{ "cells": [ { "cell_type": "code", "execution_count": null, "id": "975c5ac2", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "๐ŸŽ“ Academic mode: Using all datasets (including non-commercial)\n", "\n", "==================================================\n", "๐Ÿ”ง BIOMNI CONFIGURATION\n", "==================================================\n", "๐Ÿ“‹ DEFAULT CONFIG (Including Database LLM):\n", " Path: ./data\n", " Timeout Seconds: 600\n", " Llm: claude-sonnet-4-5\n", " Temperature: 0.7\n", " Use Tool Retriever: True\n", " Commercial Mode: Academic (all datasets)\n", "==================================================\n", "\n", "Checking and downloading missing data lake files...\n", "Using prompt-based retrieval with the agent's LLM\n", "================================\u001b[1m Human Message \u001b[0m=================================\n", "\n", "Can you generate a script to use PyLabRobot to move water from one range of wells to another using the Hamilton STAR backend?\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "I'll help you generate a PyLabRobot script to move water from one range of wells to another using the Hamilton STAR backend. Let me start by reviewing the PyLabRobot documentation and then create a working script.\n", "\n", "## Plan:\n", "1. [ ] Review PyLabRobot liquid handling documentation\n", "2. [ ] Create a script that moves water between well ranges using Hamilton STAR\n", "3. [ ] Test the script to ensure it's valid\n", "4. [ ] Provide the final working script\n", "\n", "Let me start:\n", "\n", "\n", "from biomni.tool.lab_automation import get_pylabrobot_documentation_liquid\n", "\n", "# Get the liquid handling documentation\n", "liquid_docs = get_pylabrobot_documentation_liquid()\n", "print(\"PyLabRobot Liquid Handling Documentation:\")\n", "print(\"=\" * 80)\n", "print(liquid_docs)\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "The output is too long to be added to context. Here are the first 10K characters...\n", "PyLabRobot Liquid Handling Documentation:\n", "================================================================================\n", "Notes:\n", "- Use hamilton_96_tiprack_1000uL_filter instead of HTF (deprecated). Note the capital L in uL.\n", "- Use Cor_96_wellplate_360ul_Fb instead of Corning_96_wellplate_360ul_Fb.\n", "- You must name all your plates, tip racks, and carriers.\n", "- Assign labware into carriers via slot assignment (tip_car[0] = tiprack). Assign plates to rails using lh.deck.assign_child_resource(plate_car, rails=14).\n", "- Rails must be between -4 and 32.\n", "- Make sure most liquid handling operations are done with async/await.\n", "- There are some methods that are not async, including lh.summary(). Do not use await for these methods.\n", "- When picking up tips with multiple channels, use a flat list of tips. Do not use a list of lists. ## Getting started with liquid handling on a Hamilton STAR(let)\n", "\n", "# Getting started with liquid handling on a Hamilton STAR(let)\n", "\n", "In this notebook, you will learn how to use PyLabRobot to move water from one range of wells to another.\n", "\n", "**Note: before running this notebook, you should have**:\n", "\n", "- Installed PyLabRobot and the USB driver as described in [the installation guide](../../_getting-started/installation).\n", "- Connected the Hamilton to your computer using the USB cable.\n", "\n", "Video of what this code does:\n", "\n", "\n", "\n", "## Setting up a connection with the robot\n", "\n", "Start by importing the {class}`~pylabrobot.liquid_handling.liquid_handler.LiquidHandler` class, which will serve as a front end for all liquid handling operations.\n", "\n", "Backends serve as communicators between `LiquidHandler`s and the actual hardware. Since we are using a Hamilton STAR, we also import the {class}`~pylabrobot.liquid_handling.backends.STAR_backend.STARBackend` backend.\n", "\n", "Code refs:\n", "from pylabrobot.liquid_handling import LiquidHandler\n", "from pylabrobot.liquid_handling.backends import STARBackend\n", "\n", "In addition, import the {class}`~pylabrobot.resources.hamilton.STARLetDeck`, which represents the deck of the Hamilton STAR.\n", "\n", "Code refs:\n", "from pylabrobot.resources.hamilton import STARLetDeck\n", "\n", "Create a new liquid handler using `STARBackend` as its backend.\n", "\n", "The final step is to open communication with the robot. This is done using the {func}`~pylabrobot.liquid_handling.LiquidHandler.setup` method.\n", "\n", "## Creating the deck layout\n", "\n", "Now that we have a `LiquidHandler` instance, we can define the deck layout.\n", "\n", "The layout in this tutorial will contain five sets of standard volume tips with filter, 1 set of 96 1mL wells, and tip and plate carriers on which these resources are positioned.\n", "\n", "Start by importing the relevant objects and variables from the PyLabRobot package. This notebook uses the following resources:\n", "\n", "- {class}`~pylabrobot.resources.hamilton.tip_carriers.TIP_CAR_480_A00` tip carrier\n", "- {class}`~pylabrobot.resources.hamilton.plate_carriers.PLT_CAR_L5AC_A00` plate carrier\n", "- {class}`~pylabrobot.resources.corning_costar.plates.Cor_96_wellplate_360ul_Fb` wells\n", "- {class}`~pylabrobot.resources.hamilton.tip_racks.hamilton_96_tiprack_1000ul_filter` tips\n", "\n", "Code refs:\n", "from pylabrobot.resources import (\n", "\n", "Then create a tip carrier named `tip carrier`, which will contain tip rack at all 5 positions. These positions can be accessed using `tip_car[x]`, and are 0 indexed.\n", "\n", "Use {func}`~pylabrobot.resources.abstract.assign_child_resources` to assign the tip carrier to the deck of the liquid handler. All resources contained by this carrier will be assigned automatically.\n", "\n", "In the `rails` parameter, we can pass the location of the tip carrier. The locations of the tips will automatically be calculated.\n", "\n", "Repeat this for the plates.\n", "\n", "Let's look at a summary of the deck layout using {func}`~pylabrobot.liquid_handling.LiquidHandler.summary`.\n", "\n", "## Picking up tips\n", "\n", "Picking up tips is as easy as querying the tips from the tiprack.\n", "\n", "## Aspirating and dispensing\n", "\n", "Aspirating and dispensing work similarly to picking up tips: where you use booleans to specify which tips to pick up, with aspiration and dispensing you use floats to specify the volume to aspirate or dispense in $\\mu L$.\n", "\n", "The cells below move liquid from wells `'A1:C1'` to `'D1:F1'` using channels 1, 2, and 3 using the {func}`~pylabrobot.liquid_handling.LiquidHandler.aspirate` and {func}`~pylabrobot.liquid_handling.LiquidHandler.dispense` methods.\n", "\n", "After the liquid has been aspirated, dispense it in the wells below. Note that while we specify different wells, we are still using the same channels. This is needed because only these channels contain liquid, of course.\n", "\n", "Let's move the liquid back to the original wells.\n", "\n", "## Dropping tips\n", "\n", "Finally, you can drop tips anywhere on the deck by using the {func}`~pylabrobot.liquid_handling.LiquidHandler.drop_tips` method.\n", "\n", "## iSWAP Module\n", "\n", "# Adjust iSWAP gripper parallelity\n", "\n", "The steel pointy bits at the end of the iSWAP grippers are intended to be the primary points of contact with a plate.\n", "\n", "They physically deform plastic, leading to a repeatable secure grip.\n", "\n", "Over time, the aluminum fingers leading up to the metal grippers can begin to angle outward, leaving the grip narrower toward the back of the iSWAP hand and wider at the steel pointy bits.\n", "\n", "In iSWAPs with this calibration issue, a plate can accidentally be picked up using force primarily through the smooth aluminum fingers instead of the steel pointy bits. This predisposes the plate to pivot around the smooth fingers, rotating downwards and causing catastrophic plate crashes to external hotel locations when it fails.\n", "\n", "In our testing, improper grips can be reliable for hundreds of pick/place operations, but fail after thousands. To achieve robust operation, physical adjustment is required.\n", "\n", "![](./img/adjust-iswap-gripper/before-after.jpg)\n", "\n", "## Tools\n", "- 1.5mm hex key\n", "- 2.5mm hex key\n", "\n", "## Step-by-step hardware adjustment guide\n", "\n", "Loosen by <1 turn the 4 adjustment screws (1.5mm hex) on top of the iSWAP hand corresponding to the right gripper finger. Do not fully remove the screws. This frees the slider bearing to rotate around the Z axis.\n", "\n", "There should be ~1mm of play at the end of the finger.\n", "\n", "Narrow the angle of the finger and retighten these 4 screws.\n", "\n", "A bit of force may be required initially to unstick/free the bearing to rotate, but not enough force to bend the aluminum.\n", "\n", "Remove 2 screws (2.5mm hex) holding the data wire in place on the left gripper finger. This exposes the other 4 adjustment screws. Repeat the process for these 4.\n", "\n", "![](./img/adjust-iswap-gripper/rotate-slider-bearing.jpg)\n", "\n", "\n", "You may need to run the Hamilton [iSWAP calibration macro](adjusting-iswap.md) to recalibrate grip width after making these changes, however in our testing hotel coordinate locations are altered <1mm by the physical adjustment of gripper parallelity.\n", "\n", "\n", "## Liquid level detection on Hamilton STAR(let)\n", "\n", "# Liquid level detection on Hamilton STAR(let)\n", "\n", "Liquid level detection (LLD) is a feature that allows the Hamilton STAR(let) to move the pipetting tip down slowly until a liquid is found using either a) the pressure sensor, or b) a change in capacitance, or c) both. This feature is useful if you want to aspirate or dispense at a distance relative to the liquid surface, but you don't know the exact height of the liquid in the container.\n", "\n", "To use LLD, you need to specify the LLD mode when calling the `aspirate` or `dispense` methods. Here is how you can use pressure or capacative LLD with the `aspirate` :\n", "\n", "```python\n", "await lh.aspirate([tube], vols=[300], lld_mode=[STARBackend.LLDMode.GAMMA])\n", "```\n", "\n", "The `lld_mode` parameter can be one of the following:\n", "\n", "- `STARBackend.LLDMode.OFF`: default, no LLD\n", "- `STARBackend.LLDMode.GAMMA`: capacative LLD\n", "- `STARBackend.LLDMode.PRESSURE`: pressure LLD\n", "- `STARBackend.LLDMode.DUAL`: both capacative and pressure LLD\n", "- `STARBackend.LLDMode.Z_TOUCH_OFF`: find the bottom of the container\n", "\n", "The `lld_mode` parameter is a list, so you can specify a different LLD mode for each channel.\n", "\n", "```{note}\n", "The `lld_mode` parameter is only available when using the `STAR` backend.\n", "```\n", "\n", "## Catching errors\n", "\n", "All channelized pipetting operations raise a `ChannelizedError` exception when an error occurs, so that we can have specific error handling for each channel.\n", "\n", "When no liquid is found in the container, the channel will have a `TooLittleLiquidError` error. This is useful for detecting that your container is empty.\n", "\n", "You can catch the error like this:\n", "\n", "```python\n", "from pylabrobot.liquid_handling.errors import ChannelizedError\n", "from pylabrobot.resources.errors import TooLittleLiquidError\n", "channel = 0\n", "try:\n", " await lh.aspirate([tube], vols=[300], lld_mode=[STARBackend.LLDMode.GAMMA], use_channels=[channel])\n", "except ChannelizedError as e:\n", " if isinstance(e.errors[channel], TooLittleLiquidError):\n", " print(\"Too little liquid in tube\")\n", "```\n", "\n", "\n", "## Z-probing\n", "\n", "# Z-probing\n", "\n", "With PyLabRobot, one can probe the surface of any object on a STAR(let) deck. This effectively makes the STAR act as a [Coordinate-Measurement Machine (CMM)](https://en.wikipedia.org/wiki/Coordinate-measuring_machine).\n", "\n", "There are two ways to probe the surface of an object:\n", "\n", "- Using capacitive liquid level sensors (cLLD) to map capacitive objects.\n", "- Moving the tip down onto an object until resistance is detected (a \"controlled crash\"), which works with both capacitive and non-capacitive objects.\n", "\n", "## Example setup\n", "\n", "Code refs:\n", "from pylabrobot.liquid_handling import LiquidHandler, STARBackend\n", "from pylabrobot.resources import STARLetDeck\n", "from pylabrobot.resources import (\n", "\n", "## Capacitive probing using cLLD\n", "\n", "If you are mapping a capacitive surface, you can use the cLLD sensor to detect the surface. This is safer and more accurate than the controlled crash method.\n", "\n", "```{warning}\n", "For safety purposes, we recommend using Hamilton 50ul tips for mapping surfaces. These \n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "\n", "# Now let's create a comprehensive script for moving water between well ranges\n", "script_content = '''\n", "\"\"\"\n", "PyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\n", "This script demonstrates liquid transfer between well ranges on a 96-well plate.\n", "\"\"\"\n", "\n", "from pylabrobot.liquid_handling import LiquidHandler\n", "from pylabrobot.liquid_handling.backends import STARBackend\n", "from pylabrobot.resources.hamilton import STARLetDeck\n", "from pylabrobot.resources import (\n", " TIP_CAR_480_A00,\n", " PLT_CAR_L5AC_A00,\n", " Cor_96_wellplate_360ul_Fb,\n", " hamilton_96_tiprack_1000uL_filter\n", ")\n", "\n", "async def main():\n", " # Initialize the liquid handler with Hamilton STAR backend\n", " lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\n", " \n", " # Setup connection to the robot\n", " await lh.setup()\n", " \n", " print(\"Setting up deck layout...\")\n", " \n", " # Create tip carrier and add tip racks\n", " tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n", " tip_car[0] = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\n", " tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\n", " tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\n", " tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\n", " tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\n", " \n", " # Assign tip carrier to deck at rails 1\n", " lh.deck.assign_child_resource(tip_car, rails=1)\n", " \n", " # Create plate carrier and add a 96-well plate\n", " plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\n", " plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n", " plate_car[0] = plate\n", " \n", " # Assign plate carrier to deck at rails 14\n", " lh.deck.assign_child_resource(plate_car, rails=14)\n", " \n", " # Display deck summary\n", " print(\"\\\\nDeck layout:\")\n", " print(lh.summary())\n", " \n", " # Define source and destination well ranges\n", " source_wells = \"A1:A3\" # Wells A1, A2, A3\n", " destination_wells = \"A4:A6\" # Wells A4, A5, A6\n", " \n", " print(f\"\\\\nMoving water from {source_wells} to {destination_wells}...\")\n", " \n", " # Pick up tips from the first three positions\n", " tips = tip_car[0][source_wells]\n", " await lh.pick_up_tips(tips)\n", " print(\"Tips picked up successfully\")\n", " \n", " # Aspirate liquid from source wells\n", " volume = 100 # microliters\n", " source = plate[source_wells]\n", " await lh.aspirate(source, vols=[volume, volume, volume])\n", " print(f\"Aspirated {volume} ยตL from {source_wells}\")\n", " \n", " # Dispense liquid to destination wells\n", " destination = plate[destination_wells]\n", " await lh.dispense(destination, vols=[volume, volume, volume])\n", " print(f\"Dispensed {volume} ยตL to {destination_wells}\")\n", " \n", " # Drop tips back to the tip rack\n", " await lh.drop_tips(tips)\n", " print(\"Tips dropped successfully\")\n", " \n", " print(\"\\\\nLiquid transfer complete!\")\n", " \n", " # Stop the liquid handler\n", " await lh.stop()\n", " print(\"Connection closed\")\n", "\n", "# Run the async main function\n", "if __name__ == \"__main__\":\n", " import asyncio\n", " asyncio.run(main())\n", "'''\n", "\n", "print(\"Generated PyLabRobot Script:\")\n", "print(\"=\" * 80)\n", "print(script_content)\n", "print(\"=\" * 80)\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "Generated PyLabRobot Script:\n", "================================================================================\n", "\n", "\"\"\"\n", "PyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\n", "This script demonstrates liquid transfer between well ranges on a 96-well plate.\n", "\"\"\"\n", "\n", "from pylabrobot.liquid_handling import LiquidHandler\n", "from pylabrobot.liquid_handling.backends import STARBackend\n", "from pylabrobot.resources.hamilton import STARLetDeck\n", "from pylabrobot.resources import (\n", " TIP_CAR_480_A00,\n", " PLT_CAR_L5AC_A00,\n", " Cor_96_wellplate_360ul_Fb,\n", " hamilton_96_tiprack_1000uL_filter\n", ")\n", "\n", "async def main():\n", " # Initialize the liquid handler with Hamilton STAR backend\n", " lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\n", " \n", " # Setup connection to the robot\n", " await lh.setup()\n", " \n", " print(\"Setting up deck layout...\")\n", " \n", " # Create tip carrier and add tip racks\n", " tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n", " tip_car[0] = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\n", " tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\n", " tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\n", " tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\n", " tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\n", " \n", " # Assign tip carrier to deck at rails 1\n", " lh.deck.assign_child_resource(tip_car, rails=1)\n", " \n", " # Create plate carrier and add a 96-well plate\n", " plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\n", " plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n", " plate_car[0] = plate\n", " \n", " # Assign plate carrier to deck at rails 14\n", " lh.deck.assign_child_resource(plate_car, rails=14)\n", " \n", " # Display deck summary\n", " print(\"\\nDeck layout:\")\n", " print(lh.summary())\n", " \n", " # Define source and destination well ranges\n", " source_wells = \"A1:A3\" # Wells A1, A2, A3\n", " destination_wells = \"A4:A6\" # Wells A4, A5, A6\n", " \n", " print(f\"\\nMoving water from {source_wells} to {destination_wells}...\")\n", " \n", " # Pick up tips from the first three positions\n", " tips = tip_car[0][source_wells]\n", " await lh.pick_up_tips(tips)\n", " print(\"Tips picked up successfully\")\n", " \n", " # Aspirate liquid from source wells\n", " volume = 100 # microliters\n", " source = plate[source_wells]\n", " await lh.aspirate(source, vols=[volume, volume, volume])\n", " print(f\"Aspirated {volume} ยตL from {source_wells}\")\n", " \n", " # Dispense liquid to destination wells\n", " destination = plate[destination_wells]\n", " await lh.dispense(destination, vols=[volume, volume, volume])\n", " print(f\"Dispensed {volume} ยตL to {destination_wells}\")\n", " \n", " # Drop tips back to the tip rack\n", " await lh.drop_tips(tips)\n", " print(\"Tips dropped successfully\")\n", " \n", " print(\"\\nLiquid transfer complete!\")\n", " \n", " # Stop the liquid handler\n", " await lh.stop()\n", " print(\"Connection closed\")\n", "\n", "# Run the async main function\n", "if __name__ == \"__main__\":\n", " import asyncio\n", " asyncio.run(main())\n", "\n", "================================================================================\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "Now let me update the plan and test the script:\n", "\n", "## Updated Plan:\n", "1. [โœ“] Review PyLabRobot liquid handling documentation\n", "2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\n", "3. [ ] Test the script to ensure it's valid\n", "4. [ ] Provide the final working script\n", "\n", "\n", "from biomni.tool.lab_automation import test_pylabrobot_script\n", "\n", "# Test the generated script\n", "print(\"Testing the PyLabRobot script...\")\n", "print(\"=\" * 80)\n", "test_result = test_pylabrobot_script(\n", " script_input=script_content,\n", " enable_tracking=False,\n", " timeout_seconds=60\n", ")\n", "print(\"\\nTest Result:\")\n", "print(test_result)\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "Testing the PyLabRobot script...\n", "================================================================================\n", "Setting up the liquid handler.\n", "Resource deck was assigned to the liquid handler.\n", "Resource trash was assigned to the liquid handler.\n", "Resource trash_core96 was assigned to the liquid handler.\n", "Resource waste_block was assigned to the liquid handler.\n", "Setting up deck layout...\n", "Resource tip carrier was assigned to the liquid handler.\n", "Resource plate carrier was assigned to the liquid handler.\n", "\n", "Deck layout:\n", "Rail Resource Type Coordinates (mm)\n", "=================================================================================\n", "(-6) โ”œโ”€โ”€ trash_core96 Trash (-58.200, 106.000, 229.000)\n", " โ”‚\n", "(1) โ”œโ”€โ”€ tip carrier TipCarrier (100.000, 063.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ tips_1 TipRack (106.200, 073.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_2 TipRack (106.200, 169.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_3 TipRack (106.200, 265.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_4 TipRack (106.200, 361.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_5 TipRack (106.200, 457.000, 214.950)\n", " โ”‚\n", "(14) โ”œโ”€โ”€ plate carrier PlateCarrier (392.500, 063.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ plate Plate (396.500, 071.500, 183.120)\n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚\n", "(31) โ”œโ”€โ”€ waste_block Resource (775.000, 115.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ teaching_tip_rack TipRack (780.900, 461.100, 100.000)\n", " โ”‚\n", "(32) โ”œโ”€โ”€ trash Trash (800.000, 190.600, 137.100)\n", "\n", "None\n", "\n", "Moving water from A1:A3 to A4:A6...\n", "\n", "Test Result:\n", "{'success': False, 'test_results': {'syntax_valid': True, 'imports_valid': True, 'simulation_successful': False, 'tracking_enabled': False, 'input_type': 'string'}, 'execution_summary': {'operations_performed': 0, 'tips_used': 0, 'liquid_transferred': 0.0, 'execution_time': 0.0, 'total_execution_time': 0.40647315979003906}, 'errors': [\"Script execution failed: Script execution error: 'ResourceHolder' object is not subscriptable\"], 'warnings': []}\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "I see the issue. The script has a problem with how we're accessing the wells. Let me fix this:\n", "\n", "## Updated Plan:\n", "1. [โœ“] Review PyLabRobot liquid handling documentation\n", "2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\n", "3. [โœ—] Test the script to ensure it's valid (failed - need to fix well access syntax)\n", "4. [ ] Fix the script based on test results\n", "5. [ ] Re-test the fixed script\n", "6. [ ] Provide the final working script\n", "\n", "\n", "# Fix the script - the issue is with how we access wells from tip racks and plates\n", "fixed_script = '''\n", "\"\"\"\n", "PyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\n", "This script demonstrates liquid transfer between well ranges on a 96-well plate.\n", "\"\"\"\n", "\n", "from pylabrobot.liquid_handling import LiquidHandler\n", "from pylabrobot.liquid_handling.backends import STARBackend\n", "from pylabrobot.resources.hamilton import STARLetDeck\n", "from pylabrobot.resources import (\n", " TIP_CAR_480_A00,\n", " PLT_CAR_L5AC_A00,\n", " Cor_96_wellplate_360ul_Fb,\n", " hamilton_96_tiprack_1000uL_filter\n", ")\n", "\n", "async def main():\n", " # Initialize the liquid handler with Hamilton STAR backend\n", " lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\n", " \n", " # Setup connection to the robot\n", " await lh.setup()\n", " \n", " print(\"Setting up deck layout...\")\n", " \n", " # Create tip carrier and add tip racks\n", " tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n", " tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\n", " tip_car[0] = tiprack\n", " tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\n", " tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\n", " tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\n", " tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\n", " \n", " # Assign tip carrier to deck at rails 1\n", " lh.deck.assign_child_resource(tip_car, rails=1)\n", " \n", " # Create plate carrier and add a 96-well plate\n", " plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\n", " plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n", " plate_car[0] = plate\n", " \n", " # Assign plate carrier to deck at rails 14\n", " lh.deck.assign_child_resource(plate_car, rails=14)\n", " \n", " # Display deck summary\n", " print(\"\\\\nDeck layout:\")\n", " print(lh.summary())\n", " \n", " # Define source and destination well ranges\n", " source_wells = \"A1:A3\" # Wells A1, A2, A3\n", " destination_wells = \"A4:A6\" # Wells A4, A5, A6\n", " \n", " print(f\"\\\\nMoving water from {source_wells} to {destination_wells}...\")\n", " \n", " # Pick up tips - access tips from the tiprack directly\n", " tips = tiprack[source_wells]\n", " await lh.pick_up_tips(tips)\n", " print(\"Tips picked up successfully\")\n", " \n", " # Aspirate liquid from source wells\n", " volume = 100 # microliters\n", " source = plate[source_wells]\n", " await lh.aspirate(source, vols=[volume, volume, volume])\n", " print(f\"Aspirated {volume} ยตL from {source_wells}\")\n", " \n", " # Dispense liquid to destination wells\n", " destination = plate[destination_wells]\n", " await lh.dispense(destination, vols=[volume, volume, volume])\n", " print(f\"Dispensed {volume} ยตL to {destination_wells}\")\n", " \n", " # Drop tips back to the tip rack\n", " await lh.drop_tips(tips)\n", " print(\"Tips dropped successfully\")\n", " \n", " print(\"\\\\nLiquid transfer complete!\")\n", " \n", " # Stop the liquid handler\n", " await lh.stop()\n", " print(\"Connection closed\")\n", "\n", "# Run the async main function\n", "if __name__ == \"__main__\":\n", " import asyncio\n", " asyncio.run(main())\n", "'''\n", "\n", "print(\"Fixed PyLabRobot Script:\")\n", "print(\"=\" * 80)\n", "print(fixed_script)\n", "print(\"=\" * 80)\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "Fixed PyLabRobot Script:\n", "================================================================================\n", "\n", "\"\"\"\n", "PyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\n", "This script demonstrates liquid transfer between well ranges on a 96-well plate.\n", "\"\"\"\n", "\n", "from pylabrobot.liquid_handling import LiquidHandler\n", "from pylabrobot.liquid_handling.backends import STARBackend\n", "from pylabrobot.resources.hamilton import STARLetDeck\n", "from pylabrobot.resources import (\n", " TIP_CAR_480_A00,\n", " PLT_CAR_L5AC_A00,\n", " Cor_96_wellplate_360ul_Fb,\n", " hamilton_96_tiprack_1000uL_filter\n", ")\n", "\n", "async def main():\n", " # Initialize the liquid handler with Hamilton STAR backend\n", " lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\n", " \n", " # Setup connection to the robot\n", " await lh.setup()\n", " \n", " print(\"Setting up deck layout...\")\n", " \n", " # Create tip carrier and add tip racks\n", " tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n", " tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\n", " tip_car[0] = tiprack\n", " tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\n", " tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\n", " tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\n", " tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\n", " \n", " # Assign tip carrier to deck at rails 1\n", " lh.deck.assign_child_resource(tip_car, rails=1)\n", " \n", " # Create plate carrier and add a 96-well plate\n", " plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\n", " plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n", " plate_car[0] = plate\n", " \n", " # Assign plate carrier to deck at rails 14\n", " lh.deck.assign_child_resource(plate_car, rails=14)\n", " \n", " # Display deck summary\n", " print(\"\\nDeck layout:\")\n", " print(lh.summary())\n", " \n", " # Define source and destination well ranges\n", " source_wells = \"A1:A3\" # Wells A1, A2, A3\n", " destination_wells = \"A4:A6\" # Wells A4, A5, A6\n", " \n", " print(f\"\\nMoving water from {source_wells} to {destination_wells}...\")\n", " \n", " # Pick up tips - access tips from the tiprack directly\n", " tips = tiprack[source_wells]\n", " await lh.pick_up_tips(tips)\n", " print(\"Tips picked up successfully\")\n", " \n", " # Aspirate liquid from source wells\n", " volume = 100 # microliters\n", " source = plate[source_wells]\n", " await lh.aspirate(source, vols=[volume, volume, volume])\n", " print(f\"Aspirated {volume} ยตL from {source_wells}\")\n", " \n", " # Dispense liquid to destination wells\n", " destination = plate[destination_wells]\n", " await lh.dispense(destination, vols=[volume, volume, volume])\n", " print(f\"Dispensed {volume} ยตL to {destination_wells}\")\n", " \n", " # Drop tips back to the tip rack\n", " await lh.drop_tips(tips)\n", " print(\"Tips dropped successfully\")\n", " \n", " print(\"\\nLiquid transfer complete!\")\n", " \n", " # Stop the liquid handler\n", " await lh.stop()\n", " print(\"Connection closed\")\n", "\n", "# Run the async main function\n", "if __name__ == \"__main__\":\n", " import asyncio\n", " asyncio.run(main())\n", "\n", "================================================================================\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "\n", "# Test the fixed script\n", "print(\"Testing the fixed PyLabRobot script...\")\n", "print(\"=\" * 80)\n", "test_result = test_pylabrobot_script(\n", " script_input=fixed_script,\n", " enable_tracking=False,\n", " timeout_seconds=60\n", ")\n", "print(\"\\nTest Result:\")\n", "print(test_result)\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "Testing the fixed PyLabRobot script...\n", "================================================================================\n", "Setting up the liquid handler.\n", "Resource deck was assigned to the liquid handler.\n", "Resource trash was assigned to the liquid handler.\n", "Resource trash_core96 was assigned to the liquid handler.\n", "Resource waste_block was assigned to the liquid handler.\n", "Setting up deck layout...\n", "Resource tip carrier was assigned to the liquid handler.\n", "Resource plate carrier was assigned to the liquid handler.\n", "\n", "Deck layout:\n", "Rail Resource Type Coordinates (mm)\n", "=================================================================================\n", "(-6) โ”œโ”€โ”€ trash_core96 Trash (-58.200, 106.000, 229.000)\n", " โ”‚\n", "(1) โ”œโ”€โ”€ tip carrier TipCarrier (100.000, 063.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ tips_1 TipRack (106.200, 073.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_2 TipRack (106.200, 169.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_3 TipRack (106.200, 265.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_4 TipRack (106.200, 361.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_5 TipRack (106.200, 457.000, 214.950)\n", " โ”‚\n", "(14) โ”œโ”€โ”€ plate carrier PlateCarrier (392.500, 063.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ plate Plate (396.500, 071.500, 183.120)\n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚\n", "(31) โ”œโ”€โ”€ waste_block Resource (775.000, 115.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ teaching_tip_rack TipRack (780.900, 461.100, 100.000)\n", " โ”‚\n", "(32) โ”œโ”€โ”€ trash Trash (800.000, 190.600, 137.100)\n", "\n", "None\n", "\n", "Moving water from A1:A3 to A4:A6...\n", "Picking up tips:\n", "pip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \n", " p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", "Tips picked up successfully\n", "Aspirating:\n", "pip# vol(ul) resource offset flow rate blowout lld_z \n", " p0: 100.0 plate_well_0_0 0,0,0 None None None \n", " p1: 100.0 plate_well_1_0 0,0,0 None None None \n", " p2: 100.0 plate_well_2_0 0,0,0 None None None \n", "Aspirated 100 ยตL from A1:A3\n", "Dispensing:\n", "pip# vol(ul) resource offset flow rate blowout lld_z \n", " p0: 100.0 plate_well_3_0 0,0,0 None None None \n", " p1: 100.0 plate_well_4_0 0,0,0 None None None \n", " p2: 100.0 plate_well_5_0 0,0,0 None None None \n", "Dispensed 100 ยตL to A4:A6\n", "Dropping tips:\n", "pip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \n", " p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", "Tips dropped successfully\n", "\n", "Liquid transfer complete!\n", "Stopping the liquid handler.\n", "Connection closed\n", "Setting up the liquid handler.\n", "Resource deck was assigned to the liquid handler.\n", "Resource trash was assigned to the liquid handler.\n", "Resource trash_core96 was assigned to the liquid handler.\n", "Resource waste_block was assigned to the liquid handler.\n", "Setting up deck layout...\n", "Resource tip carrier was assigned to the liquid handler.\n", "Resource plate carrier was assigned to the liquid handler.\n", "\n", "Deck layout:\n", "Rail Resource Type Coordinates (mm)\n", "=================================================================================\n", "(-6) โ”œโ”€โ”€ trash_core96 Trash (-58.200, 106.000, 229.000)\n", " โ”‚\n", "(1) โ”œโ”€โ”€ tip carrier TipCarrier (100.000, 063.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ tips_1 TipRack (106.200, 073.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_2 TipRack (106.200, 169.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_3 TipRack (106.200, 265.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_4 TipRack (106.200, 361.000, 214.950)\n", " โ”‚ โ”œโ”€โ”€ tips_5 TipRack (106.200, 457.000, 214.950)\n", " โ”‚\n", "(14) โ”œโ”€โ”€ plate carrier PlateCarrier (392.500, 063.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ plate Plate (396.500, 071.500, 183.120)\n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚ โ”œโ”€โ”€ \n", " โ”‚\n", "(31) โ”œโ”€โ”€ waste_block Resource (775.000, 115.000, 100.000)\n", " โ”‚ โ”œโ”€โ”€ teaching_tip_rack TipRack (780.900, 461.100, 100.000)\n", " โ”‚\n", "(32) โ”œโ”€โ”€ trash Trash (800.000, 190.600, 137.100)\n", "\n", "None\n", "\n", "Moving water from A1:A3 to A4:A6...\n", "Picking up tips:\n", "pip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \n", " p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", "Tips picked up successfully\n", "Aspirating:\n", "pip# vol(ul) resource offset flow rate blowout lld_z \n", " p0: 100.0 plate_well_0_0 0,0,0 None None None \n", " p1: 100.0 plate_well_1_0 0,0,0 None None None \n", " p2: 100.0 plate_well_2_0 0,0,0 None None None \n", "Aspirated 100 ยตL from A1:A3\n", "Dispensing:\n", "pip# vol(ul) resource offset flow rate blowout lld_z \n", " p0: 100.0 plate_well_3_0 0,0,0 None None None \n", " p1: 100.0 plate_well_4_0 0,0,0 None None None \n", " p2: 100.0 plate_well_5_0 0,0,0 None None None \n", "Dispensed 100 ยตL to A4:A6\n", "Dropping tips:\n", "pip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \n", " p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", " p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \n", "Tips dropped successfully\n", "\n", "Liquid transfer complete!\n", "Stopping the liquid handler.\n", "Connection closed\n", "\n", "Test Result:\n", "{'success': True, 'test_results': {'syntax_valid': True, 'imports_valid': True, 'simulation_successful': True, 'tracking_enabled': False, 'input_type': 'string'}, 'execution_summary': {'operations_performed': 1, 'tips_used': 0, 'liquid_transferred': 0.0, 'execution_time': 0.0, 'total_execution_time': 0.540640115737915}, 'errors': [], 'warnings': []}\n", "\n", "==================================\u001b[1m Ai Message \u001b[0m==================================\n", "\n", "Perfect! The script now works successfully. Let me update the final plan:\n", "\n", "## Updated Plan:\n", "1. [โœ“] Review PyLabRobot liquid handling documentation\n", "2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\n", "3. [โœ—] Test the script to ensure it's valid (failed - fixed well access syntax)\n", "4. [โœ“] Fix the script based on test results\n", "5. [โœ“] Re-test the fixed script (SUCCESS!)\n", "6. [โœ“] Provide the final working script\n", "\n", "\n", "Here's a working PyLabRobot script to move water from one range of wells to another using the Hamilton STAR backend:\n", "\n", "```python\n", "\"\"\"\n", "PyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\n", "This script demonstrates liquid transfer between well ranges on a 96-well plate.\n", "\"\"\"\n", "\n", "from pylabrobot.liquid_handling import LiquidHandler\n", "from pylabrobot.liquid_handling.backends import STARBackend\n", "from pylabrobot.resources.hamilton import STARLetDeck\n", "from pylabrobot.resources import (\n", " TIP_CAR_480_A00,\n", " PLT_CAR_L5AC_A00,\n", " Cor_96_wellplate_360ul_Fb,\n", " hamilton_96_tiprack_1000uL_filter\n", ")\n", "\n", "async def main():\n", " # Initialize the liquid handler with Hamilton STAR backend\n", " lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\n", " \n", " # Setup connection to the robot\n", " await lh.setup()\n", " \n", " print(\"Setting up deck layout...\")\n", " \n", " # Create tip carrier and add tip racks\n", " tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n", " tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\n", " tip_car[0] = tiprack\n", " tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\n", " tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\n", " tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\n", " tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\n", " \n", " # Assign tip carrier to deck at rails 1\n", " lh.deck.assign_child_resource(tip_car, rails=1)\n", " \n", " # Create plate carrier and add a 96-well plate\n", " plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\n", " plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n", " plate_car[0] = plate\n", " \n", " # Assign plate carrier to deck at rails 14\n", " lh.deck.assign_child_resource(plate_car, rails=14)\n", " \n", " # Display deck summary\n", " print(\"\\nDeck layout:\")\n", " print(lh.summary())\n", " \n", " # Define source and destination well ranges\n", " source_wells = \"A1:A3\" # Wells A1, A2, A3\n", " destination_wells = \"A4:A6\" # Wells A4, A5, A6\n", " \n", " print(f\"\\nMoving water from {source_wells} to {destination_wells}...\")\n", " \n", " # Pick up tips - access tips from the tiprack directly\n", " tips = tiprack[source_wells]\n", " await lh.pick_up_tips(tips)\n", " print(\"Tips picked up successfully\")\n", " \n", " # Aspirate liquid from source wells\n", " volume = 100 # microliters\n", " source = plate[source_wells]\n", " await lh.aspirate(source, vols=[volume, volume, volume])\n", " print(f\"Aspirated {volume} ยตL from {source_wells}\")\n", " \n", " # Dispense liquid to destination wells\n", " destination = plate[destination_wells]\n", " await lh.dispense(destination, vols=[volume, volume, volume])\n", " print(f\"Dispensed {volume} ยตL to {destination_wells}\")\n", " \n", " # Drop tips back to the tip rack\n", " await lh.drop_tips(tips)\n", " print(\"Tips dropped successfully\")\n", " \n", " print(\"\\nLiquid transfer complete!\")\n", " \n", " # Stop the liquid handler\n", " await lh.stop()\n", " print(\"Connection closed\")\n", "\n", "# Run the async main function\n", "if __name__ == \"__main__\":\n", " import asyncio\n", " asyncio.run(main())\n", "```\n", "\n", "**Key Features:**\n", "- Uses Hamilton STAR backend for liquid handling\n", "- Transfers 100 ยตL from wells A1-A3 to wells A4-A6\n", "- Includes proper deck setup with tip carriers and plate carriers\n", "- Uses async/await for all liquid handling operations\n", "- Properly manages tips (pickup and drop)\n", "- Successfully tested and validated\n", "\n", "You can modify the `source_wells`, `destination_wells`, and `volume` variables to customize the transfer for your specific needs.\n", "\n" ] }, { "data": { "text/plain": [ "(['================================\\x1b[1m Human Message \\x1b[0m=================================\\n\\nCan you generate a script to use PyLabRobot to move water from one range of wells to another using the Hamilton STAR backend?',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nI\\'ll help you generate a PyLabRobot script to move water from one range of wells to another using the Hamilton STAR backend. Let me start by reviewing the PyLabRobot documentation and then create a working script.\\n\\n## Plan:\\n1. [ ] Review PyLabRobot liquid handling documentation\\n2. [ ] Create a script that moves water between well ranges using Hamilton STAR\\n3. [ ] Test the script to ensure it\\'s valid\\n4. [ ] Provide the final working script\\n\\nLet me start:\\n\\n\\nfrom biomni.tool.lab_automation import get_pylabrobot_documentation_liquid\\n\\n# Get the liquid handling documentation\\nliquid_docs = get_pylabrobot_documentation_liquid()\\nprint(\"PyLabRobot Liquid Handling Documentation:\")\\nprint(\"=\" * 80)\\nprint(liquid_docs)\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nThe output is too long to be added to context. Here are the first 10K characters...\\nPyLabRobot Liquid Handling Documentation:\\n================================================================================\\nNotes:\\n- Use hamilton_96_tiprack_1000uL_filter instead of HTF (deprecated). Note the capital L in uL.\\n- Use Cor_96_wellplate_360ul_Fb instead of Corning_96_wellplate_360ul_Fb.\\n- You must name all your plates, tip racks, and carriers.\\n- Assign labware into carriers via slot assignment (tip_car[0] = tiprack). Assign plates to rails using lh.deck.assign_child_resource(plate_car, rails=14).\\n- Rails must be between -4 and 32.\\n- Make sure most liquid handling operations are done with async/await.\\n- There are some methods that are not async, including lh.summary(). Do not use await for these methods.\\n- When picking up tips with multiple channels, use a flat list of tips. Do not use a list of lists. ## Getting started with liquid handling on a Hamilton STAR(let)\\n\\n# Getting started with liquid handling on a Hamilton STAR(let)\\n\\nIn this notebook, you will learn how to use PyLabRobot to move water from one range of wells to another.\\n\\n**Note: before running this notebook, you should have**:\\n\\n- Installed PyLabRobot and the USB driver as described in [the installation guide](../../_getting-started/installation).\\n- Connected the Hamilton to your computer using the USB cable.\\n\\nVideo of what this code does:\\n\\n\\n\\n## Setting up a connection with the robot\\n\\nStart by importing the {class}`~pylabrobot.liquid_handling.liquid_handler.LiquidHandler` class, which will serve as a front end for all liquid handling operations.\\n\\nBackends serve as communicators between `LiquidHandler`s and the actual hardware. Since we are using a Hamilton STAR, we also import the {class}`~pylabrobot.liquid_handling.backends.STAR_backend.STARBackend` backend.\\n\\nCode refs:\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\n\\nIn addition, import the {class}`~pylabrobot.resources.hamilton.STARLetDeck`, which represents the deck of the Hamilton STAR.\\n\\nCode refs:\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\n\\nCreate a new liquid handler using `STARBackend` as its backend.\\n\\nThe final step is to open communication with the robot. This is done using the {func}`~pylabrobot.liquid_handling.LiquidHandler.setup` method.\\n\\n## Creating the deck layout\\n\\nNow that we have a `LiquidHandler` instance, we can define the deck layout.\\n\\nThe layout in this tutorial will contain five sets of standard volume tips with filter, 1 set of 96 1mL wells, and tip and plate carriers on which these resources are positioned.\\n\\nStart by importing the relevant objects and variables from the PyLabRobot package. This notebook uses the following resources:\\n\\n- {class}`~pylabrobot.resources.hamilton.tip_carriers.TIP_CAR_480_A00` tip carrier\\n- {class}`~pylabrobot.resources.hamilton.plate_carriers.PLT_CAR_L5AC_A00` plate carrier\\n- {class}`~pylabrobot.resources.corning_costar.plates.Cor_96_wellplate_360ul_Fb` wells\\n- {class}`~pylabrobot.resources.hamilton.tip_racks.hamilton_96_tiprack_1000ul_filter` tips\\n\\nCode refs:\\nfrom pylabrobot.resources import (\\n\\nThen create a tip carrier named `tip carrier`, which will contain tip rack at all 5 positions. These positions can be accessed using `tip_car[x]`, and are 0 indexed.\\n\\nUse {func}`~pylabrobot.resources.abstract.assign_child_resources` to assign the tip carrier to the deck of the liquid handler. All resources contained by this carrier will be assigned automatically.\\n\\nIn the `rails` parameter, we can pass the location of the tip carrier. The locations of the tips will automatically be calculated.\\n\\nRepeat this for the plates.\\n\\nLet\\'s look at a summary of the deck layout using {func}`~pylabrobot.liquid_handling.LiquidHandler.summary`.\\n\\n## Picking up tips\\n\\nPicking up tips is as easy as querying the tips from the tiprack.\\n\\n## Aspirating and dispensing\\n\\nAspirating and dispensing work similarly to picking up tips: where you use booleans to specify which tips to pick up, with aspiration and dispensing you use floats to specify the volume to aspirate or dispense in $\\\\mu L$.\\n\\nThe cells below move liquid from wells `\\'A1:C1\\'` to `\\'D1:F1\\'` using channels 1, 2, and 3 using the {func}`~pylabrobot.liquid_handling.LiquidHandler.aspirate` and {func}`~pylabrobot.liquid_handling.LiquidHandler.dispense` methods.\\n\\nAfter the liquid has been aspirated, dispense it in the wells below. Note that while we specify different wells, we are still using the same channels. This is needed because only these channels contain liquid, of course.\\n\\nLet\\'s move the liquid back to the original wells.\\n\\n## Dropping tips\\n\\nFinally, you can drop tips anywhere on the deck by using the {func}`~pylabrobot.liquid_handling.LiquidHandler.drop_tips` method.\\n\\n## iSWAP Module\\n\\n# Adjust iSWAP gripper parallelity\\n\\nThe steel pointy bits at the end of the iSWAP grippers are intended to be the primary points of contact with a plate.\\n\\nThey physically deform plastic, leading to a repeatable secure grip.\\n\\nOver time, the aluminum fingers leading up to the metal grippers can begin to angle outward, leaving the grip narrower toward the back of the iSWAP hand and wider at the steel pointy bits.\\n\\nIn iSWAPs with this calibration issue, a plate can accidentally be picked up using force primarily through the smooth aluminum fingers instead of the steel pointy bits. This predisposes the plate to pivot around the smooth fingers, rotating downwards and causing catastrophic plate crashes to external hotel locations when it fails.\\n\\nIn our testing, improper grips can be reliable for hundreds of pick/place operations, but fail after thousands. To achieve robust operation, physical adjustment is required.\\n\\n![](./img/adjust-iswap-gripper/before-after.jpg)\\n\\n## Tools\\n- 1.5mm hex key\\n- 2.5mm hex key\\n\\n## Step-by-step hardware adjustment guide\\n\\nLoosen by <1 turn the 4 adjustment screws (1.5mm hex) on top of the iSWAP hand corresponding to the right gripper finger. Do not fully remove the screws. This frees the slider bearing to rotate around the Z axis.\\n\\nThere should be ~1mm of play at the end of the finger.\\n\\nNarrow the angle of the finger and retighten these 4 screws.\\n\\nA bit of force may be required initially to unstick/free the bearing to rotate, but not enough force to bend the aluminum.\\n\\nRemove 2 screws (2.5mm hex) holding the data wire in place on the left gripper finger. This exposes the other 4 adjustment screws. Repeat the process for these 4.\\n\\n![](./img/adjust-iswap-gripper/rotate-slider-bearing.jpg)\\n\\n\\nYou may need to run the Hamilton [iSWAP calibration macro](adjusting-iswap.md) to recalibrate grip width after making these changes, however in our testing hotel coordinate locations are altered <1mm by the physical adjustment of gripper parallelity.\\n\\n\\n## Liquid level detection on Hamilton STAR(let)\\n\\n# Liquid level detection on Hamilton STAR(let)\\n\\nLiquid level detection (LLD) is a feature that allows the Hamilton STAR(let) to move the pipetting tip down slowly until a liquid is found using either a) the pressure sensor, or b) a change in capacitance, or c) both. This feature is useful if you want to aspirate or dispense at a distance relative to the liquid surface, but you don\\'t know the exact height of the liquid in the container.\\n\\nTo use LLD, you need to specify the LLD mode when calling the `aspirate` or `dispense` methods. Here is how you can use pressure or capacative LLD with the `aspirate` :\\n\\n```python\\nawait lh.aspirate([tube], vols=[300], lld_mode=[STARBackend.LLDMode.GAMMA])\\n```\\n\\nThe `lld_mode` parameter can be one of the following:\\n\\n- `STARBackend.LLDMode.OFF`: default, no LLD\\n- `STARBackend.LLDMode.GAMMA`: capacative LLD\\n- `STARBackend.LLDMode.PRESSURE`: pressure LLD\\n- `STARBackend.LLDMode.DUAL`: both capacative and pressure LLD\\n- `STARBackend.LLDMode.Z_TOUCH_OFF`: find the bottom of the container\\n\\nThe `lld_mode` parameter is a list, so you can specify a different LLD mode for each channel.\\n\\n```{note}\\nThe `lld_mode` parameter is only available when using the `STAR` backend.\\n```\\n\\n## Catching errors\\n\\nAll channelized pipetting operations raise a `ChannelizedError` exception when an error occurs, so that we can have specific error handling for each channel.\\n\\nWhen no liquid is found in the container, the channel will have a `TooLittleLiquidError` error. This is useful for detecting that your container is empty.\\n\\nYou can catch the error like this:\\n\\n```python\\nfrom pylabrobot.liquid_handling.errors import ChannelizedError\\nfrom pylabrobot.resources.errors import TooLittleLiquidError\\nchannel = 0\\ntry:\\n await lh.aspirate([tube], vols=[300], lld_mode=[STARBackend.LLDMode.GAMMA], use_channels=[channel])\\nexcept ChannelizedError as e:\\n if isinstance(e.errors[channel], TooLittleLiquidError):\\n print(\"Too little liquid in tube\")\\n```\\n\\n\\n## Z-probing\\n\\n# Z-probing\\n\\nWith PyLabRobot, one can probe the surface of any object on a STAR(let) deck. This effectively makes the STAR act as a [Coordinate-Measurement Machine (CMM)](https://en.wikipedia.org/wiki/Coordinate-measuring_machine).\\n\\nThere are two ways to probe the surface of an object:\\n\\n- Using capacitive liquid level sensors (cLLD) to map capacitive objects.\\n- Moving the tip down onto an object until resistance is detected (a \"controlled crash\"), which works with both capacitive and non-capacitive objects.\\n\\n## Example setup\\n\\nCode refs:\\nfrom pylabrobot.liquid_handling import LiquidHandler, STARBackend\\nfrom pylabrobot.resources import STARLetDeck\\nfrom pylabrobot.resources import (\\n\\n## Capacitive probing using cLLD\\n\\nIf you are mapping a capacitive surface, you can use the cLLD sensor to detect the surface. This is safer and more accurate than the controlled crash method.\\n\\n```{warning}\\nFor safety purposes, we recommend using Hamilton 50ul tips for mapping surfaces. These ',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n\\n# Now let\\'s create a comprehensive script for moving water between well ranges\\nscript_content = \\'\\'\\'\\n\"\"\"\\nPyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\\nThis script demonstrates liquid transfer between well ranges on a 96-well plate.\\n\"\"\"\\n\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\nfrom pylabrobot.resources import (\\n TIP_CAR_480_A00,\\n PLT_CAR_L5AC_A00,\\n Cor_96_wellplate_360ul_Fb,\\n hamilton_96_tiprack_1000uL_filter\\n)\\n\\nasync def main():\\n # Initialize the liquid handler with Hamilton STAR backend\\n lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\\n \\n # Setup connection to the robot\\n await lh.setup()\\n \\n print(\"Setting up deck layout...\")\\n \\n # Create tip carrier and add tip racks\\n tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\\n tip_car[0] = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\\n tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\\n tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\\n tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\\n tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\\n \\n # Assign tip carrier to deck at rails 1\\n lh.deck.assign_child_resource(tip_car, rails=1)\\n \\n # Create plate carrier and add a 96-well plate\\n plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\\n plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\\n plate_car[0] = plate\\n \\n # Assign plate carrier to deck at rails 14\\n lh.deck.assign_child_resource(plate_car, rails=14)\\n \\n # Display deck summary\\n print(\"\\\\\\\\nDeck layout:\")\\n print(lh.summary())\\n \\n # Define source and destination well ranges\\n source_wells = \"A1:A3\" # Wells A1, A2, A3\\n destination_wells = \"A4:A6\" # Wells A4, A5, A6\\n \\n print(f\"\\\\\\\\nMoving water from {source_wells} to {destination_wells}...\")\\n \\n # Pick up tips from the first three positions\\n tips = tip_car[0][source_wells]\\n await lh.pick_up_tips(tips)\\n print(\"Tips picked up successfully\")\\n \\n # Aspirate liquid from source wells\\n volume = 100 # microliters\\n source = plate[source_wells]\\n await lh.aspirate(source, vols=[volume, volume, volume])\\n print(f\"Aspirated {volume} ยตL from {source_wells}\")\\n \\n # Dispense liquid to destination wells\\n destination = plate[destination_wells]\\n await lh.dispense(destination, vols=[volume, volume, volume])\\n print(f\"Dispensed {volume} ยตL to {destination_wells}\")\\n \\n # Drop tips back to the tip rack\\n await lh.drop_tips(tips)\\n print(\"Tips dropped successfully\")\\n \\n print(\"\\\\\\\\nLiquid transfer complete!\")\\n \\n # Stop the liquid handler\\n await lh.stop()\\n print(\"Connection closed\")\\n\\n# Run the async main function\\nif __name__ == \"__main__\":\\n import asyncio\\n asyncio.run(main())\\n\\'\\'\\'\\n\\nprint(\"Generated PyLabRobot Script:\")\\nprint(\"=\" * 80)\\nprint(script_content)\\nprint(\"=\" * 80)\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nGenerated PyLabRobot Script:\\n================================================================================\\n\\n\"\"\"\\nPyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\\nThis script demonstrates liquid transfer between well ranges on a 96-well plate.\\n\"\"\"\\n\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\nfrom pylabrobot.resources import (\\n TIP_CAR_480_A00,\\n PLT_CAR_L5AC_A00,\\n Cor_96_wellplate_360ul_Fb,\\n hamilton_96_tiprack_1000uL_filter\\n)\\n\\nasync def main():\\n # Initialize the liquid handler with Hamilton STAR backend\\n lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\\n \\n # Setup connection to the robot\\n await lh.setup()\\n \\n print(\"Setting up deck layout...\")\\n \\n # Create tip carrier and add tip racks\\n tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\\n tip_car[0] = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\\n tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\\n tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\\n tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\\n tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\\n \\n # Assign tip carrier to deck at rails 1\\n lh.deck.assign_child_resource(tip_car, rails=1)\\n \\n # Create plate carrier and add a 96-well plate\\n plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\\n plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\\n plate_car[0] = plate\\n \\n # Assign plate carrier to deck at rails 14\\n lh.deck.assign_child_resource(plate_car, rails=14)\\n \\n # Display deck summary\\n print(\"\\\\nDeck layout:\")\\n print(lh.summary())\\n \\n # Define source and destination well ranges\\n source_wells = \"A1:A3\" # Wells A1, A2, A3\\n destination_wells = \"A4:A6\" # Wells A4, A5, A6\\n \\n print(f\"\\\\nMoving water from {source_wells} to {destination_wells}...\")\\n \\n # Pick up tips from the first three positions\\n tips = tip_car[0][source_wells]\\n await lh.pick_up_tips(tips)\\n print(\"Tips picked up successfully\")\\n \\n # Aspirate liquid from source wells\\n volume = 100 # microliters\\n source = plate[source_wells]\\n await lh.aspirate(source, vols=[volume, volume, volume])\\n print(f\"Aspirated {volume} ยตL from {source_wells}\")\\n \\n # Dispense liquid to destination wells\\n destination = plate[destination_wells]\\n await lh.dispense(destination, vols=[volume, volume, volume])\\n print(f\"Dispensed {volume} ยตL to {destination_wells}\")\\n \\n # Drop tips back to the tip rack\\n await lh.drop_tips(tips)\\n print(\"Tips dropped successfully\")\\n \\n print(\"\\\\nLiquid transfer complete!\")\\n \\n # Stop the liquid handler\\n await lh.stop()\\n print(\"Connection closed\")\\n\\n# Run the async main function\\nif __name__ == \"__main__\":\\n import asyncio\\n asyncio.run(main())\\n\\n================================================================================\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nNow let me update the plan and test the script:\\n\\n## Updated Plan:\\n1. [โœ“] Review PyLabRobot liquid handling documentation\\n2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\\n3. [ ] Test the script to ensure it\\'s valid\\n4. [ ] Provide the final working script\\n\\n\\nfrom biomni.tool.lab_automation import test_pylabrobot_script\\n\\n# Test the generated script\\nprint(\"Testing the PyLabRobot script...\")\\nprint(\"=\" * 80)\\ntest_result = test_pylabrobot_script(\\n script_input=script_content,\\n enable_tracking=False,\\n timeout_seconds=60\\n)\\nprint(\"\\\\nTest Result:\")\\nprint(test_result)\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nTesting the PyLabRobot script...\\n================================================================================\\nSetting up the liquid handler.\\nResource deck was assigned to the liquid handler.\\nResource trash was assigned to the liquid handler.\\nResource trash_core96 was assigned to the liquid handler.\\nResource waste_block was assigned to the liquid handler.\\nSetting up deck layout...\\nResource tip carrier was assigned to the liquid handler.\\nResource plate carrier was assigned to the liquid handler.\\n\\nDeck layout:\\nRail Resource Type Coordinates (mm)\\n=================================================================================\\n(-6) โ”œโ”€โ”€ trash_core96 Trash (-58.200, 106.000, 229.000)\\n โ”‚\\n(1) โ”œโ”€โ”€ tip carrier TipCarrier (100.000, 063.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ tips_1 TipRack (106.200, 073.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_2 TipRack (106.200, 169.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_3 TipRack (106.200, 265.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_4 TipRack (106.200, 361.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_5 TipRack (106.200, 457.000, 214.950)\\n โ”‚\\n(14) โ”œโ”€โ”€ plate carrier PlateCarrier (392.500, 063.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ plate Plate (396.500, 071.500, 183.120)\\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚\\n(31) โ”œโ”€โ”€ waste_block Resource (775.000, 115.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ teaching_tip_rack TipRack (780.900, 461.100, 100.000)\\n โ”‚\\n(32) โ”œโ”€โ”€ trash Trash (800.000, 190.600, 137.100)\\n\\nNone\\n\\nMoving water from A1:A3 to A4:A6...\\n\\nTest Result:\\n{\\'success\\': False, \\'test_results\\': {\\'syntax_valid\\': True, \\'imports_valid\\': True, \\'simulation_successful\\': False, \\'tracking_enabled\\': False, \\'input_type\\': \\'string\\'}, \\'execution_summary\\': {\\'operations_performed\\': 0, \\'tips_used\\': 0, \\'liquid_transferred\\': 0.0, \\'execution_time\\': 0.0, \\'total_execution_time\\': 0.40647315979003906}, \\'errors\\': [\"Script execution failed: Script execution error: \\'ResourceHolder\\' object is not subscriptable\"], \\'warnings\\': []}\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nI see the issue. The script has a problem with how we\\'re accessing the wells. Let me fix this:\\n\\n## Updated Plan:\\n1. [โœ“] Review PyLabRobot liquid handling documentation\\n2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\\n3. [โœ—] Test the script to ensure it\\'s valid (failed - need to fix well access syntax)\\n4. [ ] Fix the script based on test results\\n5. [ ] Re-test the fixed script\\n6. [ ] Provide the final working script\\n\\n\\n# Fix the script - the issue is with how we access wells from tip racks and plates\\nfixed_script = \\'\\'\\'\\n\"\"\"\\nPyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\\nThis script demonstrates liquid transfer between well ranges on a 96-well plate.\\n\"\"\"\\n\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\nfrom pylabrobot.resources import (\\n TIP_CAR_480_A00,\\n PLT_CAR_L5AC_A00,\\n Cor_96_wellplate_360ul_Fb,\\n hamilton_96_tiprack_1000uL_filter\\n)\\n\\nasync def main():\\n # Initialize the liquid handler with Hamilton STAR backend\\n lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\\n \\n # Setup connection to the robot\\n await lh.setup()\\n \\n print(\"Setting up deck layout...\")\\n \\n # Create tip carrier and add tip racks\\n tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\\n tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\\n tip_car[0] = tiprack\\n tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\\n tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\\n tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\\n tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\\n \\n # Assign tip carrier to deck at rails 1\\n lh.deck.assign_child_resource(tip_car, rails=1)\\n \\n # Create plate carrier and add a 96-well plate\\n plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\\n plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\\n plate_car[0] = plate\\n \\n # Assign plate carrier to deck at rails 14\\n lh.deck.assign_child_resource(plate_car, rails=14)\\n \\n # Display deck summary\\n print(\"\\\\\\\\nDeck layout:\")\\n print(lh.summary())\\n \\n # Define source and destination well ranges\\n source_wells = \"A1:A3\" # Wells A1, A2, A3\\n destination_wells = \"A4:A6\" # Wells A4, A5, A6\\n \\n print(f\"\\\\\\\\nMoving water from {source_wells} to {destination_wells}...\")\\n \\n # Pick up tips - access tips from the tiprack directly\\n tips = tiprack[source_wells]\\n await lh.pick_up_tips(tips)\\n print(\"Tips picked up successfully\")\\n \\n # Aspirate liquid from source wells\\n volume = 100 # microliters\\n source = plate[source_wells]\\n await lh.aspirate(source, vols=[volume, volume, volume])\\n print(f\"Aspirated {volume} ยตL from {source_wells}\")\\n \\n # Dispense liquid to destination wells\\n destination = plate[destination_wells]\\n await lh.dispense(destination, vols=[volume, volume, volume])\\n print(f\"Dispensed {volume} ยตL to {destination_wells}\")\\n \\n # Drop tips back to the tip rack\\n await lh.drop_tips(tips)\\n print(\"Tips dropped successfully\")\\n \\n print(\"\\\\\\\\nLiquid transfer complete!\")\\n \\n # Stop the liquid handler\\n await lh.stop()\\n print(\"Connection closed\")\\n\\n# Run the async main function\\nif __name__ == \"__main__\":\\n import asyncio\\n asyncio.run(main())\\n\\'\\'\\'\\n\\nprint(\"Fixed PyLabRobot Script:\")\\nprint(\"=\" * 80)\\nprint(fixed_script)\\nprint(\"=\" * 80)\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nFixed PyLabRobot Script:\\n================================================================================\\n\\n\"\"\"\\nPyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\\nThis script demonstrates liquid transfer between well ranges on a 96-well plate.\\n\"\"\"\\n\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\nfrom pylabrobot.resources import (\\n TIP_CAR_480_A00,\\n PLT_CAR_L5AC_A00,\\n Cor_96_wellplate_360ul_Fb,\\n hamilton_96_tiprack_1000uL_filter\\n)\\n\\nasync def main():\\n # Initialize the liquid handler with Hamilton STAR backend\\n lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\\n \\n # Setup connection to the robot\\n await lh.setup()\\n \\n print(\"Setting up deck layout...\")\\n \\n # Create tip carrier and add tip racks\\n tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\\n tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\\n tip_car[0] = tiprack\\n tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\\n tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\\n tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\\n tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\\n \\n # Assign tip carrier to deck at rails 1\\n lh.deck.assign_child_resource(tip_car, rails=1)\\n \\n # Create plate carrier and add a 96-well plate\\n plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\\n plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\\n plate_car[0] = plate\\n \\n # Assign plate carrier to deck at rails 14\\n lh.deck.assign_child_resource(plate_car, rails=14)\\n \\n # Display deck summary\\n print(\"\\\\nDeck layout:\")\\n print(lh.summary())\\n \\n # Define source and destination well ranges\\n source_wells = \"A1:A3\" # Wells A1, A2, A3\\n destination_wells = \"A4:A6\" # Wells A4, A5, A6\\n \\n print(f\"\\\\nMoving water from {source_wells} to {destination_wells}...\")\\n \\n # Pick up tips - access tips from the tiprack directly\\n tips = tiprack[source_wells]\\n await lh.pick_up_tips(tips)\\n print(\"Tips picked up successfully\")\\n \\n # Aspirate liquid from source wells\\n volume = 100 # microliters\\n source = plate[source_wells]\\n await lh.aspirate(source, vols=[volume, volume, volume])\\n print(f\"Aspirated {volume} ยตL from {source_wells}\")\\n \\n # Dispense liquid to destination wells\\n destination = plate[destination_wells]\\n await lh.dispense(destination, vols=[volume, volume, volume])\\n print(f\"Dispensed {volume} ยตL to {destination_wells}\")\\n \\n # Drop tips back to the tip rack\\n await lh.drop_tips(tips)\\n print(\"Tips dropped successfully\")\\n \\n print(\"\\\\nLiquid transfer complete!\")\\n \\n # Stop the liquid handler\\n await lh.stop()\\n print(\"Connection closed\")\\n\\n# Run the async main function\\nif __name__ == \"__main__\":\\n import asyncio\\n asyncio.run(main())\\n\\n================================================================================\\n',\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n\\n# Test the fixed script\\nprint(\"Testing the fixed PyLabRobot script...\")\\nprint(\"=\" * 80)\\ntest_result = test_pylabrobot_script(\\n script_input=fixed_script,\\n enable_tracking=False,\\n timeout_seconds=60\\n)\\nprint(\"\\\\nTest Result:\")\\nprint(test_result)\\n',\n", " \"==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nTesting the fixed PyLabRobot script...\\n================================================================================\\nSetting up the liquid handler.\\nResource deck was assigned to the liquid handler.\\nResource trash was assigned to the liquid handler.\\nResource trash_core96 was assigned to the liquid handler.\\nResource waste_block was assigned to the liquid handler.\\nSetting up deck layout...\\nResource tip carrier was assigned to the liquid handler.\\nResource plate carrier was assigned to the liquid handler.\\n\\nDeck layout:\\nRail Resource Type Coordinates (mm)\\n=================================================================================\\n(-6) โ”œโ”€โ”€ trash_core96 Trash (-58.200, 106.000, 229.000)\\n โ”‚\\n(1) โ”œโ”€โ”€ tip carrier TipCarrier (100.000, 063.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ tips_1 TipRack (106.200, 073.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_2 TipRack (106.200, 169.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_3 TipRack (106.200, 265.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_4 TipRack (106.200, 361.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_5 TipRack (106.200, 457.000, 214.950)\\n โ”‚\\n(14) โ”œโ”€โ”€ plate carrier PlateCarrier (392.500, 063.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ plate Plate (396.500, 071.500, 183.120)\\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚\\n(31) โ”œโ”€โ”€ waste_block Resource (775.000, 115.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ teaching_tip_rack TipRack (780.900, 461.100, 100.000)\\n โ”‚\\n(32) โ”œโ”€โ”€ trash Trash (800.000, 190.600, 137.100)\\n\\nNone\\n\\nMoving water from A1:A3 to A4:A6...\\nPicking up tips:\\npip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \\n p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\nTips picked up successfully\\nAspirating:\\npip# vol(ul) resource offset flow rate blowout lld_z \\n p0: 100.0 plate_well_0_0 0,0,0 None None None \\n p1: 100.0 plate_well_1_0 0,0,0 None None None \\n p2: 100.0 plate_well_2_0 0,0,0 None None None \\nAspirated 100 ยตL from A1:A3\\nDispensing:\\npip# vol(ul) resource offset flow rate blowout lld_z \\n p0: 100.0 plate_well_3_0 0,0,0 None None None \\n p1: 100.0 plate_well_4_0 0,0,0 None None None \\n p2: 100.0 plate_well_5_0 0,0,0 None None None \\nDispensed 100 ยตL to A4:A6\\nDropping tips:\\npip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \\n p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\nTips dropped successfully\\n\\nLiquid transfer complete!\\nStopping the liquid handler.\\nConnection closed\\nSetting up the liquid handler.\\nResource deck was assigned to the liquid handler.\\nResource trash was assigned to the liquid handler.\\nResource trash_core96 was assigned to the liquid handler.\\nResource waste_block was assigned to the liquid handler.\\nSetting up deck layout...\\nResource tip carrier was assigned to the liquid handler.\\nResource plate carrier was assigned to the liquid handler.\\n\\nDeck layout:\\nRail Resource Type Coordinates (mm)\\n=================================================================================\\n(-6) โ”œโ”€โ”€ trash_core96 Trash (-58.200, 106.000, 229.000)\\n โ”‚\\n(1) โ”œโ”€โ”€ tip carrier TipCarrier (100.000, 063.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ tips_1 TipRack (106.200, 073.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_2 TipRack (106.200, 169.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_3 TipRack (106.200, 265.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_4 TipRack (106.200, 361.000, 214.950)\\n โ”‚ โ”œโ”€โ”€ tips_5 TipRack (106.200, 457.000, 214.950)\\n โ”‚\\n(14) โ”œโ”€โ”€ plate carrier PlateCarrier (392.500, 063.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ plate Plate (396.500, 071.500, 183.120)\\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚ โ”œโ”€โ”€ \\n โ”‚\\n(31) โ”œโ”€โ”€ waste_block Resource (775.000, 115.000, 100.000)\\n โ”‚ โ”œโ”€โ”€ teaching_tip_rack TipRack (780.900, 461.100, 100.000)\\n โ”‚\\n(32) โ”œโ”€โ”€ trash Trash (800.000, 190.600, 137.100)\\n\\nNone\\n\\nMoving water from A1:A3 to A4:A6...\\nPicking up tips:\\npip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \\n p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\nTips picked up successfully\\nAspirating:\\npip# vol(ul) resource offset flow rate blowout lld_z \\n p0: 100.0 plate_well_0_0 0,0,0 None None None \\n p1: 100.0 plate_well_1_0 0,0,0 None None None \\n p2: 100.0 plate_well_2_0 0,0,0 None None None \\nAspirated 100 ยตL from A1:A3\\nDispensing:\\npip# vol(ul) resource offset flow rate blowout lld_z \\n p0: 100.0 plate_well_3_0 0,0,0 None None None \\n p1: 100.0 plate_well_4_0 0,0,0 None None None \\n p2: 100.0 plate_well_5_0 0,0,0 None None None \\nDispensed 100 ยตL to A4:A6\\nDropping tips:\\npip# resource offset tip type max volume (ยตL) fitting depth (mm) tip length (mm) filter \\n p0: tips_1_tipspot_0_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p1: tips_1_tipspot_1_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\n p2: tips_1_tipspot_2_0 0,0,0 HamiltonTip 1065 8 95.1 Yes \\nTips dropped successfully\\n\\nLiquid transfer complete!\\nStopping the liquid handler.\\nConnection closed\\n\\nTest Result:\\n{'success': True, 'test_results': {'syntax_valid': True, 'imports_valid': True, 'simulation_successful': True, 'tracking_enabled': False, 'input_type': 'string'}, 'execution_summary': {'operations_performed': 1, 'tips_used': 0, 'liquid_transferred': 0.0, 'execution_time': 0.0, 'total_execution_time': 0.540640115737915}, 'errors': [], 'warnings': []}\\n\",\n", " '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nPerfect! The script now works successfully. Let me update the final plan:\\n\\n## Updated Plan:\\n1. [โœ“] Review PyLabRobot liquid handling documentation\\n2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\\n3. [โœ—] Test the script to ensure it\\'s valid (failed - fixed well access syntax)\\n4. [โœ“] Fix the script based on test results\\n5. [โœ“] Re-test the fixed script (SUCCESS!)\\n6. [โœ“] Provide the final working script\\n\\n\\nHere\\'s a working PyLabRobot script to move water from one range of wells to another using the Hamilton STAR backend:\\n\\n```python\\n\"\"\"\\nPyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\\nThis script demonstrates liquid transfer between well ranges on a 96-well plate.\\n\"\"\"\\n\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\nfrom pylabrobot.resources import (\\n TIP_CAR_480_A00,\\n PLT_CAR_L5AC_A00,\\n Cor_96_wellplate_360ul_Fb,\\n hamilton_96_tiprack_1000uL_filter\\n)\\n\\nasync def main():\\n # Initialize the liquid handler with Hamilton STAR backend\\n lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\\n \\n # Setup connection to the robot\\n await lh.setup()\\n \\n print(\"Setting up deck layout...\")\\n \\n # Create tip carrier and add tip racks\\n tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\\n tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\\n tip_car[0] = tiprack\\n tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\\n tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\\n tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\\n tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\\n \\n # Assign tip carrier to deck at rails 1\\n lh.deck.assign_child_resource(tip_car, rails=1)\\n \\n # Create plate carrier and add a 96-well plate\\n plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\\n plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\\n plate_car[0] = plate\\n \\n # Assign plate carrier to deck at rails 14\\n lh.deck.assign_child_resource(plate_car, rails=14)\\n \\n # Display deck summary\\n print(\"\\\\nDeck layout:\")\\n print(lh.summary())\\n \\n # Define source and destination well ranges\\n source_wells = \"A1:A3\" # Wells A1, A2, A3\\n destination_wells = \"A4:A6\" # Wells A4, A5, A6\\n \\n print(f\"\\\\nMoving water from {source_wells} to {destination_wells}...\")\\n \\n # Pick up tips - access tips from the tiprack directly\\n tips = tiprack[source_wells]\\n await lh.pick_up_tips(tips)\\n print(\"Tips picked up successfully\")\\n \\n # Aspirate liquid from source wells\\n volume = 100 # microliters\\n source = plate[source_wells]\\n await lh.aspirate(source, vols=[volume, volume, volume])\\n print(f\"Aspirated {volume} ยตL from {source_wells}\")\\n \\n # Dispense liquid to destination wells\\n destination = plate[destination_wells]\\n await lh.dispense(destination, vols=[volume, volume, volume])\\n print(f\"Dispensed {volume} ยตL to {destination_wells}\")\\n \\n # Drop tips back to the tip rack\\n await lh.drop_tips(tips)\\n print(\"Tips dropped successfully\")\\n \\n print(\"\\\\nLiquid transfer complete!\")\\n \\n # Stop the liquid handler\\n await lh.stop()\\n print(\"Connection closed\")\\n\\n# Run the async main function\\nif __name__ == \"__main__\":\\n import asyncio\\n asyncio.run(main())\\n```\\n\\n**Key Features:**\\n- Uses Hamilton STAR backend for liquid handling\\n- Transfers 100 ยตL from wells A1-A3 to wells A4-A6\\n- Includes proper deck setup with tip carriers and plate carriers\\n- Uses async/await for all liquid handling operations\\n- Properly manages tips (pickup and drop)\\n- Successfully tested and validated\\n\\nYou can modify the `source_wells`, `destination_wells`, and `volume` variables to customize the transfer for your specific needs.\\n'],\n", " 'Perfect! The script now works successfully. Let me update the final plan:\\n\\n## Updated Plan:\\n1. [โœ“] Review PyLabRobot liquid handling documentation\\n2. [โœ“] Create a script that moves water between well ranges using Hamilton STAR\\n3. [โœ—] Test the script to ensure it\\'s valid (failed - fixed well access syntax)\\n4. [โœ“] Fix the script based on test results\\n5. [โœ“] Re-test the fixed script (SUCCESS!)\\n6. [โœ“] Provide the final working script\\n\\n\\nHere\\'s a working PyLabRobot script to move water from one range of wells to another using the Hamilton STAR backend:\\n\\n```python\\n\"\"\"\\nPyLabRobot script to move water from one range of wells to another using Hamilton STAR backend.\\nThis script demonstrates liquid transfer between well ranges on a 96-well plate.\\n\"\"\"\\n\\nfrom pylabrobot.liquid_handling import LiquidHandler\\nfrom pylabrobot.liquid_handling.backends import STARBackend\\nfrom pylabrobot.resources.hamilton import STARLetDeck\\nfrom pylabrobot.resources import (\\n TIP_CAR_480_A00,\\n PLT_CAR_L5AC_A00,\\n Cor_96_wellplate_360ul_Fb,\\n hamilton_96_tiprack_1000uL_filter\\n)\\n\\nasync def main():\\n # Initialize the liquid handler with Hamilton STAR backend\\n lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\\n \\n # Setup connection to the robot\\n await lh.setup()\\n \\n print(\"Setting up deck layout...\")\\n \\n # Create tip carrier and add tip racks\\n tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\\n tiprack = hamilton_96_tiprack_1000uL_filter(name=\"tips_1\")\\n tip_car[0] = tiprack\\n tip_car[1] = hamilton_96_tiprack_1000uL_filter(name=\"tips_2\")\\n tip_car[2] = hamilton_96_tiprack_1000uL_filter(name=\"tips_3\")\\n tip_car[3] = hamilton_96_tiprack_1000uL_filter(name=\"tips_4\")\\n tip_car[4] = hamilton_96_tiprack_1000uL_filter(name=\"tips_5\")\\n \\n # Assign tip carrier to deck at rails 1\\n lh.deck.assign_child_resource(tip_car, rails=1)\\n \\n # Create plate carrier and add a 96-well plate\\n plate_car = PLT_CAR_L5AC_A00(name=\"plate carrier\")\\n plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\\n plate_car[0] = plate\\n \\n # Assign plate carrier to deck at rails 14\\n lh.deck.assign_child_resource(plate_car, rails=14)\\n \\n # Display deck summary\\n print(\"\\\\nDeck layout:\")\\n print(lh.summary())\\n \\n # Define source and destination well ranges\\n source_wells = \"A1:A3\" # Wells A1, A2, A3\\n destination_wells = \"A4:A6\" # Wells A4, A5, A6\\n \\n print(f\"\\\\nMoving water from {source_wells} to {destination_wells}...\")\\n \\n # Pick up tips - access tips from the tiprack directly\\n tips = tiprack[source_wells]\\n await lh.pick_up_tips(tips)\\n print(\"Tips picked up successfully\")\\n \\n # Aspirate liquid from source wells\\n volume = 100 # microliters\\n source = plate[source_wells]\\n await lh.aspirate(source, vols=[volume, volume, volume])\\n print(f\"Aspirated {volume} ยตL from {source_wells}\")\\n \\n # Dispense liquid to destination wells\\n destination = plate[destination_wells]\\n await lh.dispense(destination, vols=[volume, volume, volume])\\n print(f\"Dispensed {volume} ยตL to {destination_wells}\")\\n \\n # Drop tips back to the tip rack\\n await lh.drop_tips(tips)\\n print(\"Tips dropped successfully\")\\n \\n print(\"\\\\nLiquid transfer complete!\")\\n \\n # Stop the liquid handler\\n await lh.stop()\\n print(\"Connection closed\")\\n\\n# Run the async main function\\nif __name__ == \"__main__\":\\n import asyncio\\n asyncio.run(main())\\n```\\n\\n**Key Features:**\\n- Uses Hamilton STAR backend for liquid handling\\n- Transfers 100 ยตL from wells A1-A3 to wells A4-A6\\n- Includes proper deck setup with tip carriers and plate carriers\\n- Uses async/await for all liquid handling operations\\n- Properly manages tips (pickup and drop)\\n- Successfully tested and validated\\n\\nYou can modify the `source_wells`, `destination_wells`, and `volume` variables to customize the transfer for your specific needs.\\n')" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from biomni.agent import A1\n", "\n", "agent = A1(expected_data_lake_files=[])\n", "agent.go(\n", " \"Can you generate a script to use PyLabRobot to move water from one range of wells to another using the Hamilton STAR backend?\"\n", ")" ] } ], "metadata": { "kernelspec": { "display_name": "biomni_e2", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.13" } }, "nbformat": 4, "nbformat_minor": 5 }