Designing with the assistant
Reviewing a change
Every edit to a sequence is saved as a revision and can be compared against the one before it. This is where you check the work rather than the description of the work.
Why the diff and not the summary
A written summary of a change is a claim about the change. The diff is the change. They usually agree — and the times they do not are exactly the times you need to know.
Diffs open as tabs, so you can leave one up beside the construct while you keep working.
What to look at, in order
- Length
- Did the construct change size by the amount you expected? A surprise here is the cheapest possible way to catch a fragment inserted twice or a region deleted that you meant to keep.
- Features gone
- The comparison shows which annotations were removed or disrupted. A missing origin, promoter or resistance marker means the plasmid will not replicate, will not express, or will not be selectable.
- Features moved
- Everything downstream of an insertion shifts. That is expected; what you are checking is that nothing landed inside something it should not have.
- The junctions
- Look at the actual bases either side of each join. This is where reading frames break, and it is not visible from a feature list.
- Anything unexplained
- A change you cannot account for is worth a question before you build on it.
Version history
Every saved state of a sequence is kept. Open Version History from the toolbar and you get a timeline of revisions, with an indicator on the ones the assistant made so you can tell your edits from its edits and filter to either.
| You want to | Do this |
|---|---|
| See what a revision changed | Select it in the timeline. The comparison opens against the state before it. |
| Compare two revisions that are not adjacent | Pick both in the comparison view — useful after a run of small edits, when what you care about is the net effect. |
| Go back | Restore an earlier revision. Nothing is lost; the restore is itself a new revision, so you can go forward again. |
When the diff does not match the description
Say what you saw
Point at the specific discrepancy. “The summary says the promoter was preserved but the diff shows it was cut” is actionable. It also tells you something useful: the description was generated from an intention, and the diff was generated from the bases. When they disagree, the bases are what you have.
Roll back first, then discuss
If a change is clearly wrong, restore the previous revision before continuing the conversation. It costs nothing, and it means the next attempt starts from a construct you trust rather than from a broken one.
After the diff
A clean diff tells you the change was what was described. It does not tell you the construct will work — for that, run verification and read the verdict before you order anything.