Getting Started

Overview

PyDrugLogics is a Python package designed for constructing, optimizing Boolean Models and performing in-silico perturbations of the models.

Core Features:

• Construct Boolean model from .sif file
• Load Boolean model from .bnet file
• Optimize Boolean model
• Generate perturbed Boolean models
• Evaluate drug synergies

Installation

PyDrugLogics can be installed via PyPI, Conda, or directly from the source.

Install PyDrugLogics from PyPI

The process involves two steps to install the PyDrugLogics core package and its necessary external dependencies.

1. Install PyDrugLogics via pip

pip install pydruglogics

2. Install External Dependency

pip install -r https://raw.githubusercontent.com/druglogics/pydruglogics/main/requirements.txt

This will install the PyDrugLogics package and handle all dependencies automatically.

Install PyDrugLogics via conda

Note: CoLoMoTo conda integration is ongoing.

conda install szlaura::pydruglogics

Install from Source

For the latest development version, clone the repository and install it directly:

git clone https://github.com/druglogics/pydruglogics.git
cd pydruglogics
pip install .
pip install -r requirements.txt

CoLoMoTo Notebook Environment

PyDrugLogics is available in the CoLoMoTo Docker and Notebook starting from version 2025-01-01.

Setup CoLoMoTo Docker and Notebook

1. Install the helper script in a terminal:

pip install -U colomoto-docker

2. Start the CoLoMoTo Notebook (a specific tag can also be given):

colomoto-docker    # or colomoto-docker -V 2025-01-01

3. Open the Jupiter Notebook and navigate to the tutorials folder to find the PyDrugLogics folder hosting the pydruglogics tutorial notebook.

See more about the CoLoMoTo Docker and Notebook in the documentation.