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Python script to simulate quinones interacting with enzymes in the E. coli electron transport chain
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ETCsimulation.py
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README.md
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example_commands.sh

README.md

This script accompanies "Viscous control of cellular respiration by membrane lipid composition" by Itay Budin, Tristan de Rond, Yan Chen, Leanne Jade G. Chan, Christopher J. Petzold, and Jay D. Keasling (https://dx.doi.org/10.1126/science.aat7925)

If you use this script in your research, please cite the above paper.

For a description of our model, please refer to the Supplementary Information of the above paper.

I have run the Python script succesfully on

  • Python 3.6.3 with NumPy 1.13.3, MatPlotLib 2.1.0, and Argparse 1.1 on Windows 10, as well as on
  • Python 2.7.9 with NumPy 1.8.2, MatPlotlib 1.4.2, and Argparse 1.1 on Debian Linux 3.16,

so it will probably work on many other versions of these packages, Python and operating systems.

I have tried to make the command line flags self-explanatory. Run python ETCsimulation.py --help to see all options and explanations

The commands in the example shell script were written for Bash 4.3.30 using Parallel 20130922 on Debian Linux

Citations for Parallel:

  • O. Tange (2018): GNU Parallel 2018, March 2018, https://doi.org/10.5281/zenodo.1146014.

  • O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. (by user @ole-tange)

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