Dry Lab

If you haven’t done Penn Onboarding and Lab Onboarding yet, start there first.

  1. Training — required training and lab-specific computing orientation
  2. Server Access — PMACS/PARCC account requests, VPN
  3. Computing Basics — IDE setup, command line, Python/R (read before the tutorials below)
  4. Project Setup — project ID → metadata sheet → folder structure → push to GitHub
  5. Tutorials — grouped by what stage of a project you’re at:
    • Access: PARCC, PMACS, GitHub
    • Coding Agents: Claude Code, Codex, Biomni
    • Analysis Pipelines: scRNAseq, Xenium Spatial, ATACseq
    • Standards: Figures

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