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The subroutine task was to store all the individuals created thus for and to generate new ones by randomly choosing from within the parameter space, thus avoiding useless copies.
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For CSlogs, we generated 7 datasets of different sizes (from 40 k trees and up to 100 k) by randomly choosing trees from the original CSlogs.
It the physical network was reconstructed by randomly choosing links from the WNS, this would give a point along a diagonal line from the left bottom to the top right corners.
The representative sequences were selected by randomly choosing one from those which were similar to each other (approximately genetic distances <2.1%), isolated from the similar host (avian or a species of mammals) in the same year and in the same country.
Since human H1N1, H2N2 and H3N2 subtypes viruses did not shown obvious geographical bias through primary analysis and they were of large numbers, their representatives were selected by randomly choosing one from those which were similar to each other and isolated in the same year no matter where they were isolated.
The control gene set was generated by randomly choosing genes from all of the annotated genes (gene length-controlled).
The non-nucleolar group was generated by randomly choosing proteins from IPI release 3.40 [ 27] that are not annotated as being nucleolar in UniProt [ 30] or HPRD [ 31].
An AUC of 0.5 reflects a reconstruction of physical network by randomly choosing links from the WNS, while AUC = 1 implies a perfect reconstruction.
Specifically, we first used the Latin hypercube sampling (4, 30 ) method to create 120 random combinations of parameter values by randomly choosing (without replacement) from 120 equiprobable parameter value intervals from ranges provided in Table 1.
The individual realizations are set up by randomly choosing reservoir properties from statistical distributions.
For comparison, 2,000 independent permutations were performed by randomly choosing 12 miRNAs from the cultivars and wild rice miRNA datasets, respectively.
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