RM Regulatory Dynamics

This repository contains the Mathematica and Python codes used to reproduce the results presented in the paper:

Nonlinear Regulatory Dynamics of Bacterial Restriction-Modification Systems Modulates Horizontal Gene Transfer Susceptibility

Authors: Magdalena Djordjevic, Lidija Zivkovic, Hong-Yu OU, Marko Djordjevic
Under review in: Nucleic Acids Research, 2024

Repository Overview

The repository is organized to ensure full reproducibility of the results and figures presented in the paper. It includes Mathematica notebooks and Python simulation scripts structured as follows:

• mathematica_notebooks/: Contains Mathematica notebooks for symbolic calculations and analytical derivations.
• python_simulations/: Contains Python scripts for numerical simulations and data analysis.

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Development Environment

To ensure reproducibility, the code was developed and tested in the following environment:

• Mathematica version: 11.2
• Python version: 3.9.19
• Conda version: 24.5.0

The code was tested on Ubuntu 24.04 LTS. Compatibility with other operating systems is not guaranteed but should generally work.

Python dependencies are managed through a conda environment.

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How to Use

Mathematica Notebooks

• Located in the mathematica_notebooks/ folder.
• Each notebook corresponds to a specific figure in the paper. For example, Figure3.nb reproduces Figure 3.
• Notebooks include code, parameters, and results together for clarity.

Python Simulations

• Python codes, data, and results are in the python_simulations/ folder.
• Scripts are located in the simulation_scripts/ subfolder. Ensure scripts are executable:

  chmod u+x <script_name>

• Scripts should be run from the parent folder (python_simulations/):

  ./simulation_scripts/<script_name>

• Inputs and outputs are handled via the Python argparse module. To view options and usage, use the -h flag:

  ./simulation_scripts/simulation_CV_MR_regulated.py -h

• Default parameter values are set to reproduce paper results. Outputs are saved to the simulation_results/ folder.

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Parallelization

Python simulation scripts are parallelized:

• Default: Uses all available CPUs (-1).
• To specify the number of CPUs, use the -w flag:

  ./simulation_scripts/simulation_CV_MR_regulated.py -w <number_of_workers>

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Reproducing Figures

Figures in the Main Text

• Figure 3: mathematica_notebooks/Figure3.nb
• Figure 4: mathematica_notebooks/Figure4.nb
• Figure 5: mathematica_notebooks/Figure5.nb
• Figure 6: mathematica_notebooks/Figure6_and_S2.nb
• Figure 7: mathematica_notebooks/Figure7.nb
• Figure 8: mathematica_notebooks/Figure8.nb
• Figure 9: Run the following scripts in order:
  1. figure9_simulation_CV_MR_constitutive.py
  2. figure9_simulation_CV_MR_regulated.py
  3. figure9_simulation_MR_stochastic_decay.py
  4. figure9_plotting.py
  • Figure is saved in the simulation_results/ folder.
• Figure 10: mathematica_notebooks/figure10.nb

Supplementary Figures

• Figure S1:
  1. Run figureS1_param_inference.py
  2. Run figureS1_R_dynamics_simulation.py
  • Figure is saved in the simulation_results/ folder.
• Figure S2: mathematica_notebooks/figure6_and_S2.nb

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License

This repository is licensed under the MIT license. For more details, see the LICENSE file.

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Citation

Please cite the paper above if you use this code in your work.