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

---

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 macOS

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.

---

Build Tools Installation

Some GENBAIT dependencies (such as shap, xgboost, or leidenalg) require system-level C++ build tools to compile extensions.

For Windows

1. Download Microsoft C++ Build Tools:
   https://visualstudio.microsoft.com/visual-cpp-build-tools/

2. In the installer, select the following:

   • C++ build tools workload
   • MSVC v14 or later (e.g., v142 or v143)
   • Windows 10 or 11 SDK

3. Install the components and restart your terminal (or system).

If these tools are missing, you may encounter errors like:
error: Microsoft Visual C++ 14.0 or greater is required

For macOS

1. Install Xcode Command Line Tools:
   Open Terminal and run:

   xcode-select --install
   

---

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)
   • pytorch
   • pytorch-lightning
   • shap
   • XGBoost

These packages will be installed automatically during the setup.

Installation takes less than 2 minutes.

---

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