siRNA knockdown

This project contains Python code for analyzing the siRNA knockdown data in the data directory.

Installation

This installation guide assumes a functioning Python3.6 setup with pip installed. To set up the project on your computer, follow these steps:

1. Clone/download the project.
2. Create a new virtual environment inside the project base folder (denoted as <TARGET>):

   python -m venv <TARGET>
   

3. Enter the <TARGET> directory, if not done yet:

   cd <TARGET>
   

4. Activate the virtual environment:

   source bin/activate
   

5. Install the required Python modules:

   pip install -r requirements.txt
   

6. Activate ipywidgets:

   jupyter nbextension enable --py widgetsnbextension --sys-prefix
   

Usage

To view (and change) the jupyter notebooks in this project, first activate the virtual environment:

source bin/activate

Then, you can start the notebook server:

jupyter notebook

Open the URL displayed on your console in your web browser to access the notebooks.

When you have finished working on the notebooks, you can deactivate the virtual environment:

deactivate

Content

There are three notebooks of interest:

• siRNA_knockdown_calibrated.ipynb is the notebook for fitting the data with fixed protein maturation and degradation rates.
• siRNA_knockdown_calibrated_nonfixed.ipynb is the notebook for fitting the data without fixing protein maturation and degradation rates.
• siRNA_knockdown_fixed.ipynb is the notebook for obtaining the protein maturation and degradation rates from separate measurements.