACM digital library, pages 209–218, September 2011. [ url ] [ pdf ] [ BibTeX ]
[SRH11]
M Schwarick , C Rohr and M Heiner:
MARCIE - Model checking And Reachability analysis done effiCIEntly;
In Proc. 8th International Conference on Quantitative Evaluation of SysTems (QEST 2011), Aachen, Germany, IEEE CS Press, pages 91–100, September 2011. [ url ] [ pdf ] [ BibTeX ]
[WSH11]
J Wegener, M Schwarick and M Heiner:
A Plugin System for Charlie;
In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2011), Biaystok University of Technology, ISBN: 978-83-62582-06-8, pages 531–554, September 2011. [ url ] [ pdf ] [ BibTeX ]
[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 ]
[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 ]
[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 ]
[WSH11.sld]
J Wegener, M Schwarick and M Heiner:
A Plugin System for Charlie;
Talk, International Workshop on Concurrency, Specification, and Programming (CSP 2011), September 2011. [ pdf ] [ BibTeX ]
[SRH11.sld]
M Schwarick, C Rohr and M Heiner:
MARCIE - Model checking And Reachability analysis done effiCIEntly;
Talk, QEST 2011, Aachen, September 2011. [ pdf ] [ BibTeX ]
[H11.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 ]
[H11.sld3]
M Heiner:
BioModel Engineering - a Petri Net Perspective;
Talk, Brunel University, DISC seminar, May 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 ]
[HH11.sld]
M. Herajy and M. Heiner:
Generalized Hybrid Petri Nets;
Talk, Formal Methods in Molecular Biology, Dagstuhl seminar, April 2011. [ pdf ] [ BibTeX ]
[H11.sld2]
M Heiner:
Biochemical Networks - a Petri Net Perspective;
Talk, Universtita Torino, PhD School (invited talk), March 2011. [ pdf ] [ BibTeX ]
[H11.sld1]
M Heiner:
Biochemically Interpreted Petri Nets, Some Open Problems;
Talk, Universtita Torino, research group Prof. G Balbo (invited talk), March 2011. [ pdf ] [ BibTeX ]

2010

[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[HS10]
M Heiner and K Sriram:
Structural Analysis to Determine the Core of Hypoxia Response Network;
PLoS ONE, 5(1):e8600, 2010. [ 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 ]
[SH10b]
S Soliman and M Heiner:
A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
PLoS ONE, 5(12):e14284, 2010. [ 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 ]
[HRSS10]
M Heiner, C Rohr, M Schwarick and S Streif:
A Comparative Study of Stochastic Analysis Techniques;
In Proc. 8th International Conference on Computational Methods in Systems Biology (CMSB 2010), Trento, ACM digital library, pages 96–106, September 2010. [ pdf ] [ doi ] [ BibTeX ]
[LH10]
F Liu and M Heiner:
Colored Petri nets to model and simulate biological systems;
In Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pages 70-84, June 2010. [ pdf ] [ BibTeX ]
[HH10]
M Herajy and M Heiner:
Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions;
In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 66–79, October 2010. [ pdf ] [ BibTeX ]
[LH10b]
F Liu and M Heiner:
Computation of Enabled Transition Instances for Colored Petri Nets;
In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 51–65, October 2010. [ pdf ] [ BibTeX ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[H10.sld2]
M Heiner:
Modularization and hierarchical representation of biomolecular networks with Petri nets transition invariants;
Talk, Workshop on Integrative Biological Pathway Analysis and Simulation (IB-PAS), Bielefeld, May 2010. [ pdf ] [ BibTeX ]
[H10.sld1]
M Heiner:
Snoopy - a unifying Petri net framework to investigate biomolecular networks;
Talk, Summer School on Integrative Biological Pathway Analysis and Simulation (IB-PAS 2010), Bielefeld (invited talk), May 2010. [ pdf ] [ BibTeX ]
[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 ]

2009

[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 ]
[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 ]
[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 ]
[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 ]
[Liu09.manual]
F Liu:
Manual for Snoopy2Prism Export;
Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2009. [ pdf ] [ BibTeX ]
[Schw09]
Marcel Schwarze:
Web-based Petri net animation (in German);
Diploma thesis, FH Lausitz, Dep. of CS, November 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 ]
[Fisc09]
Ansgar Fischer:
Reachability graph based analysis of time-dependent Petri nets (in German);
Diploma thesis, BTU Cottbus, Dep. of CS, October 2009. [ 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 ]
[H09.sld1]
M Heiner:
A Petri Net Perspective on Systems and Synthetic Biology;
Talk, Brunel University London (invited talk), June 2009. [ pdf ] [ BibTeX ]

2008

[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 ]
[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 ]
[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 ]
[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 ]
[GHR+08]
D Gilbert, M Heiner, S Rosser, R Fulton, X Gu and M Trybio:
A Case Study in Model-driven Synthetic Biology;
In IFIP WCC 2008, 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC 2008), Milano, Springer, IFIP, volume 268, pages 163–175, September 2008. [ url ] [ pdf ] [ BibTeX ]
[HRS08]
M Heiner, R Richter and M Schwarick:
Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
In Proc. International Workshop on Petri Nets Tools and APplications (PNTAP 2008, associated to SIMUTools 2008), ACM digital library, 2008. [ url ] [ pdf ] [ BibTeX ]
[BGH08]
R Breitling, D Gilbert and M Heiner:
BioModel Engineering - from Structure to Behaviour, CMSB 2008, Rostock, October 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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[Bayer08]
Denny Bayer:
Testing with Music (in German);
Bachelor thesis, BTU Cottbus, Dep. of CS, September 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 ]
[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 ]
[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 ]

2007

[GHL07b]
D Gilbert, M Heiner and S Lehrack:
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
In Proc. 5th International Conference on Computational Methods in Systems Biology (CMSB 2007), Edinburgh, Springer, LNCS/LNBI, volume 4695, pages 200-216, 2007. [ url ] [ pdf ] [ BibTeX ]
[PH07]
L Popova and M Heiner:
Quantitative Evaluation of Time Petri Nets and Applications to Technical and Biochemical Networks);
In Proc. International Workshop on Concurrency, Specification and Programming (CS&P 2007), Lagów, September 2007, volume 2, pages 473-484, 2007. [ BibTeX ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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.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.sld1]
M Heiner:
Mathematical Modelling of Biochemical Networks with Petri Nets;
Talk, FMP Berlin, February 2007. [ pdf ] [ BibTeX ]

2006

[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 ]
[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 ]
[HRT06a]
M Heiner, R Richter and A Tovchigrechko:
Snoopy - a Tool to Design and Animate / Simulate Graphs;
Poster, 2006. [ 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 ]
[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 ]
[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 ]
[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 ]
[W06.sld]
K Winder:
Strukturelle Charakterisierung der Invarianten eines Petrinetzes;
Talk, FU Berlin, DFG-Research Center Matheon, May 2006. [ pdf ] [ BibTeX ]

2005

[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 ]
[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 ]
[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 ]
[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 ]
[Dube05]
Matthias Dube:
Signing and Verifying SNOOPY-files;
Student thesis, BTU Cottbus, Dep. of CS, March 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 ]
[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.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.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.sld1]
M Heiner:
From Petri Nets to Differential Equations (ODEs);
Talk, Glasgow University, Bioinformatics Research Centre (invited talk), March 2005. [ pdf ] [ BibTeX ]

2004

[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[HK04.sld1]
M Heiner and I Koch:
Petri Net Based Model Validation in Systems Biology;
Talk, ICATPN 2004, Bologna, June 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 ]
[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 ]
[H04.sld1]
M Heiner:
Dependable Software for Embedded Systems;
Talk, VW Wolfsburg (invited talk), February 2004. [ pdf ] [ BibTeX ]

2003

[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 ]
[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 ]
[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 ]
[Mertke03]
Thomas Mertke:
A Technical Language for Formal Safety Specification of Reactive Systems;
PhD thesis, BTU Cottbus, Dep. of CS, October 2003. [ 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 ]
[H03.sld]
M Heiner:
About some Applications of Petri Net Theory - My Petri Net Picture Book;
Talk, Adventmatik 2003, Paderborn, December 2003. [ pdf ] [ BibTeX ]

2002

[RHHH02]
T Rottke, D Hatebur, M Heisel and M Heiner:
A Problem-Oriented Approach to Common Criteria Certification);
In Proc. SafeComp ’02, Catania, Sept. 2002, Springer, LNCS, volume 2434, pages 334 - 346, 2002. [ pdf ] [ BibTeX ]
[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 ]
[H02.sld1]
M Heiner:
Concurrency Patterns - A Petri Net Perspective;
Talk, Workshop Dependable Components, Schloss Dagstuhl, November 2002. [ pdf ] [ BibTeX ]
[H02.sld2]
M Heiner:
Increased Safety by Fault Tolerant Software - Just another Way to Waste Money?
Talk, Bosch-Zuverlässigkeits-Workshop, Böblingen (invited talk), October 2002. [ pdf ] [ BibTeX ]
[HK02.sld]
M Heiner and I Koch:
Biopathways & Petri Nets - Demonstrated for Apoptosis;
Talk, Charité Berlin, September 2002. [ pdf ] [ BibTeX ]

2001

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

2000

[HKS00]
M Heiner, I Koch and S Schuster:
Using Time-dependent Petri Nets for the Analysis of Metabolic Networks;
In Proc. DFG-Workshop Modelling and Simulation of Metabolic Networks, May 2000, O.-v.-Guericke-Uni Magdeburg, pages 15 - 21, 2000. [ BibTeX ]
[HM00]
M Heiner and T Menzel:
Time-related Modelling of PLC Systems with Time-less Petri Nets;
In Discrete Event Systems, Analysis and Control, Boel, R.; Stremerch, G. (eds.) Kluwer Academic Publishers, volume 2000, pages 275 - 282, 2000. [ pdf ] [ BibTeX ]
[HH00.sld]
M Heiner and R Heinrich:
Metabolic Petri Nets;
Talk, Schloss Hohenkammer, DFG-Kolloquium, October 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 ]
[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 ]

1999

[HH99]
M Heiner and M Heisel:
Modelling Safety-Critical Systems with Z and Petri Nets;
In Proc. SafeComp '99, Toulouse 1999, Springer, LNCS, volume 1698, pages 361 - 374, 1999. [ url ] [ pdf ] [ BibTeX ]
[HDS99]
M Heiner, P Deussen and J Spranger:
A Case Study in Design and Verification of Manufacturing Systems with Hierarchical Petri Nets;
In The International Journal of Advanced Manufacturing Technology 1999, volume 15, pages 139-152, 1999. [ pdf ] [ BibTeX ]
[HMS99]
M Heiner and T Menzel:
Modellierung und Analyse von SPS-Anwenderprogrammen mit Petri-Netzen;
In Proc. EKA '99, 6. Fachtagung, Braunschweig, May 1999, pages 247-265, 1999. [ pdf ] [ BibTeX ]
[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 ]
[Noac99]
Andreas Noack:
Ein ZBDD-Paket für effizientes Model Checking von Petrinetzen;
Study thesis, BTU Cottbus, Dep. of CS, June 1999. [ BibTeX ]
[H99.sld]
M Heiner:
Software Testing - State of the Art, Methods, and Limitations;
Talk, March 1999. [ pdf ] [ BibTeX ]

1998

[Deus98]
P Deussen:
Algorithmic Aspects of Concurrent Automata;
In Proc. Workshop on Concurrency, Specification &Programming 1998, Berlin, Sept. 1998), Humbolt Univ. at Berlin, Informatik-Bericht, volume 110, pages 39-70, 1998. [ pdf ] [ BibTeX ]
[H98]
M Heiner:
Petri Net Based System Analysis without State Explosion;
In Proc. Hight Performance Computing '98, Boston, April 1998, SCS Int. San Diego 1998), pages 394-403, 1998. [ pdf ] [ BibTeX ]
[HM98a]
M Heiner and T Menzel:
Instruction List Verification Using a Petri Net Semantics;
In Proc. IEEE Int. Conf. on Systems, Man, and Cybernetics, San Diego, October 1998), pages 716-721, 1998. [ pdf ] [ BibTeX ]
[HM98b]
M Heiner and T Menzel:
A Petri Net Semantics for the PLC Language Instruction List;
In Proc. IEE Workshop on Discrete Event Systems (WODES '98), Cagliari, August 1998), pages 161-165, 1998. [ pdf ] [ BibTeX ]
[Spra98]
J Spranger:
Combining structural properties and symbolic representation for efficient analysis of Petri nets;
In Proc. Workshop on Concurrency, Specification &Programming 1998, Berlin, Sept. 1998), Humbolt Univ. at Berlin, Informatik-Bericht, volume 110, pages 236-244, 1998. [ pdf ] [ BibTeX ]
[Deus98]
P Deussen:
Concurrent Automata;
Technical report I-05/1998, Brandenburg University of Technology Cottbus, Department of Computer Science, August 1998. [ pdf ] [ BibTeX ]
[H98.sld]
M Heiner:
Application of Petri Nets to Metabolic Networks (in German);
Talk, HU Berlin, August 1998. [ pdf ] [ BibTeX ]

1997

[H97a]
M Heiner:
On Exploiting the Analysis Power of Petri nets for the Validation of Discrete Event Systems;
In Proc. 2nd IMACS Symposium on Mathematical Modelling (MATHMOD VIENNA '97), ARGESIM Report, volume 11, pages 171 – 176, 1997. [ pdf ] [ BibTeX ]
[H97b]
M Heiner:
Verification and Optimization of Control Programs by Petri Nets without State Explosion;
In Proc. 2nd Int. Workshop on Manufacturing and Petri Nets held at Int. Conf. on Application and Theory of Petri Nets (ICATPN '97, Toulouse, June 1997), pages 69–84, 1997. [ pdf ] [ BibTeX ]
[HP97]
M Heiner and L Popova-Zeugmann:
On Integration of Qualitative and Quantitative Analysis of Manufacturing Systems Using Petri Nets;
In Proc. 42. Int. wissenschaftliches Kolloquium (IWK '97), Ilmenau, September 1997), TU Ilmenau, volume 1, pages 557-562, 1997. [ pdf ] [ BibTeX ]
[KUH97]
H König, A Ulrich and M Heiner:
Design for Testability: A Step-wise Approach to Protocol Testing;
In Proc. 10th Int. Workshop on Testing of Communicating Systems (IWTCS '97), Seoul, Sept. 1997), Chapman &Hall, Kim, M.; Kang, S.; Hong, K. (eds.), pages 125-140, 1997. [ pdf ] [ BibTeX ]
[PH97]
L Popova-Zeugmann and M Heiner:
Worst-case Analysis of Concurrent Systems with Duration Interval Petri Nets;
In Proc. 5. Fachtagung EKA '97, Braunschweig, May 1997, IfRA 1997), Schnieder, E.; Abel, D. (eds.), Entwurf komplexer Automatisierungssysteme `97, pages 162–179, 1997. [ pdf ] [ BibTeX ]
[Spra97]
J Spranger:
FUNlite - A Parallel Petri Net Simulator;
In Proc. 42. IWK Ilmenau, September 1997), IWK Ilmenau, page 6, 1997. [ pdf ] [ BibTeX ]
[HM97]
M Heiner and T Menzel:
Petri-Netz-Semantik für die SPS-Anwenderprogrammiersprache Anweisungsliste;
Technical report I-20/1997, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1997. [ pdf ] [ BibTeX ]
[HMMM97]
M Heiner, M Meier, T Menzel and T Mertke:
Petri-Netz basierte Methoden zur sicherheitsorientierten Zertifizierung von SPS Anwenderprogrammen;
Technical report I-19/1997, Brandenburg University of Technology Cottbus, Department of Computer Science, December 1997. [ pdf ] [ BibTeX ]
[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 ]

1996

[HD96a]
M Heiner and P Deussen:
Petri Net Based Design and Analysis of Reactive Systems;
In Proc. Int. Workshop on Discrete Event Systems (WODES '96), Edinburgh, August 1996. [ pdf ] [ BibTeX ]
[HD96b]
M Heiner and P Deussen:
A Case Study in Design and Validation of Reactive Systems by Means of Petri Nets;
In Proc. IMACS Multiconference on Computational Engineering in Systems Applications (CESA '96), Symposium "Discrete Events and Manufacturing Systems", Lille, France, July 1996. [ pdf ] [ BibTeX ]
[HDS96]
M Heiner, P Deussen and J Spranger:
A Case Study in Developing Control Software of Manufacturing Systems with Hierarchical Petri Nets;
In Proc. 1st Int. Workshop on Manufacturing and Petri Nets held at Int. Conf. on Application and Theory of Petri Nets (ICATPN '96), Osaka, Japan, June 1996. [ pdf ] [ BibTeX ]
[LHK96]
G Lindner, M Heiner and T Kobienia:
Deadlock Detection in a Distributed Implementation of a Visualization System for Medical Measurement Signals;
In Proc. IEEE In. Conf. on Systems, Man and Cybernetics, Beijing, China, IEEE Press, volume 3, pages 2299–2304, Oct. 1996. [ pdf ] [ BibTeX ]
[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 ]
[H96.sld1]
M Heiner:
Safety-related Certification of PLC Application Programs with Petri Nets;
Talk, December 1996. [ 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 ]

1995

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

1994

[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 ]
[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 ]

1992

[H92]
M Heiner:
Petri Net Based Software Validation - Prospects and Limitations;
Technical report TR-92-022, ICSI Berkeley, March 1992. [ pdf ] [ 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

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

2002

2001

2000

1999

1998

1997

1996

1995

1994

1992

… the end …