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International Conference on Applications and Theory of Petri Nets and Concurrency

PETRI NETS 2016: Application and Theory of Petri Nets and Concurrency pp 113–122Cite as

AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9698))

Abstract

We present a tool for simulation of populations of living cells interacting in spatial structures. Each cell is modelled with the Quasi-Steady Petri Net that integrates dynamic regulatory network expressed with a Petri Net (PN) and Genome Scale Metabolic Networks (GSMN) where linear programming is used to explore the steady-state metabolic flux distributions in the whole-cell model.

Similar simulations have already been conducted for single cells, but we present an architecture to simulate populations of millions of interacting cells organized in spatial structures which can be used to model tumour growth or formation of tuberculosis lesions. For that we use the Spark framework and organize the computation in an agent based “think like a vertex” fashion as in Pregel like systems. In the cluster we introduce a special kind of per node caching to speed up computation of the steady-state metabolic flux.

Our tool can be used to provide a mechanistic link between genotype and behaviour of multicellular system.

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Acknowledgements

This research was sponsored by National Science Centre based on decision DEC-2012/07/D/ST6/02492.

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Authors and Affiliations

  1. Institute of Informatics, University of Warsaw, Warsaw, Poland

    Wojciech Ptak & Jacek Sroka

  2. Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK

    Andrzej M. Kierzek

Authors
  1. Wojciech Ptak
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  2. Andrzej M. Kierzek
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  3. Jacek Sroka
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Corresponding author

Correspondence to Jacek Sroka .

Editor information

Editors and Affiliations

  1. Université Pierre and Marie Curie, Paris, France

    Fabrice Kordon

  2. Department Informatik, Universität Hamburg Department Informatik, Hamburg, Germany

    Daniel Moldt

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© 2016 Springer International Publishing Switzerland

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Ptak, W., Kierzek, A.M., Sroka, J. (2016). AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks. In: Kordon, F., Moldt, D. (eds) Application and Theory of Petri Nets and Concurrency. PETRI NETS 2016. Lecture Notes in Computer Science(), vol 9698. Springer, Cham. https://doi.org/10.1007/978-3-319-39086-4_8

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  • DOI: https://doi.org/10.1007/978-3-319-39086-4_8

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-39085-7

  • Online ISBN: 978-3-319-39086-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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