Parallel Generation and Visualization of Bacterial Genome Structures

Tobias Klein, Peter Mindek, Ludovic Autin, David Goodsell, Arthur Olson, Meister Eduard Gröller, Ivan Viola
Parallel Generation and Visualization of Bacterial Genome Structures
Computer Graphics Forum, 2019.

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Abstract

Visualization of biological mesoscale models provides a glimpse at the inner workings of living cells. One of the most complex components of these models is DNA, which is of fundamental importance for all forms of life. Modeling the 3D structure of genomes has previously only been attempted by sequential approaches. We present the first parallel approach for the instant construction of DNA structures. Traditionally, such structures are generated with algorithms like random walk, which have inherent sequential constraints. These algorithms result in the desired structure, are easy to control, and simple to formulate. Their execution, however, is very time-consuming, as they are not designed to exploit parallelism. We propose an approach to parallelize the process, facilitating an implementation on the GPU.

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BibTeX

@article{klein_2019_PGG,
  title =      "Parallel Generation and Visualization of Bacterial Genome
               Structures",
  author =     "Tobias Klein and Peter Mindek and Ludovic Autin and David
               Goodsell and Arthur Olson and Meister Eduard Gr\"{o}ller and
               Ivan Viola",
  year =       "2019",
  abstract =   "Visualization of biological mesoscale models provides a
               glimpse at the inner workings of living cells. One of the
               most complex components of these models is DNA, which is of
               fundamental importance for all forms of life. Modeling the
               3D structure of genomes has previously only been attempted
               by sequential approaches. We present the first parallel
               approach for the instant construction of DNA structures.
               Traditionally, such structures are generated with algorithms
               like random walk, which have inherent sequential
               constraints. These algorithms result in the desired
               structure, are easy to control, and simple to formulate.
               Their execution, however, is very time-consuming, as they
               are not designed to exploit parallelism. We propose an
               approach to parallelize the process, facilitating an
               implementation on the GPU.",
  journal =    "Computer Graphics Forum",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PGG/",
}