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TBDynamics: A Compartmental Model for simulating Mycobacterium tuberculosis transmission dynamics in Vietnam

Overview:

TBDynamics is a Python-based modeling tool developed to simulating Mycobacterium tuberculosis (M.tb) transmission in Vietnam . Leveraging the power of the summer, a Python-based framework for the creation and execution of compartmental models (or “state-based”) epidemiological models of infectious disease transmission, TBDynamics offers a comprehensive compartmental model that simulates TB transmission, progression, and control strategies.

Features:

  • Compartmental Modeling: Implements a sophisticated model capturing various stages of M.tb infection and TB diseases.
  • Customizable Parameters: Allows users to tailor model parameters.
  • Data Integration: Capable of incorporating real-world data for more accurate modelling.
  • Simulation and Analysis: Offers tools for running simulations over specified time periods and analyzing the outcomes.

Installation Guide:

  1. Install Conda (if not already installed):

    If Conda is not installed, follow these steps:

    • Download the latest version of Miniconda or Anaconda.

    • Follow the installation instructions for your operating system.

    • After installation, verify by opening a terminal and running:

      conda --version

  2. Install Visual Studio Code (VSCode)

    Download and install Visual Studio Code from here.

    Follow the installation instructions for your operating system.

    Once installed, open VSCode.

  3. Install Git

    Git is required for version control and cloning the repository.

    Download and install Git from here.

    After installation, verify the installation by running:

    git --version

  4. Create a Directory for TBDynamics

    In your terminal or command prompt, create a new directory where you will store the TBDynamics codebase:

    mkdir ~/tbdynamics

  5. Open VSCode and Set Up the Project

    • Launch Visual Studio Code.
    • Open the tbdynamics directory you just created by navigating to File > Open Folder in the VSCode menu.
    • Open a terminal in VSCode by pressing Ctrl + Shift + ` (or Cmd + Shift + ` on Mac).

  6. Create a Conda Environment with Python 3.10

    In the terminal, create a new Conda environment with Python 3.10:

    conda create --name tb_env python=3.10

  7. Activate the Conda Environment

    After the environment is created, activate it by running:

    conda activate tb_env

  8. Navigate to the tbdynamics Directory

    In the terminal, navigate to the tbdynamics folder where the repository will be cloned:

    cd ~/tbdynamics

  9. Clone the Git Repository

    Clone the tbdynamics repository into the current directory:

    git clone https://github.com/longbui/tbdynamics.git .

    The . at the end ensures the repository is cloned directly into the tbdynamics folder.

  10. Install the Project in Editable Mode

    Once the repository is cloned, install the project and its dependencies using the following command:

    pip install -e .

    This will install the current project in editable mode, allowing you to make changes to the code without needing to reinstall the package.