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Update an existing strain

Most day-to-day work in CellRepo is not creating new strains.

It is updating existing ones.

This workflow shows how to record changes safely and traceably without overwriting history.

When should you use this workflow?

Use this workflow whenever:

  • you modify a strain
  • you add new experimental results
  • you confirm or correct genotype information
  • you upload sequencing or analysis files
  • you make a meaningful decision that affects the strain

If you are starting from scratch, see
Track a new strain.

The core idea

In CellRepo:

you never edit the past
you always add a new commit

Instead of changing old information, you create a new checkpoint.

This preserves:

  • traceability
  • accountability
  • reproducibility

Just like a lab notebook, you add entries — you don’t erase pages.

Step 1: Open the strain repository

  • navigate to your project
  • open the repository for the strain

You should see:

  • latest commit
  • commit history
  • files and notes

The latest commit represents the current state of the strain.

Step 2: Decide if this change deserves a commit

Ask yourself:

Will future-me care that this happened?

If yes → commit it.

Good examples:

  • “Transformed with plasmid pXYZ”
  • “Sequencing confirmed deletion”
  • “Protocol changed after failed growth”
  • “Updated design following optimisation”

Not necessary:

  • small typos
  • temporary notes
  • incomplete thoughts

Think milestones, not micro-edits.

Step 3: Create a new commit

Click:

New commit / Create commit

Then:

  • write a clear message
  • add or update files if needed
  • record notes or metadata

Save.

That’s it.

You’ve extended the strain’s history.

Step 4: Attach supporting data (optional)

You can include:

  • sequencing files
  • plasmid maps
  • analysis outputs
  • images
  • protocols
  • notes

You don’t need everything every time.

Commits can be:

  • small and frequent
  • or larger summaries

Choose what fits your workflow.

Example: real lab timeline

Here’s what a typical history might look like:

  1. Initial strain created
  2. Plasmid introduced
  3. Colony screened
  4. Genotype confirmed
  5. Growth assay results added
  6. Protocol updated

Each step becomes one commit.

Anyone can now understand:

  • what happened
  • when
  • by whom
  • why

Correcting mistakes

Mistakes happen. That’s normal.

If something is wrong:

❌ Don’t delete history
✅ Create a new commit that fixes it

Example:

  • “Corrected genotype annotation after resequencing”

This keeps everything transparent and scientifically honest.

Working with others

When multiple people update the same strain:

  • commits show ownership
  • changes are visible
  • decisions are documented

No more:

  • “who changed this?”
  • “which version is correct?”

History answers those questions automatically.

Tips for clean histories

Good practice:

  • commit at logical milestones
  • write descriptive messages
  • keep one idea per commit

Avoid:

  • huge commits covering many unrelated changes
  • vague messages like “update”
  • long gaps without recording progress

Small, meaningful commits work best.

Result

After following this workflow:

  • the strain evolves safely
  • nothing is lost
  • every change is explainable

You now have a living, traceable record of the strain.

Working alone or need collaboration?

Need reports or documentation?