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Bioinformatics. 2014 Nov 1;30(21):3101-8. doi: 10.1093/bioinformatics/btu498. Epub 2014 Jul 26.

Biocellion: accelerating computer simulation of multicellular biological system models.

Author information

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.

Abstract

MOTIVATION:

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.

RESULTS:

We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies.

AVAILABILITY AND IMPLEMENTATION:

Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information.

PMID:
25064572
PMCID:
PMC4609016
DOI:
10.1093/bioinformatics/btu498
[Indexed for MEDLINE]
Free PMC Article

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