Parallel Generation and Visualization of Bacterial Genome Structures
KAUST DepartmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer Science Program
Visual Computing Center (VCC)
KAUST Grant NumberBAS/1/1680-01-01
Embargo End Date2020-11-14
Permanent link to this recordhttp://hdl.handle.net/10754/660374
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AbstractVisualization 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.
CitationKlein, T., Mindek, P., Autin, L., Goodsell, D. S., Olson, A. J., Gröller, E. M., & Viola, I. (2019). Parallel Generation and Visualization of Bacterial Genome Structures. Computer Graphics Forum, 38(7), 57–68. doi:10.1111/cgf.13816
SponsorsThis work was funded under the ILLVISATION grant by WWTF (VRG11-010). It is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. OSR-2019-CPF-4108 and BAS/1/1680-01-01. The Scripps Research Institute researchers acknowledge support from the National Institutes of Health under the grant R01-GM120604. This paper was partly written in collaboration with the VRVis Competence Center. VRVis is funded by BMVIT, BMWFW, Styria, SFG and Vienna Business Agency in the scope of COMET - Competence Centers for Excellent Technologies (854174), which is managed by FFG. The authors would like to thank Nanographics GmbH (nanographics.at) for providing the Marion Software Framework.
JournalComputer Graphics Forum