GitHub - sb2cl/Activity-Clouds: Analysis of the impact of the RBS core on gene translation

Activity-Cloud Framework Enables Robust Coarse-Grained Translation Tuning via Shine-Dalgarno Core Substitution in E. coli

This repository contains the code used for the analysis presented in the paper.

The required Python modules are listed in the requirements.txt file. Install them using:

pip install -r requirements.txt

Open your terminal or command prompt.
Navigate to the directory: where you want to work. Use the cd command (e.g., cd Documents/Activity-Clouds).
Start the Jupyter Notebook server . Type the following command and press Enter:

jupyter notebook

Open the notebook 10_tree_creation_and_prunning.ipynb in the Jupyter Notebook server.
Run the notebook.
The results are displayed in the notebook and all generated data are stored in the data directory.
Run the other notebooks in the specified order.

Name		Name	Last commit message	Last commit date
.idea		.idea
data		data
.gitignore		.gitignore
10_tree_creation_and_prunning.ipynb		10_tree_creation_and_prunning.ipynb
20_DBSCAN_clustering.ipynb		20_DBSCAN_clustering.ipynb
30_PLS_analysis.ipynb		30_PLS_analysis.ipynb
40_validation_against_uaspire.ipynb		40_validation_against_uaspire.ipynb
50_tree_regressor_on_pruned_tree.ipynb		50_tree_regressor_on_pruned_tree.ipynb
60_energy_of_clouds.ipynb		60_energy_of_clouds.ipynb
70_sequence_variations.ipynb		70_sequence_variations.ipynb
80_rbs_calc_validation.ipynb		80_rbs_calc_validation.ipynb
README.md		README.md
common.py		common.py
requirements.txt		requirements.txt