How to use the opentrons.robot.comment function in opentrons

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github Opentrons / Protocols / protocols / dna_normalization_csv / dna_normalization_csv.ot2.py View on Github external
tip_racks=tipracks)
    elif pipette_model == 'p10-Single':
        tipracks = [
            labware.load('tiprack-10ul', slot)
            for slot in tiprack_slots]
        pipette = instruments.P10_Single(
            mount=pipette_mount,
            tip_racks=tipracks)

    plate = labware.load(plate_type, '3')

    volumes = [float(cell) for cell in well_csv_to_list(volumes_csv)]

    for vol in volumes:
        if 0 < vol < pipette.min_volume:
            robot.comment(
                'WARNING: volume {} is below pipette\'s minimum volume.'
                .format(vol))

    tip_strategy = 'always' if tip_reuse == 'new tip each time' else 'once'
    pipette.transfer(volumes, source, plate, new_tip=tip_strategy)
github Opentrons / Protocols / protocols / 7d113b / 7d113b.ot2.py View on Github external
conc1 = float(y)
        vol1 = round(vol_const/conc1, 1)
        if vol1 > final_volume:
            vol1 = final_volume
        ww = final_volume - vol1
        src.append(x)
        v1.append(vol1)
        water_vol.append(ww)

    robot.comment('Adding correct amount of water to corresponding wells.')
    # transfer water
    for dest, vol in zip(src, water_vol):
        if vol > 0:
            water_transfer(dest, vol)

    robot.comment('Adding correct amount of DNA to corresponding wells')
    # transfer dna
    for dest, vol in zip(src, v1):
        dna_transfer(dest, vol)

    robot.comment('Protocol now complete.')
github Opentrons / Protocols / protocols / 569d34-part1 / nuc_acid_purification_pt1.ot2.py View on Github external
collection tubes on slot 2 using TissueLyserII, incubate at 56°C for 30 \
minutes, and centrifuge at 4,000 x g for 10 minutes')

    # carefully transfer lysate from collection tubes to corresponding wells of
    # magnetic module deep plate
    m300.set_flow_rate(aspirate=50)
    for s, d in zip(strips_multi, mag_multi):
        pick_up('m300')
        m300.transfer(
            volume_of_lysate_to_transfer_in_ul, s, d.top(), new_tip='never')
        m300.mix(10, 250, d)
        m300.blow_out(d.top())
        m300.drop_tip()
    m300.set_flow_rate(aspirate=150)

    robot.comment('Let sit at room temperature for 5 minutes, and continue \
with part 2.')
github Opentrons / Protocols / protocols / qiaseq-pt-4 / pt4_target_enrichment.ot2.py View on Github external
m50.transfer(
            11.6,
            strips.wells('A1'),
            [s for s in samples_multi],
            new_tip='always'
        )

    robot.pause('Briefly centrifuge reaction plate and replace in slot 1')

    for s in samples_multi:
        m50.pick_up_tip()
        m50.mix(7, 10, s)
        m50.blow_out(s.top())
        m50.drop_tip()

    robot.comment('Briefly centrifuge again. Program the thermal cycler \
according to the parameters prescribed in the manual, and thermocycle the \
github Opentrons / Protocols / protocols / 229e98-part2 / 229e98-part2.ot2.py View on Github external
# Step 5
    for source, dest in zip(ultratubes.wells()[:50], sampvials.wells()):
        pick_up(pip50)
        pip50.transfer(20, source, dest, new_tip='never')
        pip50.blow_out(dest.top())
        pip50.drop_tip()

    robot.pause("Samples have been transferred to sample vial. Replace the \
    centrifuge tubes in slots 2/5/8 and when ready, click RESUME.")
    for source, dest in zip(ultratubes.wells()[:50], centtubes.wells()):
        pick_up(pip300)
        pip300.transfer(180, source, dest, new_tip='never')
        pip300.blow_out(dest.top())
        pip300.drop_tip()

    robot.comment("Part 2 complete, protocol is now finished.")
github Opentrons / Protocols / protocols / 4c4650 / csv_dilution.ot2.py View on Github external
def pick_up():
        nonlocal tip1000_count
        if tip1000_count == tip1000_max:
            robot.pause('Refill 1000ul tipracks before resuming.')
            p1000.reset()
            tip1000_count = 0
        tip1000_count += 1
        p1000.pick_up_tip()

    # perform dilution transfer
    for i, (vol, dest) in enumerate(zip(volumes, all_tubes)):
        if i == 0:
            pick_up()
            p1000.move_to(dest.top())
            robot.comment('Ensure pipette tip is centered and flush with the \
opening of tube A1 of tuberack 1. Cancel run if not.')
            p1000.delay(seconds=10)
        # determine offset for dispense
        offset = -10 if vol >= 1800 else -20
        num_transfers = math.ceil(vol/1000)
        v_per_trans = vol/num_transfers
        for _ in range(num_transfers):
            if not p1000.tip_attached:
                pick_up()
            p1000.transfer(v_per_trans, te, dest.top(offset), new_tip='never')
            p1000.blow_out()
            p1000.drop_tip()
github Opentrons / Protocols / protocols / 55f974 / 55f974.ot2.py View on Github external
p300.transfer(400, zyppy_wash, mag.top(), new_tip='never')
            p300.mix(10, 280, mag)
            p300.blow_out(mag.top())
            p300.drop_tip()
        magdeck.engage(height=mag_offset)
        p300.delay(minutes=2)
        p300.set_flow_rate(aspirate=75)
        for mag in mag_plate:
            pick_up()
            p300.transfer(400, mag, liq_waste, new_tip='never')
            p300.drop_tip()
        magdeck.disengage()

    inc_cmmt = 'Incubating for '+str(incubation_time)+' minutes.'
    robot.comment(inc_cmmt)
    robot.comment('While incubating, please replace tips in slot 8.')
    p300.set_flow_rate(aspirate=150)

    p300.delay(minutes=incubation_time)

    # add elution buffer and mix
    for tips, mag in zip(used_tips, mag_plate):
        p300.pick_up_tip(tips)
        p300.transfer(40, zyppy_el, mag, new_tip='never')
        p300.mix(10, 40, mag)
        p300.blow_out(mag.top())
        p300.return_tip()

    for _ in range(10):
        p300.delay(seconds=30)
        for tips, mag in zip(used_tips, mag_plate):
            p300.pick_up_tip(tips)
github Opentrons / Protocols / protocols / 56a6a1 / protein_array.ot2.py View on Github external
dispense_locs,
            disposal_vol=0,
            new_tip='never'
        )
        m300.move_to(res_12.wells('A12').top(10))
        robot.comment('Incubating 5 minutes.')
        m300.delay(minutes=5)
        if i < 3:
            vacuum()

    m300.move_to(res_12.wells('A12').top(10))
    robot.comment('Incubating 5 minutes.')
    m300.delay(minutes=5)
    m300.drop_tip(m300.trash_container.top(15))

    robot.comment('Take off slides from FastFrame and place into 50 ml \
conical tube filled with 45 ml PBS, and wash by agitating on TeleShake for 5 \
github Opentrons / Protocols / protocols / 50486f-part2-GAP / 50486f-part2-GAP.ot2.py View on Github external
tip10_count += 1

    dest = tempplate.rows('A')

    for i in range(number_of_plates):

        # transfer 10ul of mastermix from PCR strip to plate on tempdeck

        for d in dest:
            pick_up(pip10)
            pip10.transfer(10, pcr_well.wells('A1'), d, new_tip='never')
            pip10.blow_out(d.top())
            pip10.drop_tip()

        if i == number_of_plates-1:
            robot.comment("Part 2/4 (GAP) complete. Please remove plate from \
            Slot 1 and run on PCR program. When ready, load materials and run \
            Part 3/4 (EXO) on the OT-2.")
        else:
            robot.pause("Part 2/4 (GAP), plate "+str(i+1)+" now complete. \
            Please remove plate from Slot 1 and run on PCR program. You may \
github Opentrons / Protocols / protocols / 56a6a1 / protein_array.ot2.py View on Github external
)
            m300.move_to(res_12.wells('A12').top(10))
            robot.comment('Incubating 5 minutes.')
            m300.delay(minutes=5)
            vacuum()

        m300.pick_up_tip()
        m300.distribute(
            100,
            sg_source,
            dispense_locs,
            disposal_vol=0,
            new_tip='never'
        )
        m300.move_to(res_12.wells('A12').top(10))
        robot.comment('Incubating 5 minutes.')
        m300.delay(minutes=5)
        vacuum()

        for i in range(num_final_pbst):
            m300.pick_up_tip()
            m300.distribute(
                100,
                pbst[wash_ind],
                dispense_locs,
                disposal_vol=0,
                new_tip='never'
            )
            m300.move_to(res_12.wells('A12').top(10))
            robot.comment('Incubating 5 minutes.')
            m300.delay(minutes=5)
            if final_aspirate: