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  {
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   "source": [
    "# BioTek EL406\n",
    "\n",
    "The BioTek EL406 plate washer is controlled by the {class}`~pylabrobot.plate_washing.biotek.el406.BioTekEL406Backend` class. It communicates via FTDI USB serial.\n",
    "\n",
    "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."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.plate_washing.biotek.el406 import ExperimentalBioTekEL406Backend\n",
    "from pylabrobot.resources import Cor_96_wellplate_360ul_Fb\n",
    "\n",
    "backend = ExperimentalBioTekEL406Backend()  # ExperimentalBioTekEL406Backend(device_id=\"YOUR_FTDI_ID_HERE\")\n",
    "await backend.setup()\n",
    "\n",
    "plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Manifold\n",
    "\n",
    "The wash manifold is the primary fluid system. Prime the lines before use to fill tubing with buffer."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.manifold_prime(plate, volume=10000, buffer=\"A\")  # 10 mL"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Dispense and aspirate individually, or use `manifold_wash` for repeated dispense-aspirate cycles."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.manifold_dispense(plate, volume=200, buffer=\"A\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.manifold_aspirate(plate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.manifold_wash(plate, cycles=3, buffer=\"A\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`manifold_wash` supports many options: shake/soak between cycles, secondary aspirate, bottom wash, and per-cycle pre-dispense."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.manifold_wash(\n",
    "    plate,\n",
    "    cycles=3,\n",
    "    buffer=\"A\",\n",
    "    dispense_volume=300,\n",
    "    soak_duration=10,\n",
    "    shake_duration=5,\n",
    "    shake_intensity=\"Medium\",\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Run an auto-clean cycle to flush the manifold lines."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.manifold_auto_clean(plate, buffer=\"A\", duration=60)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Syringe pump\n",
    "\n",
    "The syringe pump provides precise low-volume dispensing."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.syringe_prime(plate, syringe=\"A\", volume=5000, flow_rate=5, refills=2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.syringe_dispense(plate, volume=50, syringe=\"A\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Peristaltic pump"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.peristaltic_prime(plate, volume=300, flow_rate=\"High\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.peristaltic_dispense(plate, volume=100, flow_rate=\"High\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.peristaltic_purge(plate, volume=300, flow_rate=\"High\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Shaking"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.shake(plate, duration=30, intensity=\"Medium\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Batching\n",
    "\n",
    "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."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "async with backend.batch(plate):\n",
    "    await backend.manifold_prime(plate, volume=10000, buffer=\"A\")\n",
    "    await backend.manifold_wash(plate, cycles=3, buffer=\"A\")\n",
    "    await backend.manifold_aspirate(plate)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Queries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.request_serial_number()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.request_washer_manifold()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.request_instrument_settings()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Teardown"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await backend.stop()"
   ]
  }
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