Lab Instruments¶

A Rhylthyme program can drive lab instruments: a step names a tool and what to send it, and the runner (rhylthyme run --workcell) sends it at the right moment, ends the step on the instrument's reply or its own timer, and records every call and reply. Instruments run simulated unless you ask for a live run.

Two families of instruments are supported, each through its own package:

Workcells¶

Programs name tools by role ("tool": "balance"). A local workcell file says what each tool is and where it is; it never leaves the lab machine, and Rhylthyme scrubs its addresses from everything it publishes. One workcell can mix both families:

{
  "id": "bench-1",
  "tools": [
    { "name": "balance", "driver": "labmcp", "server": "mettler-toledo",
      "address": "/dev/ttyUSB0", "limits": { "max_series_duration_s": 300 } },
    { "name": "shaker", "type": "bioshake", "host": "localhost", "port": 50710 }
  ]
}

"driver": "labmcp" tools are LabMCP servers; tools without a driver are galago-tools tools.

Instrument steps¶

The full reference is the program schema's instrument.

{ "stepId": "tare", "name": "Tare the balance",
  "instrument": { "tool": "balance", "command": "tare" },
  "startTrigger": { "type": "programStart" } }

With command, the step sends one call when it starts and ends when the instrument replies. A step can also send phase actions, each {command, params, tool?}:

• start: in order when the step starts (and again on retry);
• until: one call whose reply ends the step, instead of command;
• end: in order when the step ends, by timer, by the operator or on a reply;
• onAbort: if the step fails or the run is aborted, instead of the default safe stops.

{ "stepId": "heat-stir", "name": "Heat to 40 °C and stir for 2 minutes",
  "duration": { "type": "fixed", "seconds": 120 },
  "instrument": { "tool": "stirrer",
    "start": [ { "command": "set_temperature", "params": { "temperature_c": 40 } },
               { "command": "start_heating" }, { "command": "start_stirring" } ],
    "end":   [ { "command": "stop_heating" } ] } }

An action may name another tool; the step holds every tool it names.

Checking and planning¶

rhylthyme validate program.json --workcell lab.json
rhylthyme plan program.json planned.json --workcell lab.json

validate checks every call against the instrument's own definition (galago commands; LabMCP's catalogue of every server's tools, input schemas and limits), the workcell's limits and command policies. Without a workcell, a step that names its toolType (bioshake, labmcp-ika) is checked the same way, also by the hosted MCP server. A step that ends on a reply and has no duration is planned with an estimate from its params, flagged in metadata.durationEstimate and drawn with ≈ on timelines.

Running safely¶

• Limits in the workcell are enforced by the instrument's server: it refuses any request beyond them, with nothing sent.
• When a step fails, its onAbort actions are sent, or else each touched instrument's default stops (for LabMCP, its safety tools: stop, terminate, outputs off). Then the operator retries, marks it done or aborts.
• Aborting a run, or quitting it part-way, stops every instrument it used.
• Pausing the schedule pauses instruments that can hold their work.
• Live runs (--live) show a pre-flight first, with each instrument's identity, mode and limits and every hazardous action, refuse to start unless every instrument is ready, and need you to type live.

Every call, reply and stop is in the run record.

From rhylthyme.com¶

rhylthyme bridge program.json --workcell lab.json runs a program and shows it live on your Bridges page, where you can pause, resume, retry or skip a failed step and abort. rhylthyme bridge --workcell lab.json waits for runs started from the page. Addresses never leave the lab machine.