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

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

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

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.