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The network of miRNAs and target genes was constructed in the software Exploratory Gene Association Networks (EGAN) [ 22].
PCA plots were constructed in the software Qlucore Omics Explorer v.2.1 using the subset of 28 transcripts shared between evaluated platforms as variable input.
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The proposed method further employs a state-of-the-art transmission line (TL) and substation equipment models for lightning-surge transient analysis, constructed in the EMTP software package.
We used our phylogenetic tree in conjunction with a branch model constructed in the PAML software package to determine the Ka, Ks, and Ka/Ks values for 4,094 separate alignments of P. erythrurus and P. putjatia.
The multiple alignment was created with MAFFT [ 33] and edited with JalView version 2.5 [ 34] after which the phylogenetic tree was constructed in the same software with the Neighbor Joining method using a BLOSUM62-based distance measure.
A 3D model of an existing two-wheel drive tractor (SH500) is constructed in the 3D design software Pro/Engineer and exported out into the virtual prototyping software ADAMS in which the slippage virtual test system is established and the slippage virtual test is carried out.
Real data on shuttle services is used as an input for the simulation model, constructed in the Arena simulation software.
A dynamic model was constructed in the high-level simulation software STELLA, using water, soil, weather, and plant data from this mesocosm study.
The MRJ-L 3′UTR shRNA (shJ8_5′-GCGCAGATGGCTAACTGAGTA) was designed using InvivoGen siRNA Wizard v3.1 software, and was constructed in the pLKO.1-puro vector (obtained from the National RNAi Core Facility, Academia Sinica, Taiwan).
The catch is that neural nets, which are modeled loosely on the structure of the human brain, are typically constructed in software rather than hardware, and the software runs on conventional computer chips.
The mid-parent expression value was constructed in SAS software's PROC MIXED by down-weighting each parent in the contrast statement by 0.5; such an approach uses the pooled variance of both parental measures.
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