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    Parallel Generation and Visualization of Bacterial Genome Structures

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    Name:
    Pacific_Graphics_2019___Parallel_Fibers.pdf
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    8.766Mb
    Format:
    PDF
    Description:
    Accepted manuscript
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    Type
    Article
    Authors
    Klein, T. cc
    Mindek, P. cc
    Autin, L. cc
    Goodsell, D. S. cc
    Olson, A. J. cc
    Gröller, E. M. cc
    Viola, Ivan cc
    KAUST Department
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Computer Science Program
    Visual Computing Center (VCC)
    KAUST Grant Number
    BAS/1/1680-01-01
    Date
    2019-11-14
    Embargo End Date
    2020-11-14
    Permanent link to this record
    http://hdl.handle.net/10754/660374
    
    Metadata
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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.
    Citation
    Klein, 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
    Sponsors
    This 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.
    Publisher
    Wiley
    Journal
    Computer Graphics Forum
    DOI
    10.1111/cgf.13816
    Additional Links
    https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13816
    ae974a485f413a2113503eed53cd6c53
    10.1111/cgf.13816
    Scopus Count
    Collections
    Articles; Computer Science Program; Visual Computing Center (VCC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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