Following the dimensionality analyses, inversion of AMT and wide-band MT data was performed using code developed by Egbert and Kelbert (2012; ModEM).
For engineering design of liquid lithium (Li) target of the International Fusion Materials Irradiation Facility (IFMIF), two-dimensional hydraulic analysis was performed using code FLUENT.
Numerical simulations for the single-compartment model were performed using code written in MatLab (MathWorks), whereas simulations for the multi-compartmental model based on the morphological reconstruction were performed using the simulation package NEURON [37, 38].
All simulations were performed using code written for Mathematica 7.0 running on a Macintosh G4 with 4MB of RAM.
Using the cDNA as a template, a real-time PCR measurement was performed using coding region primers (Table S3) for the 26 hyper-acetylated genes (Table 1) and 22 hypo-acetylated genes (Table 2) from the C1 and D1 mice.
GCA was performed using code written in MATLAB.
Blast searches of the NCBI [ 34] and Ensembl [ 35] ratC3.1 rat genome databases were performed using coding sequences from known rat PSGs (PSG36- PSG40) and mouse PSGs.
K-mer counting, which was used, in part, in datasets 1 and 3, was performed using code modified from a script that was kindly provided by Dr. William Stafford Noble of the University of Washington.
K-mer counting which was used in part for datasets 1, 2 and 8 were performed using code modified from a script kindly provided by Dr. William Stafford Noble of Washington University.
Further, for genes that were absent in RH4 [ 13, 73], BlastN searches were performed using coding sequences of bacterial species closely related to M. catarrhalis, namely Psychrobacter sp., Acinetobacter sp., and Neisseria sp. Pearson correlation analysis was utilized for comparisons of various data sets as denoted in the text.
