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. 2015 Feb 13;6:42. doi: 10.3389/fphys.2015.00042

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Copyright © 2015 Sumiyoshi, Hirata, Hiroi and Funahashi.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Performance analysis of data compression w.r.t. the number of reactions. This figure shows a plot of the ratios of the execution times of 10,240 realization of a single-gene production-reduction model on a CPU (Core i7 2.80 GHz with 12 GB of memory) and on a GPU (NVIDIA Tesla C1060) as the vertical axis, and the number of reactions (model size) as the horizontal axis. Compression of the stoichiometry matrix resulted in a further improvement by a factor of 1.4 for a model with eight reactions; this was about 130 times faster than on a CPU. On the other hand, the execution time on a GPU was notably longer for larger models (>64 reactions).