PUDA Machines

Goal

Provide machine-selection and capability guidance for PUDA workflows, then load the correct machine reference before generating commands.

Critical Rule

If you are unsure which machine should be used for a command, ask the user before proceeding.
Do not assume.

Machine Capabilities and When to Use

First Machine (machine_id: "first")

Use for liquid handling and deck operations.

Capabilities:

• Pipetting workflows: aspirate, dispense, attach tip, drop tip
• Deck and labware workflows: load deck, position-dependent operations
• Sequenced robotic handling steps in wet-lab protocols

Use this machine when:

• The task is about moving liquids between wells/labware
• The user mentions tip usage, aspiration/dispensing, or deck slots/labware setup

Before command generation:

• Refer to: first-machine
• Run puda machine commands first to understand available commands
• Follow constraints and sequencing in references/first-machine.md

PipQuBotV3 Machine (machine_id: "pipqubotv3")

Use for liquid handling and deck operations.

Capabilities:

• Pipetting workflows: aspirate, dispense, attach tip, drop tip
• Deck and labware workflows: load deck, position-dependent operations
• Sequenced robotic handling steps in wet-lab protocols

Use this machine when:

• The task is about moving liquids between wells/labware
• The user mentions tip usage, aspiration/dispensing, or deck slots/labware setup

Before command generation:

• Refer to: pipqubotv3-machine
• Run puda machine commands pipqubotv3 to understand available commands
• Follow constraints and sequencing in references/pipqubotv3-machine.md

Biologic Machine (machine_id: "biologic")

Use for electrochemical testing and characterization.

Capabilities:

• OCV (Open Circuit Voltage)
• CA (Chronoamperometry)
• PEIS / GEIS (Impedance spectroscopy)
• CV (Cyclic Voltammetry)
• MPP variants (MPP, MPP_Cycles, MPP_Tracking)

Use this machine when:

• The task is an electrochemical measurement or battery/cell characterization
• The user asks for OCV, CA, EIS, CV, or MPP tests

Before command generation:

• Refer to: biologic-machine
• Run puda machine commands biologic to understand available commands
• Follow constraints in references/biologic-machine.md

Centrifuge Machine (machine_id: "centrifuge")

Use for centrifugation, spin-downs, and phase or pellet separation.

Capabilities:

• Sample spin-downs before or after handling steps
• Separation workflows based on centrifugal force
• Pelleting, clarification, and phase-separation preparation steps

Use this machine when:

• The user asks to centrifuge, spin, spin down, pellet, or clarify samples

Before command generation:

• Refer to: centrifuge-machine
• Run puda machine commands centrifuge to understand available commands
• Follow constraints in references/centrifuge-machine.md

Dobot M1Pro Machine (machine_id: "dobot-m1pro")

Use for gripper-based tube transfers between fixed positions.

Capabilities:

• Pick-and-place tube handling with a gripper
• Moving tubes between predefined source and destination positions
• Position-based transfer steps between pipqubotv3, bioshake, centrifuge machines

Use this machine when:

• The user asks to transfer tubes with a gripper
• The workflow involves moving tubes between known hardcoded positions
• A step references Dobot M1Pro positions such as centrifuge tube or MTP coordinates

Before command generation:

• Refer to: dobot-m1pro-machine
• Run puda machine commands dobot-m1pro to understand available commands
• Follow constraints in references/dobot-m1pro-machine.md

BioShake Machine (machine_id: "bioshake")

Use for shaking, heating, and plate clamping operations.

Capabilities:

• Shaking at a specified RPM for a given duration
• Heating (or cooling) to a target temperature and holding for a given duration
• Clamping and unclamping plates on the shaker
• Homing the shaker to its locked home position

Use this machine when:

• The user asks to shake, vortex, or mix a plate on a shaker
• The user asks to heat or incubate a plate at a specific temperature
• The user asks to clamp or unclamp a plate on the BioShake
• The workflow requires holding a plate at temperature while shaking

Before command generation:

• Run puda machine commands bioshake to understand available commands

Balance Machine

Use for gravimetric mass measurement via an Arduino-based USB load-cell balance on Linux.

Capabilities:

• Continuous calibrated mass readings from a load-cell over USB serial (/dev/ttyUSB* or /dev/ttyACM*)
• Background reader thread streaming readings at ~4 Hz; no polling required
• Tare command to zero the balance before a dispense step
• Freshness check (fresh flag) to detect stale/disconnected readings
• NATS telemetry publishing via the edge service
• Custom calibration CSV support

Use this machine when:

• The workflow requires weighing a container before or after a liquid transfer
• The user asks for gravimetric calibration, transfer error calculation, or balance feedback
• The task involves viscosity or transfer accuracy experiments needing mass data

Before use:

• Refer to: balance-machine
• Ask the user for the Linux serial port (/dev/ttyUSB1, etc.) — do not assume
• Ensure the edge service is running (uv run --package balance-edge python edge/balance.py)

Opentrons Machine (machine_id: "opentrons")

Use for automated liquid handling and full protocol generation on the Opentrons OT-2 robot.

Capabilities:

• Full protocol code generation via Protocol.to_python_code() — produces valid runnable OT-2 Python
• Pipetting workflows: aspirate, dispense, mix, transfer (with auto-chunking for large volumes)
• Tip management: pick_up_tip, drop_tip
• Deck and labware setup: load_labware, load_instrument
• Flow control: flow_rate, air_gap, blow_out, touch_tip, move_to
• Protocol utilities: delay, comment, home
• CSV-driven loops: read_csv_file + loop for data-driven protocols
• Custom labware support: AMDM mass balance vials (30 mL, 50 mL) loaded inline
• All gen2 pipette types: p10, p20, p300, p1000 (single and multi-channel)
• External camera image capture: camera_capture — triggers the external camera mounted above the deck to capture and save a still image of the wellplate

Use this machine when:

• The user references an Opentrons OT-2 robot
• The task involves generating a complete OT-2 protocol or individual liquid handling commands
• The user mentions Opentrons labware (tip racks, well plates, reservoirs, NEST, Corning, mass balance vials)
• The workflow requires data-driven dispensing from a CSV file
• The workflow requires capturing a camera image of the wellplate after dispensing steps

Before command generation:

• Refer to: opentrons-machine
• Run puda machine commands opentrons to understand available commands
• Follow all command types, params, sequencing rules, and labware constraints in references/opentrons-machine.md

Selection Workflow

1. Parse user intent and identify the tasks.
2. Match intent to the machine capabilities above.
3. If machine selection is unclear or ambiguous, ask the user and wait for confirmation.
4. Load the corresponding reference file and CLI help.
5. Generate commands only after machine choice is confirmed.

Output Guidance

When answering machine-selection questions:

• State the recommended machine and a one-line reason tied to capability.
• If uncertain, ask a direct clarification question instead of guessing.

Critical sequencing rules

1. bioshake must not be shaking while any machine is operating on a Bioshake position.
2. centrifuge must not be spinning while any machine is operating on a Centrifuge position.
3. opentrons protocols must always end with no tip attached to any pipette.
4. opentrons deck slot (location) for every load_labware command must be explicitly confirmed by the user — never assume a slot.
5. opentrons capture_image must be its own standalone protocol — never combined with pipetting commands in the same protocol.
6. balance — always call startup() before reading and shutdown() after. Always tare before a dispense step. Always verify fresh == True before using a reading.