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The SEs data downloaded from dbSUPER65 was also generated using the same pipeline.
A background lightcurve is also generated using the region file back.reg, and errors using the Gehrels approximation are calculated.
In addition, the three subtype specific CoMFA models were also generated using the identical training set molecules (N = 28).
Random networks were also generated using the 'igraph' packages in R. For each network in this study, 1000 random networks were generated, and all of the network indexes were calculated individually.
In addition to the CS-ET reconstructions, a reference reconstruction was also generated using the full dataset and a conventional SIRT algorithm, implemented in Inspect3D.
A model of a solid beam was also generated using the cracked moment of inertia (Matthew 2013) and the inorganic repaired and solid beams followed closely to the model with slight deviations due to imperfections in the cast beams.
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Scatter plots were also generated using this software to inspect the reproducibility of the replicates as well as the degree of variations of the samples under comparison.
Scenario 3 was also generated using this same methodology.
Normalized heat maps were also generated using MG-RAST and the different gene pool arrays were hierarchically clustered using Kendall's tau similarity metric.
The fingerprints themselves were also generated using open-source software, so the results in this study should be fully reproducible by any researcher.
The hESC line Shef 6 was obtained from the UK Stem Cell Bank, and control iPSCs, also generated using retroviral transduction, were obtained from the laboratory of Dr Tilo Kunath.
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