Reference
An integrated approach reveals regulatory controls on bacterial translation elongation
Subramaniam AR, Zid B, O’Shea EK. Cell, 159, 1200, 2014
The four IPython Notebooks in this folder are:
- sequencing_data_analysis.ipynb — Analysis of high-throughput sequencing data from ribosome profiling and RNA-Seq
- simulation.ipynb — E. coli whole-cell translation simulation
- simulation_data_analysis.ipynb — Analysis of simulation results. Simulation results can be downloaded from Data Dryad
- yeast_simulation_and_analysis.ipynb — Modifications to simulation in Shah et al and analysis of simulation results. Simulation results can be downloaded from Data Dryad
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The hyperlinks in the table of contents of each IPython notebook do not seem to be working on github. But they are functional once downloaded locally.
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The source code is licensed under GNU GPLv3 license.