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GPU computing for systems biology

Lorenzo Dematte, Davide Prandi
The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Piazza Manci 17 38123 Povo, Trento, Italy. Tel: +39-0461-882834; Fax: +39-0461-882814; E-mail: prandi@cosbi.eu
Brief Bioinform, Vol. 11, No. 3. (1 May 2010), pp. 323-333

@article{dematte2010gpu,

   title={GPU computing for systems biology},

   author={Dematt{‘e}, L. and Prandi, D.},

   journal={Briefings in bioinformatics},

   volume={11},

   number={3},

   pages={323},

   year={2010},

   publisher={Oxford Univ Press}

}

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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 [~]$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.
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