Warning! TBsim is still in the early stages of development. It is being shared solely for transparency and to facilitate collaborative development. It is not ready to be used for real research or policy questions.
This repository contains the implementation of a new Tuberculosis (TB) model using the Starsim package. The model aims to simulate the dynamics of TB spread and treatment efficacy under various scenarios.
Try the tutorials online! Click the Binder badge above to launch an interactive environment with all tutorials ready to run.
Tuberculosis is a major global health problem, and understanding its dynamics can help in developing better strategies for control and treatment. This project uses the Starsim package to simulate TB spread in a population, considering factors like transmission rates, treatment efficacy, and social dynamics.
- TB Dynamics Simulation: Models the spread of TB in a given population.
- Treatment Scenarios: Evaluates the efficacy of different treatment strategies.
- Customizable Parameters: Allows adjustment of various parameters to simulate different scenarios.
- Visualization Tools: Includes tools for visualizing the simulation results.
- IBM and NBM: Leverages Individual-Based Models and Network-Based Models for more accurate and comprehensive simulations.
The easiest way to get started is to run the tutorials online using Binder:
- Click the Binder badge at the top of this README
- Wait for the environment to build (takes 2-3 minutes)
- Navigate to the
tutorialsdirectory - Open any tutorial notebook and start exploring!
Available tutorials:
tb_interventions_tutorial.ipynb- TB interventions modelingtbhiv_comorbidity.ipynb- TB-HIV comorbidity analysistuberculosis_sim.ipynb- Basic TB simulation
- Python 3.x
- Starsim package
- Other dependencies (listed in
requirements.txt)
- Clone the repository:
git clone https://github.com/starsimhub/tbsim.git cd tbsim - Install the required packages:
pip install -e .
The steps described below will allow you to use the latest unreleased features of starsim, it needs to be run after tbsim has been installed to allow for the package to be updated:
- Clone and install starsim:
git clone https://github.com/starsimhub/starsim.git cd starsim pip install -e .
- Navigate to the directory scripts
- Run the script:
python run_tb.py
- running this script should result in basic charts being displayed.
- Usage examples are available in the scripts folder.
TBsim is based on Starsim, please refer to Starsim documentation for additional information.
Contributions to the TBsim project are welcome! Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests.
- Daniel Klein - daniel-klein
- Minerva Enriquez - menriquez-idm
- Stewart Chang - stchang-idm
- Deven Gokhale - gokhale616
- Mike Famulare - famulare
This project is licensed under the MIT License - see the LICENSE.md file for details.
The code in this repository was developed by IDM, the Burnet Institute, and other collaborators to support our joint research on flexible agent-based modeling. We've made it publicly available under the MIT License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as permitted under the MIT License.
Epidemiological benefits of more-effective tuberculosis vaccines, drugs, and diagnostics
To build the documentation locally:
- Install the documentation dependencies:
pip install -r docs/requirements.txt
- Build the docs:
cd docs make html - The generated HTML will be in
docs/_build/html/index.html.