BioCompute: A Platform for Bioinformatics Analysis Workflow
Introduction
BioCompute is a platform designed to facilitate the documentation and communication of bioinformatics analysis workflows. Following the IEEE 2791-2020 standard, BioCompute aims to ease communication burdens between research centers, organizations, and industries by providing a standardized, human- and machine-readable format for BioCompute Objects (BCOs).
Key Features
- Standardized Documentation: Adopts the IEEE 2791-2020 standard for bioinformatics analyses.
- User-Friendly Interface: Build BioCompute Objects through an intuitive web portal.
- Extensible: Supports integration with various bioinformatics tools and databases.
- Community-Driven: Open-source and welcoming contributions from the community.
Quickstart Guide
Follow these steps to get started with BioCompute:
- Clone the Repository:
git clone https://github.com/biocompute/portal_userdb.git
cd client/
-
Switch to the desired branch:
git switch <branch_name>git pull -
Install dependencies:
npm install
- Run the Client:
npm run start
Access the Portal: Open your web browser and navigate to 'http://localhost:3000'.
Architecture
BioCompute consists of two main components:
- BCO Portal Server (UserDB):
Located in the SERVER directory.
Built with Django (Python) and uses SQLite3 for the database.
- BCO Portal Client (Portal):
Located in the CLIENT directory.
Built with React and Redux ToolKit.
Workflow Diagram
Installation
Local Deployment for Development
Clone the Repository:
git clone https://github.com/biocompute/bcodb.git cd bcodb
Install Dependencies:
pip install -r requirements.txt npm install
Run the Applications:
cd server python manage.py runserver cd ../client npm start
Follow the detailed instructions in our Local deployment Guide
Production Deployment
Follow the detailed instructions in our Production deployment Guide.
Docker Deployment
Our Docker deployment Guide is currently a work in progress. Stay tuned for updates.
Contributing
We welcome contributions from the community! To contribute:
Fork the repository on GitHub. Create a feature branch. Commit your changes. Submit a pull request. Please refer to our Contributing Guide for more details.
FAQ and Troubleshooting
Find solutions to common issues in our FAQ and trouble shooting Guide.
License
BioCompute is licensed under the Apache 2.0 License. See the [LICENSE]() file for more details.
Acknowledgements
We thank all our contributors and the wider community for their support.