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The MATLAB ® programming environment is used for programming the constrained GA optimization script.
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A generated McStas instrument file performs the Monte Carlo ray-tracing, which is controlled by iFit optimization scripts.
The scripts are designed to be as platform independent as possible, given the need to facilitate mirroring on different systems around the world, although the growing use of Linux as the operating system of choice within astronomy has led to increasing optimization of the scripts for installation on that platform.
Instead of directly generating optimized code, we extend an optimizing compiler to output its optimization decisions in POET, a scripting language designed for extensive parameterization of source-to-source program transformations.
The experimental data files, analysis scripts, and optimization programs are available at the Open Science Framework (https://osf.io/vuaxj/?view_only=489c5b2f9b8b45cbb866416ef1e50ef4).
The add-on uses Google Apps Script to send optimization problems to Google servers.
Advanced features, such as model scripting and an optimization tool, are also described.
This optimization technique enabled ordinary Matlab scripts to run at a similar speed to hand-coded PBLAS implementations.
These results are straightforward, but necessary for the validity and optimization of the algorithms and scripts used in this paper.
The model was automatically generated depending on the optimization variables using a developed pre-processor script.
Methylated peaks were annotated with HOMER (Hypergeometric Optimization of Motif EnRichment), version 4.3, using the Perl script "annotatePeaks.pl" with default parameters to identify their genomic location.
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