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We developed a novel algorithm that algebraically manipulates the weighted LD statistic into a form that can be computed using a fast Fourier transform (FFT), dramatically speeding up the computation (File S2).
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Subsequent runs of the workflow use as much as possible of the computation files from previous runs, which serves as a basic form of caching.
Addition of the metadata for reproduction of the results Since all metadata required for the reproduction of computations (files, scripts, command line strings, etc).
Linear and non-linear dynamic correlations between all pair wise combinations of time-series were measured with the SL [22], [44] (for mathematical details on the SL computation, see File S1).
All five models were compressed prior to EFM computation (Additional file 2).
In fact, the count increased to more than 2,900 genes when the experiment in which a gene deviated most from its median phase was excluded from variance computation (Additional file 2; Fig. S2b).
The regulatory network of the lac operon used in the paper was completed with the reconstruction of the regulation of the maltose operon [ 41], and then was converted in the SBML-qual format for computation (Additional file 2).
As a result of iterative computations, the file may contain multiple versions of the same record; therefore, old versions are removed to reduce local disk space usage.
All computations and file storage were performed using double precision (15 digits).
Then, we identified the gene networks for each class of tumors by using nonlinear correlation analyses and transfer entropy computation (see Additional file 1: Table S1A and Additional file 2: Table S1B).
Tests were performed with different percentages of synteny anchors kept in the jackknife computation (see Additional file 3).
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com