Code for Ferrin elife 2017 paper
This repository includes raw data and code for running simulations, analyzing data, and reproducing figures in the paper.
Raw data from experiments and simulations are in rawdata folder.
Final figures generated by running the analysis are in figures folder.
Table of Contents
# download data and scripts git clone https://github.com/rasilab/ferrin_elife_2017.git # download genome and annotations cd ferrin_elife_2017 cd annotations/simulations wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/005/845/GCA_000005845.2_ASM584v2/GCA_000005845.2_ASM584v2_genomic.fna.gz gunzip GCA_000005845.2_ASM584v2_genomic.fna.gz -c > NC_000913.fna wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/005/845/GCA_000005845.2_ASM584v2/GCA_000005845.2_ASM584v2_genomic.gff.gz gunzip GCA_000005845.2_ASM584v2_genomic.gff.gz -c > NC_000913.gff cd ../../ # install a python virtual environment for installing packages (optional) # activate environment and upgrade the package installer virtualenv py2 source py2/bin/activate pip install pip --upgrade # install python packages pip install -r python_requirements.txt # run analysis cd scripts sh masterscript.sh
To run simulations from scratch, uncomment the two lines highlighted in scripts/masterscript.sh.
> sh masterscript.sh Tue Mar 7 21:13:41 PST 2017 Compiled whole cell simulation successfully. Tue Mar 7 21:13:42 PST 2017 Compiled reporter simulation successfully. Tue Mar 7 21:13:42 PST 2017 Made directories for storing generated data and figures. Tue Mar 7 21:13:49 PST 2017 Plotted Fig 1 fluorescence data. Tue Mar 7 21:13:56 PST 2017 Plotted Fig 1 polysome qPCR data. Tue Mar 7 21:14:02 PST 2017 Plotted Fig 1 mRNA qPCR data. Tue Mar 7 21:14:24 PST 2017 Analyzed all plate reader data. Tue Mar 7 21:14:28 PST 2017 Fitted simulation results to experimental data. Tue Mar 7 21:14:37 PST 2017 Created input files for simulations based on experimental fits. Tue Mar 7 21:14:52 PST 2017 Plotting simulation results and comparison to experiments.
This will generate all the plots in the figures folder.
annotations/simulations/ecoli.mrna.concn.and.te.li.2014.csv was downloaded from Li et al. Cell 2014, Table S4, opened in Libreoffice Calc and saved as csv file.
annotations/simulations/ecoli.trna.abundance.dong1996.txt was downloaded from Dong et al. J. Mol. Biol. 1996, Table 2, and pasted into a text file. Gly1 and Ile2 entries were manually deleted from the table since these were not measured in this study. Sec tRNA was deleted since we are not considering this non-canonical translation. A typo for Val1 anticodon was corrected (TAG → TAC).
annotations/simulations/NC_000913.gff were downloaded from the corresponding ncbi genome assembly: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/005/845/GCA_000005845.2_ASM584v2.
> uname -a Linux rhino3 3.13.0-68-generic #111-Ubuntu SMP Fri Nov 6 18:17:06 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > lsb_release -a No LSB modules are available. Distributor ID:IDUbuntu Description:DescriptionUbuntu 14.04.3 LTS Release:Release14.04 Codename:Codenametrusty > g++ --version g++ (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # boost C++ library used in simulation code > dpkg -s libboost-dev | grep 'Version' Version: 184.108.40.206ubuntu1 > python --version Python 2.7.6 # for running simulations on cluster > sbatch --version slurm 15.08.7