GENBAIT: Genetic Algorithm for Bait Selection

GENBAIT is a Python package designed for bait (feature) selection in proximity labeling data using genetic algorithms.

A preprint describing the method and introducing a novel benchmarking platform is available: Kasmaeifar et al. (2024) Computational design and evaluation of optimal bait sets for scalable proximity proteomics

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Overview

Requirements

GENBAIT requires Python 3.10 or higher. We recommend creating a virtual environment to ensure smooth installation.

Git Installation

To install GENBAIT, you first need Git. Follow the instructions below to install Git on your system.

For Windows

1. Download the Git installer:

   • Go to the official Git website: https://git-scm.com/download/win.
   • Download the latest installer for Windows.

2. Run the installer:

   • Locate the downloaded file and double-click to open the installer.
   • Follow the prompts in the setup wizard. You can keep the default options or customize the installation.

For Mac

1. Install Git using Homebrew:

   • If you have Homebrew installed, open the Terminal and run:

     brew install git

   • Homebrew will handle the download and installation of Git.

2. Verify the installation:

   • In Terminal, type the following command and press Enter:

     git --version

   • You should see a Git version number, confirming that Git is installed.

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Installation

To install the genbait package, follow these steps:

1. Install GENBAIT from GitHub using pip:

   pip install git+https://github.com/camlab-bioml/genbait.git

2. Ensure all dependencies are installed: GENBAIT requires the following Python packages:

   • pandas
   • numpy
   • scipy
   • scikit-learn
   • matplotlib
   • seaborn
   • gprofiler-official
   • igraph
   • leidenalg
   • deap (for Genetic Algorithm operations)

These packages will be installed automatically during the setup.

Installation takes less than 2 minutes.

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Getting started

A detailed tutorial of how to use different functions of the package can be found here: GENBAIT Tutorial

Expected run time

For 200 baits and 10 iterations for a panel size 50, running genbait takes approximately 30 minutes on a computer with 32 GB RAM.

Authors

This software is authored by: Vesal Kasmaeifar, Kieran R Campbell

Lunenfeld-Tanenbaum Research Institute & University of Toronto