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Biocellion: accelerating computer simulation of multicellular biological system models.

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      Abstract

      Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming.

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      Affiliations
      [1 ] Computational Biology and Bioinformatics Group, High-performance Computing Group, Pacific Northwest National Laboratory, Richland, WA 99354, USA, Department of Computer Science, Utah State University, Logan, UT 84322, USA and Institute for Systems Biology, Seattle, WA 98109, USA.
      Journal
      Bioinformatics
      Bioinformatics (Oxford, England)
      1367-4811
      1367-4803
      Nov 1 2014
      : 30
      : 21
      btu498 10.1093/bioinformatics/btu498 25064572 4609016
      © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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