Whenever the story is interaction over time — an instrument protocol, a data pipeline handshake, a review workflow — a sequence diagram says it better than prose. In the Diagram tab it’s a few lines of text.

Step 1 — Participants and messages

Choose the sequence diagram type. Each participant gets a vertical lifeline; arrows between them are messages, in the order written:

participant R as Researcher
participant W as Writano
participant C as Compiler
R->>W: edit document
W->>C: compile request
C-->>W: PDF
W-->>R: preview updates

->> is a solid arrow (a request, an action); -->> is dashed (a response). The as clause gives long names a short handle you reuse.

Step 2 — Order is the syntax

There is no layout to fight: messages render top-to-bottom in the order you wrote them. Reordering the story is reordering lines — which is exactly how editing a protocol should feel.

Step 3 — Notes and phases

Notes annotate a moment; they’re how you mark timing, conditions, or the phase of an experiment:

participant S as Sample
participant D as Detector
participant PC as Acquisition
Note over S,D: alignment phase
S->>D: reference beam
D->>PC: baseline counts
Note over PC: 10 min integration
S->>D: measurement beam
D->>PC: signal counts
PC-->>PC: subtract baseline

A self-message (PC-->>PC) marks internal processing — the subtraction happens at the acquisition step, not between participants.

Step 4 — Loops and alternatives

Repetition and branching have blocks:

participant U as User
participant W as Writano
loop every autosave
  U->>W: changed text
  W-->>U: saved
end
alt compile succeeds
  W-->>U: PDF preview
else compile fails
  W-->>U: error log, offending line
end

loop … end and alt … else … end render as labelled frames — the standard notation reviewers already know how to read.

Step 5 — Export or insert

Like every diagram: pick a theme so it matches your other figures, then export a vector PDF or Insert into the paper with a \label. The saved diagram reopens as this text for the next protocol revision.

Tip: Keep participants to four or five. A sequence diagram with eight lifelines is two diagrams wearing one caption.