From Kerr Wiki

Public: RifRampCode

The code used for this project and relevant input text files are included below:

R code (version 2.15.0 used)

Input text files for R code:

Rifampicin Concentrations across Treatments (Figure 1a)
Population Survivorship across Treatments (Figure 1b)
Names of Surviving Populations (Figure 1c)
Spec Readings for Surviving Populations (Figure 1c)
Mutation Data for Sequenced Isolates (Figures 2a, 2b)
Spec Readings for Engineered Strains with Single Mutations (Figure 2c)
Spec Readings for Engineered Strains from Population G13 (Figure 4a)
Viability Assay Results for all Engineered Strains (Figures 4b, 4d; Supp Figures 3b, 3d, 4c, 4d)
Competition Results for G13 Engineered Genotypes (Figure 4b)
Spec Readings for Engineered Strains from Population G18 (Figure 4c)
Competition Results for G18 Engineered Genotypes (Figure 4d)
Competition Results to Test Neutrality of Ara Marker (Supplementary Figure 1)
Spec Readings for Re-engineered Ancestors (Supplementary Figure 2)
Spec Readings for Engineered Strains from Population M358 (Supplementary Figure 3a)
Competition Results for M358 Engineered Genotypes (Supplementary Figure 3b)
Spec Readings for Engineered Strains from Population M367 (Supplementary Figure 3c)
Competition Results for M367 Engineered Genotypes (Supplementary Figure 3d)
Spec Readings for Engineered Strains from Sudden Population (S497 & S1236) (Supplementary Figures 4a, 4b)
Competition Results for Sudden Engineered Genotypes (Supplementary Figures 4c, 4d)

Mathematica code (version 8.0 used)

Input text files for Mathematica code:

Accessibility Wall for G13 Isolate (Figure 4b):
Accessibility Wall for G18 Isolate (Figure 4d):
Accessibility Wall for M358 Isolate (Supplementary Figure 3b):
Accessibility Wall for M367 Isolate (Supplementary Figure 3d):
Accessibility Wall for S497 Isolate (Supplementary Figure 4c):
Accessibility Wall for S1236 Isolate (Supplementary Figure 4c):

Back to RifRamp Project Homepage

Retrieved from http://kerrlab.org/Public/RifRampCode

Page last modified on September 09, 2012, at 03:53 AM