Parallel Generation and Visualization of Bacterial Genome Structures

T. Klein, P. Mindek, L. Autin, D. S. Goodsell, A. J. Olson, E. M. Gröller, Ivan Viola

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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.
Original languageEnglish (US)
Pages (from-to)57-68
Number of pages12
JournalComputer Graphics Forum
Issue number7
StatePublished - Nov 14 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): BAS/1/1680-01-01
Acknowledgements: 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 ( for providing the Marion Software Framework.


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