endylab/trnacad

tRNAShuffle

Contains code corresponding to the engineering tRNA abundances for synthetic cellular systems project.

Modeling code

All modeling code is available with comment in Jupyter notebooks. Colloidal dynamics and Colloidal dynamics-Computer Aided Design (CD-CAD) algorithms used throughout can be found in analysis_utils.py and are accessed within Jupyter notebooks. Files correspond to particular modeling and simulations for as follows:

ColloidalDynamics_tRNANaturalAnalysis - Figure 1 & S1: Colloidal dynamics modeling assessing wild type E. coli

ColloidalDynamics_tRNAVaryingIO - Figure 2 & S2: Colloidal dynamics modeling assessing rationally engineered tRNA distributions

CDCAD_WTecoli - Figure 3: CD-CAD modeling for the E. coli transcriptome

CDCAD_RED20Ecoli - Figure 4, S3, S14: CD-CAD modeling for the genome reduced E. coli transcriptome

CDCAD_RED20_SingleGeneOptimization - Figure 5, S14: Optimization and analysis of tRNA distributions for RED20-encoded GFP

CDCAD_WT_PerturbationAnalysis - Figure S9, S10: CD-CAD perturubation analysis for WT E. coli

CDCAD_ompF_PerturbationAnalysis - Figure S12: CD-CAD perturbation analysis for the highest expressing gene in the E. coli transcriptome, ompF

CDCAD_RED20GFP_PerturbationAnalysis - Figure S13: CD-CAD perturubation analysis for RED20-encoded GFP

CDCAD_genestratification - Figure S11: Gene stratficiation analysis

analysis_utils - All algorithms supporting analysis (including evolutionary algorithms & elongation computation)

Experimental analysis code

Code for experimental analysis (Figure 5 and related supplemental figures) can be found in experimental_data_analysis.ipynb