TBDynamics: A Compartmental Model for simulating Mycobacterium tuberculosis transmission dynamics in Vietnam
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.
- 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.
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Install Conda (if not already installed):
If Conda is not installed, follow these steps:
-
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.
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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
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Create a Directory for TBDynamics
In your terminal or command prompt, create a new directory where you will store the TBDynamics codebase:
mkdir ~/tbdynamics
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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 + `
(orCmd + Shift + `
on Mac).
-
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
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Activate the Conda Environment
After the environment is created, activate it by running:
conda activate tb_env
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Navigate to the
tbdynamics
DirectoryIn the terminal, navigate to the
tbdynamics
folder where the repository will be cloned:cd ~/tbdynamics
-
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 thetbdynamics
folder. -
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.