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‎.pre-commit-config.yaml‎

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repos:
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- repo: local
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hooks:
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- id: make-format
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name: Run format
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entry: make format
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- id: ruff-format
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name: ruff format
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entry: ruff format
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language: system
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types: [python]
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files: ^pylabrobot/.*$
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- id: ruff-check
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name: ruff check
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entry: ruff check --fix
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language: system
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types: [python]
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files: ^pylabrobot/.*$
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- repo: https://github.com/crate-ci/typos

‎Makefile‎

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rm -rf docs/jupyter_execute
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rm -rf docs/user_guide/jupyter_execute
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TRACKED_PY = $(shell git ls-files 'pylabrobot/*.py' 'pylabrobot/*.ipynb')
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lint:
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$(BIN)python -m ruff check pylabrobot
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$(BIN)python -m ruff check $(TRACKED_PY)
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format:
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$(BIN)python -m ruff format pylabrobot
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$(BIN)python -m ruff check --fix pylabrobot --select I
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$(BIN)python -m ruff format $(TRACKED_PY)
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$(BIN)python -m ruff check --fix $(TRACKED_PY) --select I
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format-check:
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$(BIN)python -m ruff format --check pylabrobot
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$(BIN)python -m ruff check pylabrobot --select I
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$(BIN)python -m ruff format --check $(TRACKED_PY)
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$(BIN)python -m ruff check $(TRACKED_PY) --select I
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test:
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$(BIN)python -m pytest -s -v

‎docs/user_guide/00_liquid-handling/_liquid-handling.rst‎

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hamilton-prep/_hamilton-prep
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opentrons-ot2/hello-world
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tecan-evo/_tecan-evo
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plate-washing/plate-washing
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pumps/_pumps
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moving-channels-around
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tutorial_tip_inventory_consolidation

‎docs/user_guide/00_liquid-handling/plate-washing/biotek-el406.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# BioTek EL406\n",
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"\n",
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"The BioTek EL406 plate washer is controlled by the {class}`~pylabrobot.plate_washing.biotek.el406.BioTekEL406Backend` class. It communicates via FTDI USB serial.\n",
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"\n",
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"The EL406 has three fluid delivery subsystems — manifold, syringe pump, and peristaltic pump — plus an integrated plate shaker. All operations require a {class}`~pylabrobot.resources.Plate` object to configure plate-specific parameters automatically."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Setup"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from pylabrobot.plate_washing.biotek.el406 import ExperimentalBioTekEL406Backend\n",
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"from pylabrobot.resources import Cor_96_wellplate_360ul_Fb\n",
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"\n",
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"backend = ExperimentalBioTekEL406Backend() # ExperimentalBioTekEL406Backend(device_id=\"YOUR_FTDI_ID_HERE\")\n",
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"await backend.setup()\n",
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"\n",
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"plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Manifold\n",
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"\n",
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"The wash manifold is the primary fluid system. Prime the lines before use to fill tubing with buffer."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.manifold_prime(plate, volume=10000, buffer=\"A\") # 10 mL"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Dispense and aspirate individually, or use `manifold_wash` for repeated dispense-aspirate cycles."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.manifold_dispense(plate, volume=200, buffer=\"A\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.manifold_aspirate(plate)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.manifold_wash(plate, cycles=3, buffer=\"A\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"`manifold_wash` supports many options: shake/soak between cycles, secondary aspirate, bottom wash, and per-cycle pre-dispense."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.manifold_wash(\n",
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" plate,\n",
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" cycles=3,\n",
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" buffer=\"A\",\n",
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" dispense_volume=300,\n",
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" soak_duration=10,\n",
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" shake_duration=5,\n",
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" shake_intensity=\"Medium\",\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Run an auto-clean cycle to flush the manifold lines."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.manifold_auto_clean(plate, buffer=\"A\", duration=60)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Syringe pump\n",
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"\n",
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"The syringe pump provides precise low-volume dispensing."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.syringe_prime(plate, syringe=\"A\", volume=5000, flow_rate=5, refills=2)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.syringe_dispense(plate, volume=50, syringe=\"A\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Peristaltic pump"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.peristaltic_prime(plate, volume=300, flow_rate=\"High\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.peristaltic_dispense(plate, volume=100, flow_rate=\"High\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.peristaltic_purge(plate, volume=300, flow_rate=\"High\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Shaking"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.shake(plate, duration=30, intensity=\"Medium\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Batching\n",
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"\n",
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"Each step command automatically starts and cleans up a batch. To group multiple steps into a single batch (avoiding repeated start/cleanup overhead), use the `batch()` context manager."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"async with backend.batch(plate):\n",
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" await backend.manifold_prime(plate, volume=10000, buffer=\"A\")\n",
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" await backend.manifold_wash(plate, cycles=3, buffer=\"A\")\n",
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" await backend.manifold_aspirate(plate)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Queries"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.request_serial_number()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.request_washer_manifold()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.request_instrument_settings()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Teardown"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"await backend.stop()"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "env",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.25"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎docs/user_guide/00_liquid-handling/plate-washing/plate-washing.md‎

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# Plate Washing
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Plate washers automate the process of dispensing and aspirating wash buffers from microplates. They are commonly used in ELISA, cell-based assays, and other workflows that require repeated wash cycles.
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## Supported Plate Washers
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- BioTek EL406
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```{toctree}
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:maxdepth: 1
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:hidden:
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BioTek EL406 <biotek-el406>
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```

‎docs/user_guide/machines.md‎

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| Cole Parmer | Masterflex L/S 07522-20 07522-30 07551-20 07551-30 07575-30 07575-40 | Full | [PLR](https://docs.pylabrobot.org/user_guide/00_liquid-handling/pumps/cole-parmer-masterflex.html) / [OEM](https://www.masterflex.nl/assets/uploads/2017/09/07551-xx.pdf) |
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| Agrowtek | Pump Array | Full | [OEM](https://www.agrowtek.com/index.php/products/dosing_systems/dosing-pumps/agrowdose-adi-digital-persitaltic-dosing-pumps-detail) |
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### Plate Washers
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| Manufacturer | Machine | PLR-Support | Links |
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|--------------|---------|-------------|--------|
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| Agilent (BioTek) | EL406 | Mostly | [PLR](https://docs.pylabrobot.org/user_guide/00_liquid-handling/plate-washing/biotek-el406.html) / [OEM](https://www.agilent.com/en/product/microplate-instrumentation/microplate-washers-dispensers/biotek-el406-washer-dispenser-795212) |
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---
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## Material Handling

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