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The last metric is CPU time that measures running time of each algorithm (Karimi et al. 2010).
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These expected values were then subtracted from the measured running time results and the outcome was evaluated for each device and the CPU.
Mice were acclimated to a motorized treadmill (Columbus Instruments) for 3 consecutive days and physical performance was characterized by measuring running time and distance to failure using a previously described protocol modified for ob/ob mice (initial speed of 8 m/min, increase of 2 m/min every 3 min; 0% grade) [7], [17].
We measure running time in the same computational environment to assess realistic applicability of compared methods.
We measured running time using the time reported by the Linux command, and peak memory usage using the Linux command.
To measure running time and maximum sizes of memory during the program's runs we used POSIX's "getrusage" function twice: before and after processing to measure data size excluding program code itself.
We measured running times with a memoization that memorizes the neighborhoods of 10,000 different structures.
We have measured running times per output and memory usage as function of input size and output size (see Table 1 and Additional file 2, Figure S2).
Open image in new window Fig. 9 Measured run time, standardised run time, and linear fit of the standardised run time of GIMME, applied to 1,000 line locations with various numbers of segments.
Since he is only measuring run time, he doesn't need to worry about the sensitivity of these alignments, just speed.
To measure run time, three non-synthetic metagenomic samples representing a viral metagenome (SRX022172), a human microbiome metagenome (ERR011121) and a single species raw read 'metagenome' (DRR000184) were taken from the SRA.
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