MIRELLA

MIRELLA is the repository that contains the Python code that supports the findings of the study: 'MIRELLA: A mathematical model explains the effect of miRNA (MI) REgulation on intracellular resource aLLocAtion.'

Repo Contents

• Notebooks
• Docs

System Requirements

Hardware Requirements

MIRELLA does not require any specific hardware to run the code using Python.

OS Requirements

MIRELLA does not require any specific OS to run the code. The package has been tested on macOS Monterey v12.6.

Software Dependencies

• Standard Python Libraries
• Scientific Python Libraries: SciPy, NumPy, Pandas, Seaborn

Installation Guide

• Using pip

1. Clone the repository git clone https://github.com/giansimone/MIRELLA.git.
2. Create a virtual environment python3 -m venv mirella_venv
3. Activate the virtual environment source mirella_venv/bin/activate
4. Navigate to the repo cd ./MIRELLA/
5. Install the dependencies pip install -r requirements.txt.

• Using conda

1. Clone the repository git clone https://github.com/giansimone/MIRELLA.git.
2. Navigate to the repo cd ./MIRELLA/
3. Create a conda environment conda env create -f environment.yml

Demo

See the Instructions for Use section.

Instructions for Use

• Use the notebook 1_Notebook_Ribosome_Reallocation.ipynb to generate the simulations shown in Fig. 2c, Fig. 3a,b, and Supplementary Fig. S7.
• Use the notebook 2_Notebook_RNase_Realloaction.ipynb to generate the simulations shown in Fig. 4b, Supplementary Fig. S4, and Supplementary Fig. S5.
• Use the notebook 3_Notebook_SI.ipynb to generate the computational analysis shown in Supplementary Fig. S3, and Supplementary Fig. S6.

License

This code is licensed under the MIT License.