BenchBaze

BenchBaze is a Django-based laboratory inventory and purchasing management system. It provides a highly customized Django admin experience for managing biological collection items, approvals, GMO compliance (AKA Formblatt Z in Germany), purchasing, user access, as well as an built-in DNA map viewer.

Key features

• Inventory management for plasmids, cell lines, strains (yeast and bacteria), oligos, antibodies, viruses, and related assets
• Purchasing and order tracking workflows
• Approval forms and document attachments
• GMO compliance support for German laboratories
• Custom user roles and OIDC-aware authentication
• Open Vector Editor (OVE) integration for DNA map visualization
• REST API endpoints for frontend integration

Repository structure

• config/ - Django configuration, settings, URL routing, and WSGI entrypoint
• collection/ - inventory app modules for biological collections and shared utilities
• purchasing/ - purchasing, orders, cost units, and hazardous materials support
• approval/ - approval workflows and forms
• common/ - shared models, admin site customizations, authentication backends, and utilities
• formz/ - form-related models and management logic
• frontend/ - Vue 3 + Vite frontend project used for client-side UI components (very much in development)
• requirements/ - Python dependency manifests and environment definitions
• templates/ - Django templates used by the admin and authentication views
• staticfiles/ - static assets
• uploads/ - media upload directory

Technology stack

• Python 3.11
• Django 4.2
• PostgreSQL
• Vue 3 + Vite for frontend UI
• Mozilla Django OIDC for authentication
• django-guardian for object permissions
• django-import-export, djangoql, django-simple-history, background_task
• Open Vector Editor (OVE) integration for DNA map support

Setup

1. Create private_settings.py

Copy the template and update the values for your environment:

cp config/private_settings_template.py config/private_settings.py

Edit config/private_settings.py to set relevant values for your database, email, and other environment-specific settings.

2. Install Python dependencies

Install from the pinned requirement file:

conda create -n benchbaze -f requirements/conda.yml
conda activate benchbaze

python -m pip install -r requirements/prod.txt

For development dependencies:

python -m pip install -r requirements/dev.txt

3. Initialize the database

Create and migrate the PostgreSQL database:

python manage.py migrate

Create a superuser:

python manage.py createsuperuser

4. Collect static assets

python manage.py collectstatic --noinput

Running the application

For local development, use Django's built-in server:

python manage.py runserver

License

See LICENSE for project licensing details.