Tutorials

These tutorials are the primary learning resource for IDTrack. They are written for wet-lab researchers (basic Python familiarity) and bioinformaticians (advanced patterns), and they cover both cross-release and cross-assembly identifier mapping.

Learning path

Part

What you will learn

Start here

Part 0

The mental model (time axis vs space axis, snapshot boundary, outcomes 1→0/1→1/1→n)

Part 0 — Conceptual Foundation

Part 1

Installation and a clean, reusable local repository directory

Part 1 — Environment Setup & Installation

Part 2

External database configuration (YAML) for human, mouse, pig (and how to add a new organism)

Part 2 — External Database Configuration

Part 3

Build snapshot graphs (multi-assembly where applicable), reuse caches, and manage rebuilds across organisms and output assemblies

Part 3 — Graph Initialization & Management

Part 4

Core API usage (single + batch conversion, explainability, introspection)

Part 4 — Core API Deep-Dive (Human Example)

Part 5

Real dataset workflows (harmonization, integration hygiene, legacy rescue)

Part 5 — Real-World Experiments: Harmonization

Part 6

Cross-species “humanization” workflows and comparative-analysis preparation

Part 6 — Cross-Species Workflows: Humanization

Part 7

Production patterns (profiles, automation, diagnostics, pipelines)

Part 7 — Advanced Topics

Appendix

Self-tests, sanity checks, and troubleshooting helpers

Appendix