autoimmune_model
This repository contains the code for modeling T cell development and persistent infection that may lead to autoimmunity.
Science Score: 44.0%
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✓CITATION.cff file
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○Scientific vocabulary similarity
Low similarity (6.7%) to scientific vocabulary
Repository
This repository contains the code for modeling T cell development and persistent infection that may lead to autoimmunity.
Basic Info
- Host: GitHub
- Owner: pinkzephyr
- License: mit
- Language: Python
- Default Branch: main
- Size: 473 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Simulating T cell thymic selection and persistent/major infection
This repository contains the code for the paper "How persistent infection overcomes peripheral tolerance mechanisms to cause T cell–mediated autoimmune disease". Specifically, it contains the code for modeling T cell development and persistent infection that may lead to autoimmunity. The peptide_files.zip contains csv files of foreign IAb peptides with corresponding IAb mouse peptide homologs. The title of each file is the Mycobacterium tuberculosis IAb-binding 15mer peptide followed by its 9mer core, and in the csv file contains the corresponding IAb 15mer mouse peptide and its 9mer core.
Installation
Clone the repository:
bash git clone https://github.com/pinkzephyr/autoimmune_model.git cd autoimmune_modelCreate and activate a virtual environment:
bash python -m venv model source model/bin/activateInstall the dependencies:
bash pip install -r requirements.txtOr with Conda:
bash conda env create -f environment.yml conda activate env-name
Usage
To run the main script: ```bash python src/model.py
Owner
- Name: Rose Yin
- Login: pinkzephyr
- Kind: user
- Repositories: 1
- Profile: https://github.com/pinkzephyr
Citation (CITATION.cff)
cff-version: 1.2.0
message: If you use this software, please cite it as below.
title: How persistent infection overcomes peripheral tolerance mechanisms to cause T cell–mediated autoimmune disease
authors:
- name: Rose Yin
- name: Samuel Melton
- name: Eric S. Huseby
- name: Mehran Kardar
orcid: https://orcid.org/0000-0002-1112-5912
- name: Arup K. Chakraborty
version: 1.0.0
doi: 10.1073/pnas.2318599121
license: MIT
repository-code: https://github.com/pinkzephyr/autoimmune_model