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biocompute

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:

  1. Clone the Repository:

git clone https://github.com/biocompute/portal_userdb.git cd client/

  1. Switch to the desired branch: git switch <branch_name> git pull

  2. Install dependencies:

npm install

  1. 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

BCO Portal git workflow drawio

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.