Keeping records
Experiments and protocols
The write-up lives in the same project as the plasmid it describes, and links to it — so six months later the construct and the reason for it are one click apart.
Three kinds of writing
- Experiments
- One run of one thing. Has a status, an objective, linked sequences, steps, notes and a conclusion. This is your notebook entry.
- Protocols
- A method you run more than once. Write it once, reuse it, and link each experiment to the version you used.
- Documents
- Everything else — design rationale, a summary for a lab meeting, a list of things to try next.
All three open as tabs beside your sequences and use the same editor.
Writing an experiment
Create one from New Experiment in the Projects panel, or Lab Entry in the Create menu. An entry has:
| Field | What it is for |
|---|---|
| Status | Where the experiment has got to. Set it as you go rather than at the end. |
| Objective | One line on what you were trying to find out. The most valuable field and the most skipped. |
| Linked sequences | The constructs involved, clickable straight through to the map. |
| Protocol | The steps you actually followed. |
| Notes | The free-form body — observations, gel images, what went wrong. |
| Conclusion | Appears once the experiment is complete. What you concluded, including a negative result. |
| Tags | Your own labels, for finding things later. |
Entries can be pinned or starred to keep them near the top, and there is an AI summary if you want a condensed version of a long entry.
Protocols
Protocols are step-based and built to be reused. Write your standard miniprep, transformation or ligation once and link to it from every experiment that used it, rather than pasting the same steps repeatedly.
If you run liquid-handling robots, a protocol is also the starting point for automating it — Protocols and robots.
The editor
Rich text with markdown underneath. Type / anywhere for the block menu:
| Block | Use it for |
|---|---|
| Headings 1–3 | Sectioning a long entry. |
| Bullet and numbered lists | Observations; ordered steps. |
| Task list | Checkboxes you tick off — good for a protocol you are working through at the bench. |
| Quote | Something from a paper or a colleague. |
| Code block | Primer sequences, command lines, calculations. |
| Table | Conditions against results. |
| Divider | Separating a run from the next one. |
Select text for the formatting bar — bold, italic, underline, strikethrough, inline code and highlight. Typing @ mentions something else in the project.
Working with the assistant
From the bench into the notebook
Select a region on a sequence map, right-click, and choose Document in Lab Notebook. It carries the construct and the region with it, so you are not retyping coordinates.
From the notebook into a conversation
Right-click a block in the editor and add it to the chat — useful for “here is what happened, what would you try next?” without rewriting the account of it.
Drafting
The assistant can draft a protocol or an experiment write-up from a conversation. Treat it as a first draft written by someone who was not in the room: it does not know your incubator ran hot or that you substituted a reagent. Read it before you keep it.
What is not there yet
The AI Complete option in the editor's block menu is a placeholder and does nothing. Documents and experiments also have no dedicated export — export is a sequence-level feature. To get an entry out today, copy from the editor.