A protocol written as a numbered list implies that the steps happen one after another. Most of them do not. The steps overlap, and the list gives you no way to see where.
Sort the steps by how much they care
Before timing anything, divide the steps into two groups: the ones where the duration changes the result, and the ones where it does not. This is the single most useful thing you can know about a protocol, and it is almost never written down.
- Critical: enzymatic reactions with a defined stop, fixation, anything where over-incubation degrades the sample, anything light-sensitive
- Forgiving: most washes, most blocking steps, most equilibrations — where "at least" is the real constraint and longer does no harm
Once the steps are sorted, the schedule almost writes itself: slack goes into the forgiving steps, and the critical ones get your attention and an alarm.
Plan backwards from the step that cannot wait
Find the step in the protocol with the least tolerance — the one that must happen at a specific point relative to something else. Place that step in the day first, then work outwards in both directions. Planning forwards from step one produces a schedule where the critical step lands at 17:40, which is how protocols end up being rushed at exactly the point they should not be.
Run the timers as a schedule, not as a stack
Several named countdowns running at once is not clutter — it is the schedule made visible. The reason it works is that each alarm arrives with the context of what it is for, so you are not deciding what to do next, you are being told.
The alternative, a single timer restarted at each step, works right up until two steps overlap. Then it stops working entirely, usually without announcing that it has.
Write the timings into the protocol, not into your memory
If a protocol has a step that is always started while another is running, say so in the protocol. "Start the block while the samples are spinning" is a real instruction that saves ten minutes every run and is currently living in one person's head.
That sentence is the whole difference between a protocol that lists what to do and a protocol that tells you how the afternoon goes.