Run a PCR with a plate transfer

You need: the setup from the cookbook front page (install plus the two simulated instruments). About ten minutes.

1. Ask for the experiment

   In your agent, type:

   Run a 3-cycle PCR at 95/58/72 on the plate in deck slot A1, hold it at 4 °C afterwards, and put the plate back in A2.

   Three cycles keeps the simulated run short. On a real instrument you would say 30.

2. The agent looks for a recipe

   Behind the scenes it calls mhp_lab op="recipes" with your sentence and gets back pcr-with-plate-transfer, which needs a robot arm and a thermocycler. You may see it say something like "There is a tested recipe for this. I'll use it."

3. The agent finds the instruments and reads their notes

   It calls mhp_find for an idle thermocycler and an idle arm, then mhp_describe on each. The thermocycler's notes say the lid must be closed and the lid heater should be on before loading. The arm's notes say to use 30% speed near open plates. The agent will follow both without being told.

4. The agent rehearses and shows you the plan

   It runs the recipe in plan mode. Nothing moves. You see a plan like this:

   Plan for pcr-with-plate-transfer (cycles=3, plate_slot=deck_A1, return_slot=deck_A2)
    1  arm-01           set speed = 30                          ok
    2  arm-01           read homed → false
    3  arm-01           home                                    ok
    4  thermocycler-01  read lid_closed → true
    5  arm-01           pick_plate from deck_A1                 ok
    6  arm-01           place_plate at thermocycler             ok
    7  thermocycler-01  set lid_heater = true                   ok
    8  thermocycler-01  run_protocol (3 steps × 3 cycles)       ok   long-running
    9  thermocycler-01  set target_temperature = 4              ok
   10  arm-01           pick_plate from thermocycler            ok
   11  arm-01           place_plate at deck_A2                  ok
   Verdict: ok; no human confirmation needed. Shall I run it?

   Every step passed the instrument's safety checks. If you had asked for a 110 °C step, step 8 would show REFUSED: step temp 110 outside block limits and the agent would stop here and ask you what to do.

5. Say go

   Yes, run it.

   The agent runs the same recipe for real. With three cycles on the simulator this takes about ten seconds. On a real thermocycler with 30 cycles it would start the run in the background and tell you the run id.

6. Read the result

   The agent reports what the instruments actually did, from the recipe's output:

   pcr done on thermocycler-01: {'cycles_completed': 3, 'final_block_temperature': 72}; plate at deck_A2; block 4.0 C

   Notice it reports the block temperature it read (4.0 °C), not the one it set. Ask "where is the plate now?" and it reads the arm's holding_plate and position to answer.

7. Try a step that needs a human

   Now open the thermocycler lid.

   The thermocycler's owner marked open_lid as "a person must confirm", because the lid may be hot. In Claude Code you get a confirmation prompt from the server itself; in a harness without that feature, the agent asks you in the chat and only proceeds after you say yes. Either way the answer is written to the run log.

8. See the record

   Show me what happened in that run.

   The agent reads the run log and the run's output file (mhp_data) and lists every write, action and reading with timestamps. This is the record you would paste into a notebook.

Doing it on real instruments

1. Onboard your thermocycler (say "onboard my thermocycler"; serial or hand-operated needs no code) or add a community package. Keep the action name run_protocol with steps and cycles, and the recipe works unchanged.
2. Add your plate mover the same way. If you do not have one, onboard a "manual" arm: the agent will ask the operator to move the plate at steps 5, 6, 10 and 11 and wait.
3. Use "30 cycles" and let the agent run it in the background. Ask for the result when it is done, or ask it to notify you.

The recipe file

You do not need to read it, but it is openmhp/recipes/pcr_with_plate_transfer.py in the repository. The parameters the agent fills from your sentence:

PARAMS = {"arm": None, "thermocycler": None,        # None = pick an idle one by search
          "plate_slot": "deck_A1", "return_slot": "deck_A2",
          "steps": [{"temp": 95, "hold_s": 30}, {"temp": 58, "hold_s": 30}, {"temp": 72, "hold_s": 45}],
          "cycles": 30, "hold_c": 4}