Designing with the assistant
What needs your approval
Some things always stop and wait for you. Others depend on the mode you are in. This page is the honest version of both.
What always stops
Regardless of mode, these hand control back to you and go no further until you respond.
- Deleting a file
- Always asks, every time, in every mode. Deletion is the one action that is not recoverable from version history.
- A plan, before it is executed
- You read it and choose Execute, Refine or Cancel. Plan and Act.
- A question it needs answered
- Which host, which marker, which of two designs. It stops rather than guessing, and your answer becomes a constraint on the rest of the work.
- Running a protocol on a robot
- Physical actions always require explicit approval, with the protocol, a checklist and an estimate in front of you. Protocols and robots.
- When it is stuck
- If it cannot make progress it asks for help rather than churning. Being asked is not a failure — it is the alternative to a confident wrong answer.
What depends on the mode
Editing a sequence inside your own project is the case that changes.
| Mode | What happens when it wants to edit a sequence |
|---|---|
| Plan | It cannot. The operations that write to files are not available in Plan mode. |
| Act | It generally goes ahead. You gave permission for that class of work by switching to Act. |
What an approval card shows
When a sequence change does come to you for approval, you get more than a yes/no prompt.
- A plain-English summary
- What is being changed, where it sits in the construct, and where the new sequence came from.
- The surrounding context
- The region around the insertion point, so you can see what it lands next to rather than trusting a coordinate.
- Property badges
- Short flags on the operation itself — whether it preserves the reading frame, whether it is reversible, whether the inserted sequence is being reverse-complemented.
- The exact parameters
- Hidden behind a toggle. Open it when the summary is not specific enough and you want the precise numbers.
Your options are Approve or Reject.
What to actually check
Reading the summary is not the same as checking the change. The things worth thirty seconds:
| Look at | Because |
|---|---|
| The position | Is it landing where you expect, relative to the promoter and the ribosome binding site? |
| The frame badge | If it is not frame-preserving and it should be, stop. |
| The source | Where did the inserted sequence come from? A fetched record with an accession is verifiable; something with no stated origin is not. |
| The strand | Reverse-complemented when you did not expect it usually means a directional cloning assumption differs from yours. |
Rejecting well
Rejecting stops the operation. It does not end the conversation — say why in the next message and the work continues from there. “No, that cuts the ribosome binding site” is far more useful than a bare rejection, because the reason is the thing that lets it produce a correct version instead of the same one again.
What it never does
It does not act outside the project you are working in. It does not delete anything without asking. It does not order DNA, contact a vendor, or spend money. And it does not drive a robot without an explicit, separate approval carrying the protocol you are approving.