Biofilter Documentation

Lightweight, user-focused documentation for running Biofilter today.

This documentation is intentionally practical:

• install/configure quickly (PyPI, source, or Docker)

• bootstrap database and run ETL

• run reports via CLI/API

• troubleshoot common operational issues

Getting Started

• Getting Started
  • Choose your path
  • What you’ll need
  • Where this guide stops
• Installing Biofilter
  • Which one should I use?
  • pip (recommended)
  • Docker
  • From source
  • Next step
• Connecting to a Database
  • Option A — Connect to an existing database
  • Option B — Bootstrap a new local database
  • Next step
• Finding a Report
  • 1. Browse the catalog
  • 2. Ask the GPT assistant
  • 3. Use the CLI to introspect
  • Common starting points
  • Next step
• Running Your First Report
  • CLI — quickest path
  • Python API — best for notebooks and scripts
  • A complete first example
  • Next steps

Reference

• System Overview
  • What Is Biofilter 4 (BF4)?
  • High-Level Architecture
  • Deployment Modes
  • ETL Data Lifecycle
  • Provenance and Reproducibility
  • Report Explain Guides
• Entity Model and Omics Domains
  • Why Entity Exists
  • Core Entity Objects
  • Domain-Specific Master Data
  • Omics Domains in BF4
  • How This Appears in ETL and Reports
• Developer Extensions
  • Add a New DTP
  • Add a New Report
  • CLI Parameter Model for Reports
  • Suggested Development Checklist
• Configuration
  • Common Commands
  • Typical Keys
  • Tips
• Database Operations
  • Core Commands
  • Recommended Flow
• Database Schema
  • ER Diagram
  • Key design notes
• ETL Operations
  • Main Commands
  • Monitoring Pair
  • File Lifecycle (Raw and Processed)
  • ETL Package Tracking
• Reports
  • Discover and Inspect
  • Run Reports
  • Dynamic Parameter Injection
  • Explain Guides
  • Practical Examples
• Report Catalog
  • Running any report
  • ETL & Platform Monitoring
  • Entity & Relationship
  • Annotation Masters
  • Variant Analysis
  • Variant Interaction Modeling
  • SNP×SNP Interaction Pipeline
  • Pathway Burden Pipeline
  • Utilities
  • Coverage summary
• CLI Reference
  • Global
  • Config
  • DB
  • ETL
  • Report
• Troubleshooting
  • Report Not Found
  • Input Conflict in report run
  • Explain Page Not Found
  • PostgreSQL-only Reports
  • Migration/Upgrade Issues
  • ETL Batch Resume
  • Report Output Not Found (Docker)