Initial commit

skills/opentrons-integration/scripts/basic_protocol_template.py

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+#!/usr/bin/env python3
+"""
+Basic Opentrons Protocol Template
+
+This template provides a minimal starting point for creating Opentrons protocols.
+Replace the placeholder values and add your specific protocol logic.
+"""
+
+from opentrons import protocol_api
+
+# Metadata
+metadata = {
+    'protocolName': 'Basic Protocol Template',
+    'author': 'Your Name <email@example.com>',
+    'description': 'A basic protocol template for Opentrons',
+    'apiLevel': '2.19'
+}
+
+# Requirements
+requirements = {
+    'robotType': 'Flex',  # or 'OT-2'
+    'apiLevel': '2.19'
+}
+
+def run(protocol: protocol_api.ProtocolContext):
+    """
+    Main protocol function.
+
+    Args:
+        protocol: The protocol context provided by Opentrons
+    """
+
+    # Load tip racks
+    tips_200 = protocol.load_labware('opentrons_flex_96_tiprack_200ul', 'D1')
+
+    # Load labware
+    source_plate = protocol.load_labware(
+        'nest_96_wellplate_200ul_flat',
+        'D2',
+        label='Source Plate'
+    )
+
+    dest_plate = protocol.load_labware(
+        'nest_96_wellplate_200ul_flat',
+        'D3',
+        label='Destination Plate'
+    )
+
+    # Load pipette
+    pipette = protocol.load_instrument(
+        'p300_single_flex',
+        'left',
+        tip_racks=[tips_200]
+    )
+
+    # Protocol commands
+    protocol.comment('Starting protocol...')
+
+    # Example: Transfer from A1 to B1
+    pipette.transfer(
+        volume=50,
+        source=source_plate['A1'],
+        dest=dest_plate['B1'],
+        new_tip='always'
+    )
+
+    protocol.comment('Protocol complete!')

skills/opentrons-integration/scripts/pcr_setup_template.py

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+#!/usr/bin/env python3
+"""
+PCR Setup Protocol Template
+
+This template demonstrates how to set up PCR reactions using the Thermocycler module.
+Includes master mix distribution, sample addition, and PCR cycling.
+"""
+
+from opentrons import protocol_api
+
+metadata = {
+    'protocolName': 'PCR Setup with Thermocycler',
+    'author': 'Opentrons',
+    'description': 'Automated PCR setup and cycling protocol',
+    'apiLevel': '2.19'
+}
+
+requirements = {
+    'robotType': 'Flex',
+    'apiLevel': '2.19'
+}
+
+def run(protocol: protocol_api.ProtocolContext):
+    """
+    Sets up PCR reactions and runs thermocycler.
+
+    Protocol performs:
+    1. Distributes master mix to PCR plate
+    2. Adds DNA samples
+    3. Runs PCR cycling program
+    """
+
+    # Load thermocycler module
+    tc_mod = protocol.load_module('thermocyclerModuleV2')
+    tc_plate = tc_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')
+
+    # Load tips and reagents
+    tips_20 = protocol.load_labware('opentrons_flex_96_tiprack_50ul', 'C1')
+    tips_200 = protocol.load_labware('opentrons_flex_96_tiprack_200ul', 'C2')
+    reagent_rack = protocol.load_labware(
+        'opentrons_24_tuberack_nest_1.5ml_snapcap',
+        'D1',
+        label='Reagents'
+    )
+
+    # Load pipettes
+    p20 = protocol.load_instrument('p50_single_flex', 'left', tip_racks=[tips_20])
+    p300 = protocol.load_instrument('p300_single_flex', 'right', tip_racks=[tips_200])
+
+    # Define liquids
+    master_mix = protocol.define_liquid(
+        name='PCR Master Mix',
+        description='2x PCR master mix',
+        display_color='#FFB6C1'
+    )
+
+    template_dna = protocol.define_liquid(
+        name='Template DNA',
+        description='DNA samples',
+        display_color='#90EE90'
+    )
+
+    # Load liquids
+    reagent_rack['A1'].load_liquid(liquid=master_mix, volume=1000)
+    for i in range(8):  # 8 samples
+        reagent_rack.wells()[i + 1].load_liquid(liquid=template_dna, volume=50)
+
+    # PCR setup parameters
+    num_samples = 8
+    master_mix_volume = 20  # µL per reaction
+    template_volume = 5  # µL per reaction
+    total_reaction_volume = 25  # µL
+
+    protocol.comment('Starting PCR setup...')
+
+    # Open thermocycler lid
+    tc_mod.open_lid()
+    protocol.comment('Thermocycler lid opened')
+
+    # Step 1: Distribute master mix
+    protocol.comment(f'Distributing {master_mix_volume}µL master mix to {num_samples} wells...')
+    p300.distribute(
+        master_mix_volume,
+        reagent_rack['A1'],
+        tc_plate.wells()[:num_samples],
+        new_tip='once',
+        disposal_volume=10  # Extra volume to prevent shortage
+    )
+
+    # Step 2: Add template DNA
+    protocol.comment('Adding template DNA to each well...')
+    for i in range(num_samples):
+        p20.transfer(
+            template_volume,
+            reagent_rack.wells()[i + 1],  # Sample tubes
+            tc_plate.wells()[i],  # PCR plate wells
+            mix_after=(3, 10),  # Mix 3x with 10µL
+            new_tip='always'
+        )
+
+    protocol.comment('PCR reactions prepared')
+
+    # Close lid and start PCR
+    tc_mod.close_lid()
+    protocol.comment('Thermocycler lid closed')
+
+    # Set lid temperature
+    tc_mod.set_lid_temperature(celsius=105)
+    protocol.comment('Lid heating to 105°C')
+
+    # Initial denaturation
+    protocol.comment('Initial denaturation...')
+    tc_mod.set_block_temperature(
+        temperature=95,
+        hold_time_seconds=180,
+        block_max_volume=total_reaction_volume
+    )
+
+    # PCR cycling profile
+    protocol.comment('Starting PCR cycling...')
+    profile = [
+        {'temperature': 95, 'hold_time_seconds': 15},  # Denaturation
+        {'temperature': 60, 'hold_time_seconds': 30},  # Annealing
+        {'temperature': 72, 'hold_time_seconds': 30}   # Extension
+    ]
+
+    num_cycles = 35
+    tc_mod.execute_profile(
+        steps=profile,
+        repetitions=num_cycles,
+        block_max_volume=total_reaction_volume
+    )
+
+    # Final extension
+    protocol.comment('Final extension...')
+    tc_mod.set_block_temperature(
+        temperature=72,
+        hold_time_minutes=5,
+        block_max_volume=total_reaction_volume
+    )
+
+    # Hold at 4°C
+    protocol.comment('Cooling to 4°C for storage...')
+    tc_mod.set_block_temperature(
+        temperature=4,
+        block_max_volume=total_reaction_volume
+    )
+
+    # Deactivate and open
+    tc_mod.deactivate_lid()
+    tc_mod.open_lid()
+
+    protocol.comment('PCR complete! Plate ready for removal.')
+    protocol.comment(f'Completed {num_cycles} cycles for {num_samples} samples')

skills/opentrons-integration/scripts/serial_dilution_template.py

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+#!/usr/bin/env python3
+"""
+Serial Dilution Protocol Template
+
+This template demonstrates how to perform a serial dilution across a plate row.
+Useful for creating concentration gradients for assays.
+"""
+
+from opentrons import protocol_api
+
+metadata = {
+    'protocolName': 'Serial Dilution Template',
+    'author': 'Opentrons',
+    'description': 'Serial dilution protocol for creating concentration gradients',
+    'apiLevel': '2.19'
+}
+
+requirements = {
+    'robotType': 'Flex',
+    'apiLevel': '2.19'
+}
+
+def run(protocol: protocol_api.ProtocolContext):
+    """
+    Performs a serial dilution across plate rows.
+
+    Protocol performs:
+    1. Adds diluent to all wells except the first column
+    2. Transfers stock solution to first column
+    3. Performs serial dilutions across rows
+    """
+
+    # Load labware
+    tips = protocol.load_labware('opentrons_flex_96_tiprack_200ul', 'D1')
+    reservoir = protocol.load_labware('nest_12_reservoir_15ml', 'D2', label='Reservoir')
+    plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 'D3', label='Dilution Plate')
+
+    # Load pipette
+    p300 = protocol.load_instrument('p300_single_flex', 'left', tip_racks=[tips])
+
+    # Define liquids (optional, for visualization)
+    diluent = protocol.define_liquid(
+        name='Diluent',
+        description='Buffer or growth media',
+        display_color='#B0E0E6'
+    )
+
+    stock = protocol.define_liquid(
+        name='Stock Solution',
+        description='Concentrated stock',
+        display_color='#FF6347'
+    )
+
+    # Load liquids into wells
+    reservoir['A1'].load_liquid(liquid=diluent, volume=15000)
+    reservoir['A2'].load_liquid(liquid=stock, volume=5000)
+
+    # Protocol parameters
+    dilution_factor = 2  # 1:2 dilution
+    transfer_volume = 100  # µL
+    num_dilutions = 11  # Number of dilution steps
+
+    protocol.comment('Starting serial dilution protocol')
+
+    # Step 1: Add diluent to all wells except first column
+    protocol.comment('Adding diluent to wells...')
+    for row in plate.rows()[:8]:  # For each row (A-H)
+        p300.transfer(
+            transfer_volume,
+            reservoir['A1'],  # Diluent source
+            row[1:],  # All wells except first (columns 2-12)
+            new_tip='once'
+        )
+
+    # Step 2: Add stock solution to first column
+    protocol.comment('Adding stock solution to first column...')
+    p300.transfer(
+        transfer_volume * 2,  # Double volume for first well
+        reservoir['A2'],  # Stock source
+        [row[0] for row in plate.rows()[:8]],  # First column (wells A1-H1)
+        new_tip='always'
+    )
+
+    # Step 3: Perform serial dilution
+    protocol.comment('Performing serial dilutions...')
+    for row in plate.rows()[:8]:  # For each row
+        p300.transfer(
+            transfer_volume,
+            row[:num_dilutions],  # Source wells (1-11)
+            row[1:num_dilutions + 1],  # Destination wells (2-12)
+            mix_after=(3, 50),  # Mix 3x with 50µL after each transfer
+            new_tip='always'
+        )
+
+    protocol.comment('Serial dilution complete!')
+    protocol.comment(f'Created {num_dilutions} dilutions with {dilution_factor}x dilution factor')