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

  • Wojciech Ptak
  • Andrzej M. Kierzek
  • Jacek SrokaEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, 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.

Notes

Acknowledgements

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

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© Springer International Publishing Switzerland 2016

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 2.5 International License (http://creativecommons.org/licenses/by-nc/2.5/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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Authors and Affiliations

  • Wojciech Ptak
    • 1
  • Andrzej M. Kierzek
    • 2
  • Jacek Sroka
    • 1
    Email author
  1. 1.Institute of InformaticsUniversity of WarsawWarsawPoland
  2. 2.Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK

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