🧬 🧿 BioOptuna: Hyperparameter Optimization for Bioinformatics

BioOptuna is a streamlined hyperparameter optimization template tailored for bioinformatics applications. Built upon the robust Optuna framework, this toolkit is designed to effortlessly optimize parameters for various bioinformatics tools and pipelines.

Features

• Modular Python codebase for easy integration.
• Comprehensive examples specific to bioinformatics.
• Supports various bioinformatics tools and software.
• User-friendly configuration for defining search spaces.

Installation

1. Clone this repository:

   git clone https://github.com/SaberHQ/BioOptuna.git
   

2. Navigate to the cloned directory and install the required packages:

   cd BioOptuna
   pip install -r requirements.txt
   

Quick Start

1. Define your hyperparameter search space and objective function in config.py.
2. Run the optimization script:

   python optimize.py
   

3. Check the results in the generated output file.

Examples

Check out the examples/ directory for practical applications of BioOptuna with popular bioinformatics tools.

Contributing

We welcome contributions! Please check the CONTRIBUTING.md file for guidelines on submitting pull requests and reporting issues.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• The Optuna team for developing such a versatile optimization framework.
• BTL Lab members for their feedback and support.