fix

protocols/010d6c/010d6c.ot2.apiv2.py

@@ -1,5 +1,10 @@
 # flake8: noqa
 
+def get_values(*names):
+    import json
+    _all_values = json.loads("""{"csv_samp":"source slot,source well,dest well\\n8,A1,A4\\n8,A1,A5","plate_standard":true,"diluent_buff_col":1,"duplicate_plating":true,"user_input_pause":true,"m300_mount":"right","p300_mount":"left"}""")
+    return [_all_values[n] for n in names]
+
 metadata = {
     'protocolName': 'Ribogreen Assay',
     'author': 'Rami Farawi <[email protected]>',
@@ -10,24 +15,28 @@
 
 def run(ctx):
 
-    [csv_samp, plate_standard, diluent_buff_col,
-        duplicate_plating, m300_mount, p300_mount] = get_values(  # noqa: F821
-        "csv_samp", "plate_standard", "diluent_buff_col",
-            "duplicate_plating", "m300_mount", "p300_mount")
-
-    # p300_mount = 'left'
-    # m300_mount = 'right'
-    # plate_standard = True
-    # diluent_buff_col = 4
-    # duplicate_plating = False
-    # csv_samp = """
-    #
-    # source slot, source well, dest well
-    # 7, A1, A1
-    # 8, A1, A2
-    # 7, A3, A3
-    #
-    # """
+    # [csv_samp, plate_standard, diluent_buff_col,
+    #     duplicate_plating, user_input_pause, m300_mount, p300_mount] = get_values(  # noqa: F821
+    #     "csv_samp", "plate_standard", "diluent_buff_col",
+    #         "duplicate_plating", "user_input_pause", "m300_mount", "p300_mount")
+
+    p300_mount = 'left'
+    m300_mount = 'right'
+    plate_standard = True
+    diluent_buff_col = 4
+    duplicate_plating = False
+    csv_samp = """
+
+
+
+    source slot, source well, dest well
+    7, A1, A1
+    8, A1, A2
+    7, A3, A3
+
+    """
+
+    user_input_pause = True
 
     def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):
         # Split transfer up to allow for more control over touch tip height
@@ -169,7 +178,7 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):
         m300.touch_tip(v_offset=1)
 
         for well in dispense_wells:
-            m300.dispense(50, well.bottom(z = 3))
+            m300.dispense(50, well.bottom(z = 4))
 
             # Added in touch tip
             m300.move_to(well.top(z = -3))
@@ -191,14 +200,15 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):
         m300.touch_tip(v_offset=1)
 
         for well in dispense_wells:
-            m300.dispense(50, well.bottom(z = 3))
+            m300.dispense(50, well.bottom(z = 4))
 
             # Added in touch tip
             m300.move_to(well.top(z = -3))
             m300.touch_tip(v_offset=1)
 
         m300.drop_tip()
 
+
     ctx.comment('\n------------ADDING SAMPLE------------\n\n')
 
     # Modified for faster sample addition with less tip wastage
@@ -216,11 +226,19 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):
 
         # Only pick up tip and aspirate if start of new replicate batch
         if index%reps == 0:
-            p300.pick_up_tip()
-            p300.mix(1, 50*reps, source_well.bottom(z = 4)) # Added in pre-wet
-            p300.aspirate(50*reps, source_well.bottom(z = 4))
-            p300.move_to(source_well.top(-3))
-            p300.touch_tip(v_offset=1)
+            if csv_slot == 8:  # DIFFERENT Z HEIGHTS DEPENDING ON SLOT
+                print('going to 2mL on 8')
+                p300.pick_up_tip()
+                p300.mix(1, 50*reps, source_well.bottom(z = 4))
+                p300.aspirate(50*reps, source_well.bottom(z = 4))
+                p300.move_to(source_well.top(-3))
+                p300.touch_tip(v_offset=1)
+            elif csv_slot == 7:
+                print('going to 5mL on 7')
+                p300.mix(1, 50*reps, source_well.bottom(z=1)) # CHANGED ASPIRATION HEIGHT BACK TO DEFAULT FOR 5ML TUBES
+                p300.aspirate(50*reps, source_well.bottom(z=1))
+                p300.move_to(source_well.top(-3))
+                p300.touch_tip(v_offset=1)
 
         p300.dispense(50, hs_plate.wells_by_name()[dest_well].bottom(z = 3)) # Set z offset
         p300.move_to(hs_plate.wells_by_name()[dest_well].top(-3))
@@ -284,7 +302,7 @@ def Transfer_With_TT(Pipette, Source, Destination, Vol, Dispense_Top):
             ctx.delay(minutes=5)
 
     except:
-        ctx.delay(minutes=10)
+        ctx.pause('The protocol did not do the heater shaker steps - please cancel')
 
     ctx.comment('\n------------PLATING DYE------------\n\n')
 

protocols/kapa-amp-cleanup/README.md

@@ -30,7 +30,7 @@ This protocol performs a post-amplification 1X Purification using AMPure Beads.
 
 
 ### Deck Setup
-![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/kapa-qubit/CLEANUP.png)
+![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/kapa-amp/Screen+Shot+2024-01-25+at+11.44.39+AM.png)
 
 
 

protocols/kapa-amp-cleanup/kapa-amp-cleanup.ot2.apiv2.py

@@ -16,8 +16,10 @@ def run(ctx):
     # m300_mount = 'left'
 
     # labware
-    mag_mod = ctx.load_module('magnetic module gen2', 1)
-    mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')
+    # mag_mod = ctx.load_module('magnetic module gen2', 1)
+    mag_stand = ctx.load_labware('genericmagnet_96_wellplate_1500ul', 1)
+    mag_plate = ctx.load_labware('generic_96_wellplate_1500ul', 4)
+    # mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')
     reservoir = ctx.load_labware('nest_12_reservoir_15ml', 3)
     elute_plate = ctx.load_labware('agilent_96_wellplate_270ul', 2)
     tips = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)
@@ -33,6 +35,7 @@ def run(ctx):
     trash = reservoir['A12'].top()
 
     sample_cols = mag_plate.rows()[0][:num_col]
+    sample_cols_stand = mag_stand.rows()[0][:num_col]
 
     def slow_tip_withdrawal(pipette, well_location, to_center=False):
         if pipette.mount == 'right':
@@ -61,12 +64,12 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False):
 
     ctx.delay(minutes=5)
 
-    mag_mod.engage()
+    ctx.pause('Move plate to magnetic stand, then select resume')
 
     ctx.delay(minutes=3)
 
     ctx.comment('\n---------------REMOVING SUPER----------------\n\n')
-    for col in sample_cols:
+    for col in sample_cols_stand:
         m300.pick_up_tip()
         m300.aspirate(140, col, rate=0.1)
         m300.aspirate(20, col.bottom(z=0.6), rate=0.1)
@@ -77,7 +80,7 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False):
     for _ in range(2):
 
         m300.pick_up_tip()
-        for col in sample_cols:
+        for col in sample_cols_stand:
             m300.aspirate(200, ethanol)
             slow_tip_withdrawal(m300, ethanol)
             m300.dispense(200, col.top())
@@ -86,7 +89,7 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False):
 
         ctx.delay(seconds=30)
 
-        for col in sample_cols:
+        for col in sample_cols_stand:
             if not m300.has_tip:
                 m300.pick_up_tip()
             m300.aspirate(180, col, rate=0.1)
@@ -98,7 +101,7 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False):
 
     ctx.delay(minutes=bead_dry_time)
 
-    mag_mod.disengage()
+    ctx.pause('Move magplate to slot 4, then select resume')
 
     ctx.comment('\n---------------Resuspend----------------\n\n')
     for col in sample_cols:
@@ -108,10 +111,10 @@ def slow_tip_withdrawal(pipette, well_location, to_center=False):
         m300.mix(15, 19, col.bottom(z=0.7))
         m300.drop_tip()
 
-    mag_mod.engage()
+    ctx.pause('Move plate to magnetic stand, then select resume')
     ctx.delay(minutes=3)
 
-    ctx.comment('\n---------------REMOVING SUPER----------------\n\n')
+    ctx.comment('\n---------------Transfer Elute----------------\n\n')
     for s, d in zip(sample_cols, elute_plate.rows()[0]):
         m300.pick_up_tip()
         m300.aspirate(20, s.bottom(z=0.7), rate=0.1)