MResProject

This is a repository containing all the code and data used for the project 'Predicting the thermal niche of a ubiquitous bacterium using whole genome sequence'

This repository contains the code, and data required to recreate the simulations perfomed to quantify the growth rate of E. coli across a range of temperatures. It contains three directories: 'code', 'data', 'results', 'models'

Languages

• R(v4.1.2)
• Python(v3.10.0)

Dependencies

• COBRApy(v0.26.3)
• Gurobi LP solver(v9.5.1rc2)
• Scikit-learn
• tidyverse
• cowplot

Code

This directory contains all the code files used:

• GEMS.py -> For laoding the infput files in correct data strucutres
• LoopySimulation.ipynb -> Prediction of growth rates over all empirical using final parameter values
• onlyKcat.ipynb -> Addition of only enzyme activity information to ecGEM
• onlyNGAM -> Addition of only cell maintenence information to ecGEM
• onlyTm -> Additon of intracellular enzyme concentration information to ecGEM
• plotting.R -> Creating plots required with simuaiton results
• plotting2.R -> Code for plotting the effet of each temperature variant factor
• plottingMedia.R -> Creating plots for changing media simulations
• plottingInset.R -> Creating inset plots
• relaxingBounds.ipynb -> Temperature dependent simulation by relaxing bounds on reactions denoting enzyme abundance
• simulateGEM.ipynb -> Temperature dependent simulation with initial paramters
• SimulationLB.ipynb -> Temperature dependent simulation with final parameters and LB medium
• SimulationMM.ipynb -> Temperature dependent simulation with final parameters and Minimal medium
• TmToptCor.R -> Code for checking the correlation in Tm and Topt in initial parameters
• ToptFixed.ipynb -> Temperature dependent simulation by increasing the values for Topt
• ToptTmTopt.ipynb -> Multiple temperature dependent simulations following the algorithm presented
• TPCPlot.R -> Code to plot TPC in Fig. 1b
• wigCp.ipynb -> Code to check the effect of heat capacity change on model predictions
• wigTm.ipynb -> Code to check the effect of enzyme melting temperaure on model predictions
• wigCp.ipynb -> Code to check the effect of temperautre of maximum enzyme activity on model predictions
• etcpy/etc.py -> This file contains the temperature dependence modification code
• etcpy/tempDepCode.py -> This file contains the code for parameter sampling

Data

This directory contains the data required for simulations:

• BestParamsTopt.csv -> Best parameter estimates achieved by increasing Topt
• BestParamsTopt129.csv -> Best parameter estimate
• ExpGrwoth.csv -> Empirical growth data used for model prediction and validation
• model_enzyme_params_new_tageed.csv -> Initial parameter estimates
• model_enzyme_params_new.csv -> Initial parameter estimates
• model_enzyme_params.csv -> Initial parameter estimates
• media.csv -> File containing media information

Models

This directory contains the ecGEM used for incorporating temperature dependence of enzyme function

Results

This directory contains results of the simulations