https://github.com/biohacker0/containerized_bio_ml_models
Docker containers for popular bio ML models (RFdiffusion, ESMFold, AlphaFold2) with simplified setup and standardized interfaces. Eliminates complex dependencies and configuration, allowing researchers to focus on science rather than troubleshooting installation issues.
https://github.com/biohacker0/containerized_bio_ml_models
Last synced: 6 months ago
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Docker containers for popular bio ML models (RFdiffusion, ESMFold, AlphaFold2) with simplified setup and standardized interfaces. Eliminates complex dependencies and configuration, allowing researchers to focus on science rather than troubleshooting installation issues.
- Host: GitHub
- URL: https://github.com/biohacker0/containerized_bio_ml_models
- Owner: biohacker0
- License: other
- Created: 2025-04-07T08:14:35.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-28T19:55:37.000Z (about 1 year ago)
- Last Synced: 2025-07-01T21:37:19.256Z (about 1 year ago)
- Language: Dockerfile
- Size: 40 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: readme.md
- License: LICENSE
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README
# Containerized Bio ML Models
A collection of containerized machine learning models for computational biology and bioinformatics research. This repository simplifies the installation, configuration, and deployment of state-of-the-art bio ML models, allowing researchers to focus on science rather than setup.
## Overview
Setting up computational biology models often requires navigating complex dependencies, environment configurations, and installation procedures that can take days to resolve. This project provides ready-to-use Docker containers for popular bio ML models with:
- Simple commands to run each model
- Consistent interfaces across different models
- Comprehensive documentation with practical examples
- Docker Compose integration for running multiple models (planned)
## Available Models
| Model | Description | Status |
| ----------- | ---------------------------------------------- | ----------- |
| RFdiffusion | Protein structure generation with diffusion | Available |
| ESMFold | Fast and accurate protein structure prediction | Coming soon |
| AlphaFold2 | State-of-the-art protein structure prediction | Coming soon |
| ProteinMPNN | Protein sequence design | Available |
## System Requirements
- Docker (latest version recommended)
- NVIDIA GPU with CUDA 11.6+ support
- NVIDIA Container Toolkit
- 16GB+ RAM recommended
- Storage space for model weights
## Quick Start
Each model has its own directory with specific setup instructions and documentation.
## Documentation
Each model has its own comprehensive documentation located in its directory:
- Additional models: Coming soon
## Contributing
Contributions are welcome! You can help by:
- Adding new containerized models
- Improving documentation and examples
- Reporting bugs or issues