A Django-based metadata collection and management system for microbiome sequencing facilities. Streamlines the process of collecting sequencing orders, managing sample metadata according to MIxS standards, and submitting data to the European Nucleotide Archive (ENA).
Learn how researchers can create projects, submit sequencing orders, and manage sample metadata.
See how sequencing center staff can manage orders, update status, and process samples.
Learn how to register samples and submit metadata to the European Nucleotide Archive.
Discover how to run the nf-core/mag pipeline directly from the platform.
This project, "Establishing data broker functionalities at HZI for optimizing omics data submissions to public repositories," is funded by HZI through the NFDI4Microbiota Strategy Funds in 2023. The initiative aims to enhance the submission process of omics data to public repositories, making it more efficient and streamlined.
- Sequencing Order Management: Create and track sequencing orders with comprehensive metadata
- MIxS Standards Compliance: Built-in support for 17 MIxS environmental checklists
- ENA Integration: Direct submission to European Nucleotide Archive
- Pipeline Integration: Execute nf-core/mag and other bioinformatics pipelines
- Excel Import/Export: Bulk data management through spreadsheets
- Multi-facility Support: Customizable for different sequencing centers
- Dynamic Forms: Flexible form system that adapts to facility needs
- Python 3.8 or newer
- Git
- Nextflow (for bioinformatics pipelines)
# Clone the repository
git clone https://github.com/hzi-bifo/Broker4Microbiota.git
cd Broker4Microbiota
# Run the automated setup script
./setup.shThe setup script will:
- Create a virtual environment
- Install all dependencies
- Set up the database
- Configure initial settings
# Activate virtual environment
source venv/bin/activate
# Start the development server
cd project
python manage.py runserverAccess the application at http://127.0.0.1:8000/
In a separate terminal:
source venv/bin/activate
cd project
python manage.py qcluster- Register at ENA
- Wait 24 hours before attempting submissions
- Configure credentials through Admin Settings interface
Copy TEMPLATE.env to .env and configure:
- ENA credentials
- Field encryption key
- Project paths
- HPC/Slurm settings (if applicable)
For detailed documentation on:
- Installation and setup
- Configuration options
- Development guidelines
- API endpoints
- Troubleshooting
For issues, questions, or contributions:
This project is supported by the NFDI4Microbiota Strategy Funds, granted by the Helmholtz Centre for Infection Research (HZI).