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Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks

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Bacterial Molecular Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 804))

Abstract

Using the example of phosphate regulation in enteric bacteria, we demonstrate the particular suitability of stochastic Petri nets to model biochemical phenomena and their simulative exploration by various features of the software tool Snoopy.

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References

  1. Petri CA, Reisig W. (2008) Petri net. Scholarpedia, 3(4):6477 [http://www.scholarpedia.org/article/Petri_net].

  2. Marwan W, Wagler A, Weismantel R. (2011) Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks. J Nat Comput, 10(2):639–654.

    Google Scholar 

  3. Baldan P, Cocco N, Marin A, Simeoni M. (2010) Petri nets for modelling metabolic pathways: a survey. J Nat Comput, 955–989.

    Google Scholar 

  4. Heiner M, Gilbert D, Donaldson R. (2008) Petri nets in systems and synthetic biology. Lect Notes Comput Sci, 5016:215–264.

    Article  Google Scholar 

  5. Rohr C, Marwan W, Heiner M. (2010) Snoopy – a unifying Petri net framework to investigate biomolecular networks. Bioinformatics, 26(7):974–975.

    Article  PubMed  CAS  Google Scholar 

  6. Heiner M, Donaldson R, Gilbert D. (2010) Petri Nets for Systems Biology. In Symbolic Systems Biology: Theory and Methods, Chapter 3. Edited by Iyengar MS, Jones & Bartlett Publishers, LLC.

    Google Scholar 

  7. Petri Nets World: Online Services for the International Petri Nets Community, [http://www.informatik.uni-hamburg.de/TGI/PetriNets/].

  8. SBML Software Summary, [http://sbml.org/SBML_Software_Guide/SBML_Software_Summary].

  9. Bitesize Bio – Free Online Bioinformatics tools, [http://bitesizebio.com/2009/01/06/free-online-bioinformatics-tools/].

  10. Systems Biology – Software, [http://systems-biology.org/software/].

  11. Tovchigrechko A. (2008) Efficient symbolic analysis of bounded Petri nets using Interval Decision Diagrams. PhD thesis, BTU Cottbus, Germany.

    Google Scholar 

  12. Heiner M, Lehrack S, Gilbert D, Marwan W. (2009) Extended stochastic petri nets for model-based design of wet-lab experiments. Lect Notes Bioinformatics, 5750:138–163.

    Google Scholar 

  13. Gillespie DT. (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem, 81(25):2340–2361.

    Article  CAS  Google Scholar 

  14. Neidhardt FC, Ingraham JL et al. (1990) Physiology of the bacterial cell – a molecular approach. Sinauer Associates, Sunderland, 370.

    Google Scholar 

  15. Yi-Ju Hsieh Y-J, Wanner BL (2010) Global regulation by the seven-component Pi signaling system. Curr Opin Microbiol, 13:198–203.

    Article  PubMed  Google Scholar 

  16. Franzke A. (2009) Charlie 2.0 – a multi-threaded Petri net analyser. Diploma thesis, BTU Cottbus, Germany.

    Google Scholar 

  17. Heiner M, Koch I. (2004) Petri net based system validation in systems biology. Lect Notes Comput Sci, 3099:216–237.

    Article  Google Scholar 

  18. Palsson BO (2006) Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, Cambridge.

    Google Scholar 

  19. Heiner M. (2009) Understanding Network Behaviour by Structured Representations of Transition Invariants – A Petri Net Perspective on Systems and Synthetic Biology. In Algorithmic Bioprocesses. Edited by Condon A, Harel D, Kok JN, Salomaa A, Winfree E. Springer, Natural Computing Series, 367–389.

    Chapter  Google Scholar 

  20. Heiner M, Schwarick M, Tovchigrechko A. (2009) DSSZ-MC – a tool for symbolic analysis of extended petri nets. Lect Notes Comput Sci, 5606:323–332.

    Article  Google Scholar 

  21. Schwarick M, Heiner M. (2009) CSL model checking of biochemical networks with Interval Decision Diagrams. Lect Notes Bioinformatics, 5688:296–312.

    Google Scholar 

  22. MC2(PLTLc) – Monte Carlo Model Checker for PLTLc properties, University of Glasgow, [http://www.brc.dcs.gla.ac.uk/software/mc2/].

  23. Breitling R, Gilbert D, Heiner M, Orton R. (2008) A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Brief Bioinformatics, 9:404–421.

    Article  PubMed  CAS  Google Scholar 

  24. Heiner M, Sriram K. (2010) Structural analysis to determine the core of hypoxia response network. PLoS ONE, 5(1):e8600.

    Article  PubMed  Google Scholar 

  25. Breitling R, Donaldson RA, Gilbert D, Heiner M. (2010) Biomodel engineering – from structure to behavior. Lect Notes Bioinformatics, 5945:1–12.

    Google Scholar 

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Acknowledgement

Christian Rohr is funded by the International Max Planck Research School for Analysis, Design, and Optimisation in Chemical and Biochemical Process Engineering, Magdeburg.

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Authors and Affiliations

  1. Otto von Guericke University & Magdeburg Centre for Systems Biology, c/o Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany

    Wolfgang Marwan & Christian Rohr

  2. Department of Computer Science, Brandenburg University of Technology, Cottbus, Germany

    Monika Heiner

Authors
  1. Wolfgang Marwan
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  2. Christian Rohr
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  3. Monika Heiner
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Corresponding author

Correspondence to Monika Heiner .

Editor information

Editors and Affiliations

  1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, bd. du Triomphe, Bruxelles, 1050, Belgium

    Jacques van Helden

  2. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bvd. du Triomphe, Bruxelles, 1050, Belgium

    Ariane Toussaint

  3. INSERM 1024, Institut de Biologie de l'Ecole Normale, rue d'Ulm 46, Paris, 75230, France

    Denis Thieffry

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Marwan, W., Rohr, C., Heiner, M. (2012). Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_21

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  • DOI: https://doi.org/10.1007/978-1-61779-361-5_21

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-360-8

  • Online ISBN: 978-1-61779-361-5

  • eBook Packages: Springer Protocols

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