# Bears Machines > Discover PUDA machine capabilities at bears 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/bears-machines` (Agent Skill, multi-file: 6 files) - Install (CLI): `npx skillmds@latest add pudap/bears-machines` - Raw SKILL.md: https://api.skillmd.com/api/skills/pudap/bears-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/bears-machines --- # BEARS 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` ### 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` ### 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`, `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) discovered from the Opentrons driver labware catalogue and loaded through normal `load_labware` commands - 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) - Before any physical Opentrons run, load and follow [puda-opentrons-vision-validation](../puda-opentrons-vision-validation/SKILL.md): capture a fresh deck image, verify every protocol slot is occupied by the expected labware/item, and ask the user to confirm uncertain or mismatched labware before execution. - Run `puda machine commands opentrons` to understand available commands - Follow all command types, params, sequencing rules, and labware constraints in `references/opentrons-machine.md` ### Elephant Machine (`machine_id: "elephant"`) Use for **6-axis robot arm manipulation, Cartesian/joint motion, electric gripper actions, scan/reset flows, and camera-guided vision steps**. Capabilities: - Cartesian pose motion and relative moves - Joint-angle and single-axis motion controls - Scan positioning and reset-oriented recovery workflows - Electric gripper operations: `init_gripper`, `open_gripper`, `close_gripper` - Pi-camera and livestream image capture for vision-guided tasks - Pixel-to-robot offset conversion for calibrated camera workflows Use this machine when: - The task requires a robot arm to move to coordinates or execute pick-and-place style steps - The user asks for Elephant arm motion, scan/reset behavior, or arm recovery after stop/power loss - The workflow includes gripper control, Pi-camera capture, or livestream snapshot capture from the Elephant setup Before command generation: - Refer to: [elephant-machine](references/elephant.md) - Run `puda machine commands elephant` to understand available commands - Follow motion, gripper, camera, and sequencing constraints in `references/elephant.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 - `opentrons` protocols must always end with no tip attached to any pipette. - `opentrons` deck slot (`location`) for every `load_labware` command must be explicitly confirmed by the user - **never assume a slot**. - Before any physical `opentrons` run, perform vision validation of deck-slot occupation/labware; do not run if a required slot is empty, mismatched, obstructed, or not visible unless the user explicitly approves. - `opentrons` `capture_image` must be its own standalone protocol - never combined with pipetting commands in the same protocol. - `balance` - always call `startup()` before reading and `shutdown()` after. Always tare before a dispense step. Always verify `fresh == True` before using a reading. - `elephant` - ensure the arm is connected and powered before motion. For electric gripper workflows after a power cycle, call `init_gripper()` before `open_gripper()` or `close_gripper()`. Prefer `scan()` before camera-guided work.