Guides Overview

Getting started

• Installation — Docker setup, first run, and analysis access
• Story — one read walkthrough — End-to-end narrative of what the tool does
• How it works — Pipeline stages, data provenance, access model

Usage

• Analysis container — VS Code Dev Containers, Jupyter Lab, local execution
• PBI-Scope package — Python API for sequence retrieval and ML datasets
• Machine learning — Negative examples, feature engineering, model training
• Private data ingestion — Adding custom datasets
• Pipeline logs — Log files, reports, and intermediate CSVs

Reference

• Commands — CLI and Docker command reference
• API — REST API endpoints and examples
• Database — Schema and statistics
• Host resolution — How host genomes are resolved

Developer

• Code structure — Project layout, schema contracts, development workflow