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data structures and software dependability

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brandenburg university of technology cottbus - senftenberg

Snoopy's bibliography - Case Studies

latest update: February 20, 2019, at 03:20 PM

Please use the following reference to give credits to Snoopy:
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

This list contains papers providing case studies done with Snoopy. The papers are sorted according to the application area and types of models used (not exhaustive).

  • coloured Petri nets
  • QPN-SPN-CPN-HPN - case studies discussed in several paradigms
  • SPN - stochastic Petri nets
  • CPN - continuous Petri nets
  • HPN - hybrid Petri nets
  • TPN - timed Petri nets
  • QPN1 - qualitative Petri nets of signal transduction networks
  • QPN2 - qualitative Petri nets of metabolic networks
  • QPN3 - qualitative Petri nets of further biochemical networks
  • QPN4 - qualitative Petri net for control software of production cells

Biological Case Studies

COLOURED PETRI NETS

  • [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 ] (Representing Network Reconstruction Solutions)
  • [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 ] (Bacterial colony growth)
  • [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 ] (Spatial modelling for Biomodelkit)
  • [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 ] (Repressilator as coloured HPN)
  • [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 ] (Brusselator - pattern development)
  • [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 ] (C. elegans vulval development)
  • [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 ] (Drosophila)
  • [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 ] (Bacterial colony growth)
  • [LH13a]
    F Liu and M Heiner:
    Modeling membrane systems using colored stochastic Petri nets;
    Nat. Computing, 12(4):617 - 629, 2013. [ url ] [ doi ] [ BibTeX ] (Membrane systems)
  • [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 ] (Ca2+ channels)
  • [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 ] (Bacterial colony growth)
  • [Gao13]
    Q Gao:
    A Systems Biology Approach to Multi-Scale Modelling and Analysis Of Planar Cell Polarity In Drosophila Melanogaster Wing;
    PhD thesis, Brunel University, London/Uxbridge, February 2013. [ url ] [ BibTeX ] (Drosophila)
  • [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 ]
  • Petri nets for multiscale Systems Biology
  • [Liu12]
    Fei Liu:
    Colored Petri Nets for Systems Biology;
    PhD thesis, BTU Cottbus, Dep. of CS, January 2012. [ 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 ] (Drosophila)
  • [Fongwa11]
    Fongwa, EA:
    A business modelling approach using Petri nets to preserve ecosystem services by community-based financial participation;
    PhD thesis, Brandenburg University of Technology Cottbus, 2011. [ url ] [ 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 ]
  • [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 ]

CASE STUDIES DISCUSSED IN SEVERAL PARADIGMS (QUALITATIVE, STOCHASTIC, CONTINUOUS, HYBRID)

  • [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 ] (Circadian oscillation)
  • [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 ] (Repressilator)
  • [GTR+10]
    Gu, X., Trybio, M., Ramsay, S., Jensen, M., Fulton, R., Rosser, S. and Gilbert, D.:
    Engineering a novel self-powering electrochemical biosensor;
    Systems and synthetic biology, 2010. [ url ] [ BibTeX ] (Biosensor)
  • [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 ] (RKIP)
  • [HS10]
    M Heiner and K Sriram:
    Structural Analysis to Determine the Core of Hypoxia Response Network;
    PLoS ONE, 5(1):e8600, 2010. [ doi ] [ BibTeX ] (Hypoxia)
  • [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 ] (Biosensor)
  • [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 ] (MAPK)
  • [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 ] (MAPK)
  • [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 ] (MAPK)

STOCHASTIC PETRI NETS (SPN)

  • [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 ] (autism spectrum disorder and inflammatory bowel disease)
  • [ATBK13]
    L Albergante, J Timmis, L Beattie and PM Kaye:
    A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection;
    PLoS Comput Biol, 9(11):e1003334, 2013. [ doi ] [ BibTeX ] (Granulomatous Inflammation)
  • [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 ] (Phosphate regulation in enteric bacteria)
  • [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 ] (AKAP scaffold-mediated crosstalk)
  • [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 ]
  • [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 ] (Circadian clock}
  • [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 ] (Lac operon)
  • [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 ]

CONTINUOUS PETRI NETS (CPN)

  • [GP13]
    DE Gratie and I Petre:
    Quantitative Petri Nets Models for the Heat Shock Response;
    Technical report 1068, 2013. [ pdf ] [ BibTeX ] (Heat Shock Response)
  • [HI11]
    Hardy, S. and Iyengar, R.:
    Analysis of Dynamical Models of Signaling Networks with Petri Nets and Dynamic Graphs;
    Modeling in Systems Biology, 2011. [ url ] [ BibTeX ]
  • [GHBO10]
    D Gilbert, M Heiner, R Breitling and R Orton:
    Computation modelling of kinase signalling cascades;
    In MAP Kinase Signaling Protocols, (R Seger, Ed.) Pages 369–384, 2010. [ url ] [ doi ] [ BibTeX ] (MAPK)
  • [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 ]
  • [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 ] (RKIP)
  • [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 ]
  • [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 ]

HYBRID PETRI NETS (HPN)

  • [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 ] (Repressilator as coloured HPN)
  • [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 ]
  • [Herajy13]
    Mostafa Herajy:
    Computational Steering of Multi-Scale Biochemical Networks;
    PhD thesis, BTU Cottbus, Dep. of CS, January 2013. [ 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 ]
  • [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 ]
  • [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 ]

TIMED PETRI NETS (TPN)

  • [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 ]
  • [PZ11]
    Popova-Zeugmann, L.:
    Quantitative evaluation of time-dependent Petri nets and applications to biochemical networks;
    Natural Computing, 10(3):1017–1043, 2011. [ url ] [ BibTeX ]
  • [PZP11]
    L Popova-Zeugmann and E Pelz:
    Studying Steady States in Biochemical Reaction Systems by Time Petri Nets;
    In Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 71–86, June 2011. [ 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 ]
  • [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 ]
  • [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 ]

QUALITATIVE PETRI NETS OF SIGNAL TRANSDUCTION NETWORKS

  • [CKV14]
    RV Carvalho, J Kleijn and F Verbeek:
    A multi-scale extensive Petri net model of the bacterial-macrophage interaction;
    In Proc. of the 5rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 15–29, June 2014. [ url ] [ pdf ] [ BibTeX ] (bacterial macrophage)
  • [MPG+14]
    G Minervini, E Panizzoni, M Giollo, A Masiero, C Ferrari and SCE Tosatto:
    Design and Analysis of a Petri Net Model of the Von Hippel-Lindau (VHL) Tumor Suppressor Interaction Network;
    PloS one, 9(6):e96986, 2014. [ doi ] [ BibTeX ] (Von Hippel-Lindau (VHL) Tumor Suppressor)
  • [Majumdar12]
    A Majumdar:
    Modeling of Yeast Pheromone Pathway using Petri Nets;
    Master thesis, University of Nebraska, Lincoln, Computer Science and Engineering Dep., December 2012. [ url ] [ BibTeX ] (Yeast Pheromone)
  • [BMM11]
    MA Blätke, S Meyer and W Marwan:
    Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform;
    In Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 117–134, June 2011. [ pdf ] [ BibTeX ]
  • [RRR+11]
    Rodriguez, E.M., Rudy, A., del Rosario, R.C.H., Vollmar, A.M. and Mendoza, E.R.:
    A discrete Petri net model for cephalostatin-induced apoptosis in leukemic cells;
    Natural Computing, 10(3):993–1015, 2011. [ url ] [ BibTeX ]
  • [Albergante10]
    Albergante, L.:
    A Petri Net Model of Liver Response to Visceral Leishmaniasis: Self-Regulation and Complex Interplay in the Vertebrate Immune System;
    PhD thesis, Università degli Studi di Milano, 2010. [ url ] [ BibTeX ]
  • [BMSM10]
    MA Blätke, S Meyer, C Stein and W Marwan:
    Petri Net Modeling via a Modular and Hierarchical Approach Applied to Nociception;
    In Proc. International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, ISBN: 978-972-8692-53-7, pages 131–143, June 2010. [ pdf ] [ BibTeX ]
  • [DTKC10]
    Donaldson, R., Talcott, C., Knapp, M. and Calder, M.:
    Understanding signalling networks as collections of signal transduction pathways;
    In Proceedings of the 8th International Conference on Computational Methods in Systems Biology, ACM, pages 86–95, 2010. [ url ] [ BibTeX ]
  • [LYL09]
    Low, I.W.J., Yang, Y. and Lin, H.:
    Validation of Petri net apoptosis models using P-invariant analysis;
    In Control and Automation, 2009. ICCA 2009. IEEE International Conference on, IEEE, pages 416–421, 2009. [ url ] [ 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 ]
  • [Sackmann08]
    A Sackmann:
    Network algorithms and bioinformatics problems;
    PhD thesis, Poznan University Of Technology, Institute of Computing Science, May 2008. [ 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 ]
  • [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 ]
  • [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 ]

QUALITATIVE PETRI NETS OF METABOLIC NETWORKS

  • [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 ] (Glycolysis and Pentose Phosphate pathway (G/PPP))
  • [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 ] (Potato tuber)
  • [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 ] (Glycolysis and Pentose Phosphate pathway (G/PPP))

FURTHER QUALITATIVE PETRI NETS

  • [Yang11]
    Yang, Y.:
    Investigation of the Regulatory Roles of Micrornas by Systems Biology Approaches;
    PhD thesis, National University of Singapore, Electrical & Computer Engineering, 2011. [ url ] [ BibTeX ]
  • [BSK10]
    Bortfeldt, RH, Schuster, S. and Koch, I.:
    Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.;
    In Silico Biology, 10, 0007, 2010. [ url ] [ BibTeX ]
  • [Grunwald09]
    Grunwald, S.:
    Identification and characterisation of muscular dystrophy Duchenne modifying genes and signal transduction pathways;
    PhD thesis, Humboldt University, 2009. [ url ] [ 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 ]
  • [KBSK09]
    Kielbassa, J., Bortfeldt, R., Schuster, S. and Koch, I.:
    Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets;
    Computational biology and chemistry, 33(1):46–61, 2009. [ url ] [ BibTeX ]
  • [RMO09]
    del Rosario, RCH, Mendoza, E. and Oesterhelt, D.:
    Modelling the Bioenergetics of Halobacterium Salinarum with Petri Nets;
    Journal of Computational and Theoretical Nanoscience, 6(8):1965–1976, 2009. [ url ] [ BibTeX ]

Some Technical and Academic Case Studies

CONTROL SOFTWARE OF PRODUCTION CELLS

  • [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 ]
  • [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 ]

GAMES

  • P. H. Starke. Halma net. Petri Net Newsletter, 28:3-8, 1987.

… the end …

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