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ab4

https://github.com/2023ab4/ab4

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: biorxiv.org
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (16.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: 2023ab4
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 92.3 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
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Created over 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.md

Inference and design of antibody specificity

This repository hosts the Julia code for the paper:

Inference and design of antibody specificity: from experiments to models and back

Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, Kvin Ricard, Francesca Anselmi, Clment Nizak, Andrea Pagnani, Olivier Rivoire

bioRxiv 2023.10.23.563570; doi: https://doi.org/10.1101/2023.10.23.563570

See the full paper at this link. If you use this code in your work, please cite using the included CITATION.bib file.

Installation

The code is written in Julia. To install Julia, follow the instructions at JuliaLang Downloads.

Steps to Install the Package

  1. Clone this repository using git:

bash git clone https://github.com/2023ab4/ab4.git

  1. In the Julia REPL, add the package:

julia import Pkg Pkg.add("<path-to-cloned-repository>")

Pluto and Jupyter Notebooks

Pluto Notebooks

The notebooks directory contains Pluto notebooks that provide examples for:

  • Training models.
  • Performing various analyses.
  • Reproducing the figures and plots from the paper.

We recommend using Julia 1.10 for the best compatibility. To launch these, open a Julia REPL, and run:

julia using Pluto Pluto.run()

Then, navigate to the notebooks folder and select the desired notebook.

Jupyter Notebooks

Jupyter notebooks are also available in the notebooks directory to help reproduce the results from the paper. To use them:

  1. Install Python and Jupyter. For example, you can use https://www.anaconda.com/download.
  2. Install the IJulia kernel. Follow instructions here: https://github.com/JuliaLang/IJulia.jl.
  3. Start a Jupyter session:

bash jupyter notebook

  1. Navigate to the notebooks directory, and ensure that the code is executed within the Ab4Paper2023 environment, and with the IJulia kernel selected.

As with Pluto, we suggest using Julia 1.10 for compatibility.

Project Structure

  • src/: Contains the source code for the project.
  • notebooks/: Contains Pluto and Jupyter notebooks for reproducing results.
  • data/: Input data used in the paper's analysis.
  • test/: Contains test module for simple testing functionality

Issues and contributions

If you encounter any problems, please open an issue on this GitHub repository. We also welcome contributions to the codebase. Please open a pull request with your improvements.

License

MIT license

Owner

  • Name: 2023ab4
  • Login: 2023ab4
  • Kind: organization

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