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As no significant amounts of excreted products (besides CO2) are produced under phototrophic as well as aerobic conditions [ 6] the excretion of products except CO2 is disabled (rate set to zero) by default but will be allowed when simulating fermentative metabolism.
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Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity [ 14] with min_kmer_cov set to two by default and all other parameters set default.
The number of intervals for the read count data is set to two by default and can be modified by the user.
Transcriptome de novo assembly was carried out with the short read assembling program Trinity (r20140413p1) [ 69, 70] with min_kmer_cov set to two by default and all other parameters also set as default.
The parameter ε was set to zero (default) to obtain a sparse spanning network.
This threshold is, by default, set to zero (so that only identical sequences are excluded) The set of reference points R can now be used directly to embed the input sequences (see step 3).
For psRNATarget the maximum expectation was set to two and all other options left as default.
Default settings were used, except in HHpred, which was set to eight iterations, and where query-template alignments were realigned by a Maximum Accuracy algorithm.
The default path length is set to two, or in other words one intermediate node.
Default values for both the minimum number of genes and conditions have been set to two.
For each initial matching M1 of the startsimplex S1 exp to an arbitrary S k theo,the number of trials (singleTrials) to validate M1 is limited by the threshold maxSingleTrials (set to one million by default).
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