Rif Ramp Code
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