Your workspace
Projects
A project is one piece of work and everything that belongs to it — the constructs, the write-ups, the protocols, and the conversations about them.
What goes in a project
Five kinds of thing live in the project tree. They sit side by side, so the protocol that made a plasmid is one click from the plasmid.
- Sequences
- Your plasmids and fragments. Each one opens into the sequence workspace with its maps and analysis tools.
- Documents
- Free-form notes — design rationale, a summary for your PI, a list of things to try next.
- Experiments
- Notebook entries with a status, an objective, linked sequences, steps, notes and a conclusion.
- Protocols
- Reusable step-by-step methods you run more than once.
- Folders
- Ordinary nesting. Use them however your lab already thinks — by construct, by aim, by date.
There is also one special file at the root of every project: PLASMID.md. It holds the standing facts about the work — your host strain, your available enzymes, your lab's conventions — and the assistant reads it at the start of every conversation in that project. It cannot be renamed, moved or deleted. Project instructions covers what to put in it.
Creating a project
Use Create New — the + at the top of the icon rail — and pick Project. On your first sign-in you are offered a starter workspace instead, either a pUC19 cloning starter or a pBR322 starter, so there is something real to open before you import anything of your own.
Switch between projects with the dropdown at the top of the Projects panel. Starred projects sort to the top.
Working in the file tree
The tree behaves the way a file browser behaves. Drag to reorder or to move something into a folder. Press F2 to rename in place. Right-click anything for the full menu.
What the right-click menu does
| Action | What happens |
|---|---|
| Open | Opens the item in a new editor tab. |
| New Folder | Creates a folder inside the one you clicked. |
| Rename F2 | Edits the name in place. |
| Copy Name | Puts the name on your clipboard. |
| Duplicate | Makes an independent copy. Useful before an edit you are unsure about. |
| Export | Sequences only — FASTA, GenBank or JSON straight from the tree. |
| Move to… | Relocates without dragging, for deep trees. |
| Delete ⌘⌫ | Asks first, and names what it is about to remove. |
Finding things
The panel has a filter bar — All, Seq, Docs, Proto, Exp — and a search box that matches names within the current project. Sort order is yours to set: Manual, Name A–Z, Name Z–A, Newest First, Oldest First or Group by Type. Manual is the default, so the order you drag things into is the order they stay in.
To search across everything rather than one project, press ⌘K. Shortcuts covers the rest of what that can do.
Adding things to a project
The + at the top of the Projects panel is the fastest route. It offers:
- New Folder
- Paste Sequence — for a sequence you have on your clipboard
- Import File — GenBank, FASTA and the other formats on the importing page
- New Document
- New Experiment
You can also drag a file straight from your desktop onto the panel, which is usually quicker than opening the modal.
How to organise them
One project per construct family works well for most people: the backbone, the variants built from it, the protocols used, and the notebook entries recording what happened. It keeps the assistant's context tight, which makes its answers better — it can see the other constructs in the project and the conventions in PLASMID.md.
A project per aim also works if you are comparing approaches. What works badly is one enormous project holding a year of unrelated work, because everything in it becomes background noise for every question you ask.
Deleting and recovering
Deleting a sequence asks for confirmation and names what it is about to remove. Deleting is not the same as editing: if you have changed a construct and want the old bases back, use version history rather than deleting and re-importing — every saved revision is kept.