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Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology
VISUS - Visualization Research Center, University of Stuttgart, Germany.ORCID iD: 0000-0003-1511-5006
VISUS - Visualization Research Center, University of Stuttgart, Germany.
VISUS - Visualization Research Center, University of Stuttgart, Germany.
Automatic Control Laboratory, BISON Group, ETH Zürich,Switzerland.
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2011 (English)In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB'112011, ACM Press, 2011, p. 73-82Conference paper, Published paper (Refereed)
Abstract [en]

The complexity of biological systems is enormous, even when considering a single cell where a multitude of highly parallel and intertwined processes take place on the molecular level. This paper focuses on the parallel simulation of signal transduction processes within a cell carried out solely on the graphics processing unit (GPU). Each signaling molecule is represented by an agent performing a discretetime continuous-space random walk to model its diffusion through the cell. Since the interactions and reactions between the agents can be competitive and are interdependent, we propose spatial partitioning for the reaction detection to overcome the data dependencies in the parallel execution of reactions. In addition, we present a simple way to simulate the Michaelis-Menten kinetics in our particle-based method using a per-particle delay. We apply this agent-based simulation to model signal transduction in the MAPK (Mitogen-Activated Protein Kinase) cascade both with and without cytoskeletal filaments. Finally, we compare the speed-up of our GPU simulation with a parallelized CPU version resulting in a twelvefold speedup.

Place, publisher, year, edition, pages
ACM Press, 2011. p. 73-82
Keyword [en]
agent-based simulation, GPU computing, GPU parallelization, MAPK, systems biology
National Category
Media and Communication Technology
Identifiers
URN: urn:nbn:se:liu:diva-143703DOI: 10.1145/2037509.2037521ISBN: 978-1-4503-0817-5 (electronic)OAI: oai:DiVA.org:liu-143703DiVA: diva2:1166255
Conference
International Conference on Computational Methods in Systems Biology (CMSB 2011), Paris; France; 21 September 2011 through 23 September 2011
Available from: 2017-12-14 Created: 2017-12-14 Last updated: 2018-01-13

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Publisher's full texthttp://doi.acm.org/10.1145/2037509.2037521

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CiteExportLink to record
Permanent link

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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf