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Publication and Reproducibility

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How do we reference the exact protocol version used in a paper?

When submitting a manuscript, freeze the repository state:

Terminal window
git tag -a paper_2026_submission -m "Protocols used in manuscript"

This marks a permanent reference point.

Why Tagging Matters

Section titled “Why Tagging Matters”
Section titled Why Tagging Matters

Tagging enables:

  • Exact reconstruction of methods
  • Transparent reviewer responses
  • Long-term reproducibility
  • Clear linkage between data and protocol version

From Documents to Infrastructure

Section titled “From Documents to Infrastructure”
Section titled From Documents to Infrastructure

By managing SOPs in a Git repository, you transform:

Static documents into Versioned scientific knowledge infrastructure.

This is not just about Git.

It is about making laboratory knowledge structured, traceable, and reproducible.