adabmDCA 2.0 - Direct Coupling Analysis in Julia

Authors:

• Lorenzo Rosset (Sorbonne Université, Sapienza Università di Roma)
• Roberto Netti (Sorbonne Université)
• Anna Paola Muntoni (Politecnico di Torino)
• Martin Weigt (Sorbonne Université)
• Francesco Zamponi (Sapienza Università di Roma)

Maintainer: Roberto Netti

Overview

adabmDCA 2.0 is a flexible yet easy-to-use implementation of Direct Coupling Analysis (DCA) based on Boltzmann machine learning. This package provides tools for analyzing residue-residue contacts, predicting mutational effects, scoring sequence libraries, and generating artificial sequences, applicable to both protein and RNA families. The package is designed for flexibility and performance, supporting multiple programming languages (C++, Julia, Python) and architectures (single-core/multi-core CPUs and GPUs).
This repository contains the Julia version of adabmDCA, maintained by Roberto Netti.

The project's main repository can be found at adabmDCA 2.0.

Features

• Direct Coupling Analysis (DCA) based on Boltzmann machine learning.
• Support for dense and sparse generative DCA models.
• Available on multiple architectures: single-core and multi-core CPUs, GPUs.
• Ready-to-use for residue-residue contact prediction, mutational-effect prediction, and sequence design.
• Compatible with protein and RNA family analysis.

Installation

After installing Julia on your system, you can install the package in one of the following ways:

Option 1: Using bash command

Open a terminal in the desired folder, and run the following commands:

# Download scripts from Github
wget -O adabmDCA.sh https://raw.githubusercontent.com/spqb/adabmDCA.jl/refs/heads/main/adabmDCA.sh
wget -O execute.jl https://raw.githubusercontent.com/spqb/adabmDCA.jl/refs/heads/main/execute.jl
chmod +x adabmDCA.sh

# Install ArgParse and adabmDCA.jl from the GitHub repo
julia --eval 'using Pkg; Pkg.add("ArgParse"); Pkg.add(PackageSpec(url="https://github.com/spqb/adabmDCA.jl"))'

This will install all necessary dependencies and set up the package.

Option 2: Manual Installation via Julia

1. Open Julia and install the package by running:

   using Pkg
   Pkg.add(url="https://github.com/spqb/adabmDCA.jl")
   Pkg.add("ArgParse")

2. Download the files adabmDCA.sh and execute.jl into the same folder.

3. Make the script executable by opening a terminal in the folder and running:

   chmod +x adabmDCA.sh

This will set up the package for use.

Usage

To get started with adabmDCA in Julia, please refer to the documentation or the tutorials for detailed examples of how to apply DCA to real-world protein and RNA datasets.

License

This package is open-sourced under the MIT License.

Citation

If you use this package in your research, please cite:

Rosset, L., Netti, R., Muntoni, A.P., Weigt, M., & Zamponi, F. (2024). adabmDCA 2.0: A flexible but easy-to-use package for Direct Coupling Analysis.

Acknowledgments

This work was developed in collaboration with Sorbonne Université, Sapienza Università di Roma, and Politecnico di Torino.