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Fix if volume > 0, lower asp height for samples #4897

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Fix if volume > 0, lower asp height for samples #4897

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8dab6d1
Fix if volume > 0, lower asp height for samples
parrishpayne12 Sep 21, 2023
b39a271
Make temp mod optional, add temp setting
parrishpayne12 Sep 22, 2023
43cd2aa
Update fields
parrishpayne12 Sep 22, 2023
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89 changes: 56 additions & 33 deletions protocols/08207f/08207f.ot2.apiv2.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,20 @@

def run(ctx):

[input_csv, init_vol_buff, labware_pcr_plate, labware_temp_deck,
p20_mount, p300_mount] = get_values( # noqa: F821
"input_csv", "init_vol_buff", "labware_pcr_plate", "labware_temp_deck",
"p20_mount", "p300_mount")

[input_csv, init_vol_buff, labware_pcr_plate, dna_plate_lname,
temp_mod_lname, temperature, p20_mount, p300_mount] = get_values( # noqa: F821
"input_csv", "init_vol_buff", "labware_pcr_plate", "dna_plate_lname",
"temp_mod_lname", "temperature","p20_mount", "p300_mount")

if not 4 <= temperature <= 95:
raise Exception(
"Temperature module range is between 4 and 95ºC")

# modules
temp_mod = None
if temp_mod_lname:
temp_mod = ctx.load_module("temperature module gen2", '3')

# labware
tiprack20 = [
ctx.load_labware('opentrons_96_filtertiprack_20ul', slot,
Expand All @@ -24,8 +33,14 @@ def run(ctx):
ctx.load_labware(
'opentrons_96_filtertiprack_200ul', slot, '200ul tiprack')
for slot in ['2', '9']]
tempdeck = ctx.load_module('temperature module gen2', '3')
dna_plate = tempdeck.load_labware(labware_temp_deck) # noqa: E501

dna_plate = None
if temp_mod:
dna_plate = temp_mod.load_labware(dna_plate_lname, 'sample plate')
else:
dna_plate = ctx.load_labware(dna_plate_lname, '3', 'sample plate')


tube_rack = ctx.load_labware(
'opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', '5')
dest_plate = ctx.load_labware(labware_pcr_plate, '6', 'end-point-plate') # noqa: E501
Expand Down Expand Up @@ -65,8 +80,13 @@ def slow_withdraw(pip, well, delay_seconds=2.0):
pip.move_to(well.top())
pip.default_speed *= 16

# mapping
# Set temperature module temperature
if temp_mod:
ctx.comment("\n\nSetting temperature module to {} ºC\n".
format(temperature))
temp_mod.set_temperature(temperature)

# mapping
buffer = tube_rack.wells_by_name()['A3']

# parse
Expand All @@ -80,17 +100,18 @@ def slow_withdraw(pip, well, delay_seconds=2.0):
dest_well = dest_plate.wells_by_name()[well]
volume = float(row[7])

if volume > 20:
if not p300.has_tip:
p300.pick_up_tip()
p300.aspirate(volume, buffer.bottom(h_buff))
p300.dispense(volume, dest_well)
if volume > 0:
if volume > 20:
if not p300.has_tip:
p300.pick_up_tip()
p300.aspirate(volume, buffer.bottom(h_buff))
p300.dispense(volume, dest_well)

else:
if not p20.has_tip:
p20.pick_up_tip()
p20.aspirate(volume, buffer.bottom(h_buff))
p20.dispense(volume, dest_well)
else:
if not p20.has_tip:
p20.pick_up_tip()
p20.aspirate(volume, buffer.bottom(h_buff))
p20.dispense(volume, dest_well)

adjust_height(volume)

Expand All @@ -108,19 +129,21 @@ def slow_withdraw(pip, well, delay_seconds=2.0):

volume = float(row[6])
mix_reps = 2
tip_height = 0.5

if volume > 0:
if volume > 20:
p300.pick_up_tip()
p300.aspirate(volume, source_well.bottom(tip_height))
p300.dispense(volume, dest_well)
p300.mix(mix_reps, 20)
p300.blow_out()
p300.drop_tip()

if volume > 20:
p300.pick_up_tip()
p300.aspirate(volume, source_well)
p300.dispense(volume, dest_well)
p300.mix(mix_reps, 20)
p300.blow_out()
p300.drop_tip()

else:
p20.pick_up_tip()
p20.aspirate(volume, source_well)
p20.dispense(volume, dest_well)
p20.mix(mix_reps, 10)
p20.blow_out()
p20.drop_tip()
else:
p20.pick_up_tip()
p20.aspirate(volume, source_well.bottom(tip_height))
p20.dispense(volume, dest_well)
p20.mix(mix_reps, 10)
p20.blow_out()
p20.drop_tip()
25 changes: 21 additions & 4 deletions protocols/08207f/fields.json
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,28 @@
},
{
"type": "dropDown",
"label": "Labware on the Temperature Module",
"name": "labware_temp_deck",
"label": "(Optional) Temperature module with aluminum block",
"name": "temp_mod_lname",
"options": [
{ "label": "eppendorftwin.tec96_96_aluminumblock_150ul", "value": "eppendorftwin.tec96_96_aluminumblock_150ul" },
{ "label": "starlab_96_aluminumblock_200ul", "value": "starlab_96_aluminumblock_200ul" }
{"label": "No temperature module", "value": false},
{"label": "Temperature module + aluminum block ", "value": true}
]
},
{
"type": "float",
"label": "Set temperature of the temperature module",
"name": "temperature",
"default": 4
},
{
"type": "dropDown",
"label": "Labware for Sample Plate",
"name": "dna_plate_lname",
"options": [
{ "label": "eppendorftwin.tec96 on aluminum block_150ul", "value": "eppendorftwin.tec96_96_aluminumblock_150ul" },
{ "label": "starlab_96 on aluminum block_200ul", "value": "starlab_96_aluminumblock_200ul" },
{ "label": "eppendorftwin.tec_96_wellplate_150ul", "value": "eppendorftwin.tec_96_wellplate_150ul" },
{ "label": "starlab_96_wellplate_200ul", "value": "starlab_96_wellplate_200ul" }
]
},
{
Expand Down