# Ntu Machines > Discover PUDA machine capabilities in ntu lab and choose the right machines for protocol generation. Use when you need to know more about a machine, how to use a machine, or how to generate commands and protocols for any PUDA-connected machine - Skill: `pudap/ntu-machines` (Agent Skill, multi-file: 9 files) - Install (CLI): `npx skillmds@latest add pudap/ntu-machines` - Raw SKILL.md: https://api.skillmd.com/api/skills/pudap/ntu-machines/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - Author: pudap (https://skillmd.com/u/pudap) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/pudap/ntu-machines --- # 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](references/first-machine.md) - 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](references/pipqubotv3-machine.md) - 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](references/biologic-machine.md) - 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](references/centrifuge-machine.md) - 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](references/dobot-m1pro-machine.md) - 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](references/balance-machine.md) - 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](references/opentrons-machine.md) - 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.