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review · Briefings in Bioinformatics · 2010

GPU computing for systems biology

Lorenzo Dematté, Davide Prandi

Cited by 134Open access

Abstract

The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological systems. However, the computational power required by these simulations often exceeds that available on common desktop computers and thus expensive high performance computing solutions are required. An emerging alternative is represented by general-purpose scientific computing on graphics processing units (GPGPU), which offers the power of a small computer cluster at a cost of approximately $400. Computing with a GPU requires the development of specific algorithms, since the programming paradigm substantially differs from traditional CPU-based computing. In this paper, we review some recent efforts in exploiting the processing power of GPUs for the simulation of biological systems.

Cite this paper

APA 7

Dematté, L., & Prandi, D. (2010). GPU computing for systems biology. Briefings in Bioinformatics, 11(3), 323–333. https://doi.org/10.1093/bib/bbq006

MLA 9

Dematté, Lorenzo, and Davide Prandi. “GPU computing for systems biology.” Briefings in Bioinformatics, vol. 11, no. 3, 2010, pp. 323–33, https://doi.org/10.1093/bib/bbq006.

Chicago

Dematté, Lorenzo, and Davide Prandi. 2010. “GPU computing for systems biology.” Briefings in Bioinformatics 11 (3): 323–33. https://doi.org/10.1093/bib/bbq006.

Harvard

Dematté, L. and Prandi, D. (2010) ‘GPU computing for systems biology’, Briefings in Bioinformatics, 11(3), pp. 323–333. Available at: https://doi.org/10.1093/bib/bbq006.

BibTeX
@article{dematte2010computing,
  title = {{GPU computing for systems biology}},
  author = {Dematté, Lorenzo and Prandi, Davide},
  journal = {Briefings in Bioinformatics},
  volume = {11},
  number = {3},
  pages = {323--333},
  year = {2010},
  doi = {10.1093/bib/bbq006}
}

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