Parallel Generation and Visualization of Bacterial Genome Structures

Information

• Publication Type: Journal Paper with Conference Talk
• Workgroup(s)/Project(s):
  • Visualization Group
• Date: November 2019
• Journal: Computer Graphics Forum
• Volume: 38
• Number: 7
• Lecturer: Tobias Klein
• Event: Pacific Graphics 2109
• DOI: 10.1111/cgf.13816
• Call for Papers: Call for Paper
• Conference date: 2019
• Pages: 57 – 68

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.

Additional Files and Images

Weblinks

• Entry in the publication database of TU-Wien
• DOI: 10.1111/cgf.13816

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 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.",
  month =      nov,
  journal =    "Computer Graphics Forum",
  volume =     "38",
  number =     "7",
  doi =        "10.1111/cgf.13816",
  pages =      "57--68",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PGG/",
}