Merge branch 'release/1.10'

Author: saramonzon

CHANGELOG

@@ -1,3 +1,19 @@
+## Version 1.10
+
+New features:
+- New labware configuration: Biotix tips for 300 and 1000 configured in all protocols.
+- New labware configuration: axygen pcr plate configured in required protocols.
+
+Protocol modifications:
+- Waste disposal height modified, now the liquid waste is dispensed above the reservoir.
+- Aspiration in washes is modified from 220 to 210 ul to avoid the liquid touching the tip filters.
+- Change magnet height to 23 mm when using vwr deep well plates.
+- Removed reuse tips for elution steps in extraction protocol.
+- Now remove trash pause is prompted before the incubation pause.
+
+Documentation:
+- Added calibration docs. Protocol, multichannel pipette and magdeck calibration.
+
 ## Version 1.9
 
 New features:

calibration_check/stationA_protocol1_buffer_S3_calibration.py

@@ -23,6 +23,7 @@
 BUFFER_LABWARE = 'opentrons plastic 30ml tubes'
 DESTINATION_LABWARE = 'opentrons plastic 2ml tubes'
 DEST_TUBE = '2ml tubes'
+TIPS1000 = 'biotix'
 VOLUME_BUFFER = 300
 LANGUAGE = 'esp'
 RESET_TIPCOUNT = False
@@ -43,6 +44,10 @@
 """
 NUM_SAMPLES is the number of samples, must be an integer number
 
+TIPS 1000
+    biotix
+    opentrons
+
 BUFFER_LABWARE must be one of the following:
     opentrons plastic 50ml tubes
     opentrons plastic 30ml tubes
@@ -56,6 +61,10 @@
 
 
 # Constants
+TIPS1000_LW_DICT = {
+    'biotix': 'biotix_96_tiprack_1000ul',
+    'opentrons': 'opentrons_96_tiprack_1000ul'
+}
 BUFFER_LW_DICT = {
     'opentrons plastic 50ml tubes': 'opentrons_6_tuberack_falcon_50ml_conical',
     'opentrons plastic 30ml tubes': 'opentrons_6_tuberack_generic_30ml_conical'
@@ -221,8 +230,11 @@ def run(ctx: protocol_api.ProtocolContext):
         reset_tipcount()
 
     # define tips
-    tips1000 = [robot.load_labware('opentrons_96_filtertiprack_1000ul',
-                                     3, '1000µl tiprack')]
+    tips1000 = [
+        robot.load_labware(TIPS1000_LW_DICT[TIPS1000], slot,
+                         '1000µl filter tiprack')
+        for slot in ['3']
+    ]
 
     # define pipettes
     p1000 = robot.load_instrument('p1000_single_gen2', 'left', tip_racks=tips1000)

calibration_check/stationA_protocol2_beads_S3_calibration.py

@@ -22,6 +22,7 @@
 BEADS_LABWARE = 'opentrons plastic 30ml tubes'
 PLATE_LABWARE = 'nest deep generic well plate'
 VOLUME_BEADS = 410
+TIPS1000 = 'biotix'
 DILUTE_BEADS = True
 LANGUAGE = 'esp'
 RESET_TIPCOUNT = False
@@ -42,6 +43,10 @@
 """
 NUM_SAMPLES is the number of samples, must be an integer number
 
+TIPS 1000
+    biotix
+    opentrons
+
 BEADS_LABWARE must be one of the following:
     opentrons plastic 50 ml tubes
     opentrons plastic 30ml tubes
@@ -52,6 +57,11 @@
     vwr deep generic well plate
 """
 
+TIPS1000_LW_DICT = {
+    'biotix': 'biotix_96_tiprack_1000ul',
+    'opentrons': 'opentrons_96_tiprack_1000ul'
+}
+
 BD_LW_DICT = {
     'opentrons plastic 50 ml tubes': 'opentrons_6_tuberack_falcon_50ml_conical',
     'opentrons plastic 30ml tubes': 'opentrons_6_tuberack_generic_30ml_conical'
@@ -241,8 +251,11 @@ def run(ctx: protocol_api.ProtocolContext):
         reset_tipcount()
 
     # load tips
-    tips1000 = [robot.load_labware('opentrons_96_filtertiprack_1000ul',
-                                     3, '1000µl tiprack')]
+    tips1000 = [
+        robot.load_labware(TIPS1000_LW_DICT[TIPS1000], slot,
+                         '1000µl filter tiprack')
+        for slot in ['3']
+    ]
 
     # load pipette
     p1000 = robot.load_instrument(

calibration_check/stationA_protocol3_lysates_S3_calibration.py

@@ -23,6 +23,7 @@
 NUM_SAMPLES = 96
 LYSATE_LABWARE = 'opentrons plastic 2ml tubes'
 PLATE_LABWARE = 'nest deep generic well plate'
+TIPS1000 = 'biotix'
 VOLUME_LYSATE = 400
 BEADS = False
 LANGUAGE = 'esp'
@@ -47,6 +48,10 @@
 """
 NUM_SAMPLES is the number of samples, must be an integer number
 
+TIPS 1000
+    biotix
+    opentrons
+
 LYSATE_LABWARE must be one of the following:
     opentrons plastic 2ml tubes
 
@@ -56,6 +61,11 @@
     vwr deep generic well plate
 """
 
+TIPS1000_LW_DICT = {
+    'biotix': 'biotix_96_tiprack_1000ul',
+    'opentrons': 'opentrons_96_tiprack_1000ul'
+}
+
 LY_LW_DICT = {
     'opentrons plastic 2ml tubes': 'opentrons_24_tuberack_generic_2ml_screwcap'
 }
@@ -224,8 +234,11 @@ def run(ctx: protocol_api.ProtocolContext):
         reset_tipcount()
 
     # load tips
-    tips1000 = [robot.load_labware('opentrons_96_filtertiprack_1000ul',
-                                     3, '1000µl tiprack')]
+    tips1000 = [
+        robot.load_labware(TIPS1000_LW_DICT[TIPS1000], slot,
+                         '1000µl filter tiprack')
+        for slot in ['3']
+    ]
 
     # load pipette
     p1000 = robot.load_instrument(

calibration_check/stationB_protocol1_extraction_S3_calibration.py

@@ -38,10 +38,13 @@
 REAGENT_LABWARE = 'nest 12 reservoir plate'
 MAGPLATE_LABWARE = 'nest deep generic well plate'
 WASTE_LABWARE = 'nest 1 reservoir plate'
+TIPS300 = 'opentrons'
+TIPS1000 = 'opentrons'
 ELUTION_LABWARE = 'opentrons aluminum nest plate'
+REUSE_TIPS = "False"
 DISPENSE_BEADS = False
 LANGUAGE = 'esp'
-RESET_TIPCOUNT = False
+RESET_TIPCOUNT = True
 
 # End Parameters to adapt the protocol
 
@@ -59,6 +62,14 @@
 """
 NUM_SAMPLES is the number of samples, must be an integer number
 
+TIPS 300
+    biotix
+    opentrons
+
+TIPS 1000
+    biotix
+    opentrons
+
 REAGENT_LABWARE must be one of the following:
     nest 12 reservoir plate
 
@@ -82,18 +93,31 @@
 # Calculated variables
 if MAGPLATE_LABWARE == 'nest deep generic well plate':
     MAGNET_HEIGHT = 22
+    ASPIRATE_HEIGHT= 1.5
 elif MAGPLATE_LABWARE == 'vwr deep generic well plate':
-    MAGNET_HEIGHT = 22
+    MAGNET_HEIGHT = 23
+    ASPIRATE_HEIGHT= 1.5
 elif MAGPLATE_LABWARE == 'ecogen deep generic well plate':
     MAGNET_HEIGHT = 21
+    ASPIRATE_HEIGHT= 1.5
 else:
     MAGNET_HEIGHT = 22
+    ASPIRATE_HEIGHT= 1.5
 
 # End Parameters to adapt the protocol
 ACTION = "StationB-protocol1-extraction"
 PROTOCOL_ID = "0000-AA"
 
 # Constants
+TIPS300_LW_DICT = {
+    'biotix': 'biotix_96_tiprack_300ul_flat',
+    'opentrons': 'opentrons_96_tiprack_300ul'
+}
+
+TIPS1000_LW_DICT = {
+    'biotix': 'biotix_96_tiprack_1000ul',
+    'opentrons': 'opentrons_96_tiprack_1000ul'
+}
 REAGENT_LW_DICT = {
     'nest 12 reservoir plate': 'nest_12_reservoir_15ml'
 }
@@ -379,7 +403,7 @@ def run(ctx: protocol_api.ProtocolContext):
     following:\nnest 1 reservoir plate')
 
     waste = robot.load_labware(
-        WASTE_LW_DICT[WASTE_LABWARE], '11', 'waste reservoir').wells()[0].top(-10)
+        WASTE_LW_DICT[WASTE_LABWARE], '11', 'waste reservoir').wells()[0].top(1)
 
     ## REAGENT RESERVOIR
     if REAGENT_LABWARE not in REAGENT_LW_DICT:
@@ -392,16 +416,33 @@ def run(ctx: protocol_api.ProtocolContext):
     ## TIPS
     # using standard tip definition despite actually using filter tips
     # so that the tips can accommodate ~220µl per transfer for efficiency
-    tips300 = [
+    if REUSE_TIPS == True:
+        tips300 = [
+            robot.load_labware(
+                TIPS300_LW_DICT[TIPS300], slot, '300µl filter tiprack')
+            for slot in ['8', '6', '2', '3']
+        ]
+        tipsreuse = [
+            robot.load_labware(
+                'opentrons_96_tiprack_300ul', slot, '200µl filter tiprack')
+            for slot in ['7']
+        ]
+        tips1000 = [
+            robot.load_labware(TIPS1000_LW_DICT[TIPS1000], slot,
+                             '1000µl filter tiprack')
+            for slot in ['5']
+        ]
+    else:
+        tips300 = [
         robot.load_labware(
-            'opentrons_96_tiprack_300ul', slot, '200µl filter tiprack')
-        for slot in ['2', '3', '5', '6', '9','4']
-    ]
-    tips1000 = [
-        robot.load_labware('opentrons_96_filtertiprack_1000ul', slot,
-                         '1000µl filter tiprack')
-        for slot in ['8']
-    ]
+            TIPS300_LW_DICT[TIPS300], slot, '300µl filter tiprack')
+            for slot in ['2', '3', '5', '6', '9','4']
+        ]
+        tips1000 = [
+            robot.load_labware(TIPS1000_LW_DICT[TIPS1000], slot,
+                             '1000µl filter tiprack')
+            for slot in ['8']
+        ]
 
     # reagents and samples
     num_cols = math.ceil(NUM_SAMPLES/8)
@@ -436,10 +477,10 @@ def run(ctx: protocol_api.ProtocolContext):
     for position in [mag_samples_s[0], mag_samples_s[-1]]:
         p1000.move_to(position.top())
         robot.pause(f"Is it at the top of the well?")
-        p1000.aspirate(800, position.bottom(1))
+        p1000.aspirate(850, position.bottom(ASPIRATE_HEIGHT))
         p1000.move_to(position.top())
         robot.pause(f"Did it aspirate correctly?")
-        p1000.dispense(800, waste)
+        p1000.dispense(850, waste)
         p1000.move_to(waste)
         robot.pause(f"Did it dispense all the liquid?")
     drop(p1000)
@@ -458,19 +499,22 @@ def run(ctx: protocol_api.ProtocolContext):
     m300.dispense(200, mag_samples_m[0].bottom(5))
     m300.move_to(mag_samples_m[0].top())
     robot.pause(f"Did it dispense all the liquid?")
-    m300.aspirate(200, mag_samples_m[0].bottom(1))
+    magdeck.engage(height_from_base=MAGNET_HEIGHT)
+    m300.aspirate(210, mag_samples_m[0].bottom(ASPIRATE_HEIGHT))
     m300.move_to(mag_samples_m[0].top())
     robot.pause(f"Did it aspirate correctly?")
     m300.move_to(mag_samples_m[-1].top())
     robot.pause(f"Is it at the top of the well?")
-    m300.dispense(200, mag_samples_m[-1].bottom(5))
+    magdeck.disengage()
+    m300.dispense(210, mag_samples_m[-1].bottom(5))
     m300.move_to(mag_samples_m[-1].top())
+    magdeck.engage(height_from_base=MAGNET_HEIGHT)
     robot.pause(f"Did it dispense all the liquid?")
-    m300.aspirate(200, mag_samples_m[-1].bottom(1))
+    m300.aspirate(210, mag_samples_m[-1].bottom(ASPIRATE_HEIGHT))
     m300.move_to(mag_samples_m[-1].top())
     robot.pause(f"Did it aspirate correctly?")
     # waste
-    m300.dispense(200, waste)
+    m300.dispense(210, waste)
     m300.move_to(waste)
     robot.pause(f"Did it dispense all the liquid?")
     drop(m300)

calibration_check/stationC_protocol1_pcr_S3_calibration.py

@@ -25,6 +25,7 @@
 PCR_LABWARE = 'opentrons aluminum nest plate'
 ELUTION_LABWARE = 'opentrons aluminum nest plate'
 PREPARE_MASTERMIX = True
+TIPS300 = 'biotix'
 MM_TYPE = 'MM1'
 VOLUME_ELUTION = 7
 TRANSFER_MASTERMIX = True
@@ -48,6 +49,10 @@
 """
 NUM_SAMPLES is the number of samples, must be an integer number
 
+TIPS 300
+    biotix
+    opentrons
+
 MM_LABWARE must be one of the following:
     opentrons plastic block
     pentrons aluminum block
@@ -97,6 +102,11 @@
     VOLUME_MMIX = 20
 
 # Constants
+TIPS300_LW_DICT = {
+    'biotix': 'biotix_96_tiprack_300ul_flat',
+    'opentrons': 'opentrons_96_tiprack_300ul'
+}
+
 MM_LW_DICT = {
     'opentrons plastic block': 'opentrons_24_tuberack_generic_2ml_screwcap',
     'opentrons aluminum block': 'opentrons_24_aluminumblock_generic_2ml_screwcap',
@@ -433,8 +443,11 @@ def run(ctx: protocol_api.ProtocolContext):
         robot.load_labware('opentrons_96_filtertiprack_20ul', slot)
         for slot in ['6', '9', '8', '7']
     ]
-    tips300 = [robot.load_labware('opentrons_96_filtertiprack_200ul', '3')]
-
+    tips300 = [
+        robot.load_labware(
+            TIPS300_LW_DICT[TIPS300], slot, '300µl filter tiprack')
+        for slot in ['3']
+    ]
     # define pipettes
     p20 = robot.load_instrument('p20_single_gen2', 'right', tip_racks=tips20)
     p300 = robot.load_instrument('p300_single_gen2', 'left', tip_racks=tips300)

doc/S3/05_magdeck_v1_calibration_and_modifications.md

@@ -0,0 +1,23 @@
+# OT-2 Magnetic Module V1 (magdeck) calibration and modifications
+
+Magdecks V1 may have all their magnets in an unbalanced surface, making the magnets to be an uneven distance from the wells when engaging.
+
+![magdeck_unbalanced.jpg](https://github.com/BU-ISCIII/opentrons_covid19/blob/develop/img/magdeck_unbalanced.jpg?raw=true)
+
+You must make sure that all magnets are at the same high across its surface by using a level and following the next steps.
+
+## Steps
+
+1) Use a levelling tool to check where your magdeck suffers this issue or not.
+
+2) The magdeck can be completely disassembled using only a screw driver, but you will probably not need to go so far in most cases. Here is a n example of all the pieces in the magedck, in case you want to tinker with it or you need to fix something inside.
+
+![magdeck_to_pieces.jpg](https://github.com/BU-ISCIII/opentrons_covid19/blob/develop/img/magdeck_to_pieces.jpg?raw=true)
+
+3) Usually you will only need to level this platform, on top of which is located the surface with the magnets.
+
+![magdeck_calibration_platform.jpg](https://github.com/BU-ISCIII/opentrons_covid19/blob/develop/img/magdeck_calibration_platform.jpg?raw=true)
+
+4) In order to find the right position of the platform, you do not even need to dismantle the magdeck. Just find these four screws on the side and loose them a little until the platform gets loose. Put it in a levelled position and carefully screw them back in position trying to keep the balance. You may need to leave one or two a little loose to achieve a decent calibration.
+
+![magdeck_calibration_screws.jpg](https://github.com/BU-ISCIII/opentrons_covid19/blob/develop/img/magdeck_calibration_screws.jpg?raw=true)