fix

protocols/0ca318/0ca318.ot2.apiv2.py

@@ -65,6 +65,8 @@ def pick_up(pip):
 
     # mapping
     num_full_cols = math.floor(num_samp/8)
+    dispense_wells = [well for column in pcr_plate.columns()[1:11]
+                      for well in column[1:7]][:num_samp]
 
     remainder = False if num_samp % 8 == 0 else True
 
@@ -119,7 +121,7 @@ def pick_up(pip):
         ctx.comment('\n\nTRANSFERRING MASTERMIX TO PLATE\n')
         p20.pick_up_tip()
 
-        for i, (s, d) in enumerate(zip(mmx, pcr_plate.wells()[:num_samp])):
+        for i, (s, d) in enumerate(zip(mmx, dispense_wells)):
 
             if i % 4 == 0 and i > 0:
                 if m20.has_tip:
@@ -135,19 +137,13 @@ def pick_up(pip):
             ctx.comment('\n')
         p20.drop_tip()
 
-    # transfer sample
-    sample_wells = [
-                    well for column in pcr_plate.columns()[1:11]
-                    for well in column[1:7]
-                    ]
-
     if source_type == "tuberack":
         ctx.comment('\n\nTRANSFERRING SAMPLE TO PCR PLATE\n')
-        for tube, dest in zip(sample_tubes, sample_wells):
+        for tube, dest in zip(sample_tubes, dispense_wells):
             p20.pick_up_tip()
             p20.aspirate(2.5, tube, rate=0.5)
             p20.dispense(2.5, dest)
-            p20.mix(3, 20, dest)
+            p20.mix(6, 20, dest, rate=0.5)
             p20.blow_out(dest.top())
             p20.touch_tip()
             p20.drop_tip()

protocols/0ca318/fields.json

@@ -12,17 +12,17 @@
     "label": "Where are the samples?",
     "name": "source_type",
     "options": [
-      {"label": "Already in the 96 well plate on thermocycler", "value": "wellplate"},
-      {"label": "In tube racks", "value": "tuberack"}
+      {"label": "In tube racks", "value": "tuberack"},
+      {"label": "Already in the 96 well plate on thermocycler", "value": "wellplate"}
     ]
   },
   {
     "type": "dropDown",
     "label": "What is the mastermix in in slot 3 temperature module?",
     "name": "mmx_type",
     "options": [
-      {"label": "In a 96 wellplate aluminum block", "value": "mmx_wellplate"},
-      {"label": "Nest 1.5mL in a 24 aluminum block", "value": "mmx_tuberack"}
+      {"label": "Nest 1.5mL in a 24 aluminum block", "value": "mmx_tuberack"},
+      {"label": "In a 96 wellplate aluminum block", "value": "mmx_wellplate"}
     ]
   },
   {

protocols/1464-2/ELISA_protocol_part2.ot2.apiv2.py

@@ -22,7 +22,7 @@ def run(ctx):
         'corning_96_wellplate_360ul_flat', '9')
 
     tipracks_300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)
-                    for slot in ['3', '10']]
+                    for slot in ['3']]
     tiprack_m300 = ctx.load_labware('opentrons_96_tiprack_300ul', '7')
 
     # instrument setup

protocols/1464-3/ELISA_protocol_part3.ot2.apiv2.py

@@ -29,8 +29,8 @@ def run(ctx):
         tip_racks=tiprack_m300)
 
     # reagent setup
-    TMB_substrate = trough.wells_by_name()['A6'].bottom(z=0)
-    stop_solution = trough.wells_by_name()['A12'].bottom(z=0)
+    TMB_substrate = trough.wells_by_name()['A6']
+    stop_solution = trough.wells_by_name()['A12']
 
     """
     Adding TMB substrate
@@ -40,11 +40,9 @@ def run(ctx):
         100,
         TMB_substrate,
         [col[0].top() for col in plate.columns()[:number_of_columns]],
-        blow_out=False,
-        disposal_volume=0.05,
-
-        new_tip='never')
-    m300.aspirate(20, plate.columns()[number_of_columns-1][0].top())
+        blow_out=TMB_substrate,
+        new_tip='never',
+        rate=0.75)
     m300.drop_tip()
 
     ctx.delay(minutes=30)

protocols/1464/ELISA_protocol_part1.ot2.apiv2.py

@@ -10,9 +10,9 @@
 
 def run(ctx):
     [starting_buffer_volume, number_of_standards,
-     concentration_csv] = get_values(  # noqa: F821
+     concentration_csv, init_vol_buff] = get_values(  # noqa: F821
      'starting_buffer_volume', 'number_of_standards',
-     'concentration_csv')
+     'concentration_csv', "init_vol_buff")
 
     # labware setup
     tuberack_1 = ctx.load_labware(
@@ -41,6 +41,26 @@ def run(ctx):
     samples = tubes[2 + number_of_standards:]
     dilution_buffer = tuberack_1.wells_by_name()['A3']
 
+    v_naught_buff = init_vol_buff*1000
+
+    radius_sds = dilution_buffer.diameter/2
+
+    h_naught_buff = 0.85*v_naught_buff/(math.pi*radius_sds**2)
+
+    h_buff = h_naught_buff
+
+    def adjust_height(volume_from_loop):
+        nonlocal h_buff
+
+        radius = radius_sds
+
+        dh = (volume_from_loop/(math.pi*radius**2))*1.33
+
+        h_buff -= dh
+
+        if h_buff < 12:
+            h_buff = 1
+
     dil_dests = [row for deep_plate in deep_plates
                  for row in deep_plate.rows()]
 
@@ -94,16 +114,13 @@ def run(ctx):
                  for c_list in concs for conc in c_list]
         for volume, dest in zip(volumes, dests):
             p1000.pick_up_tip()
-            buffer_height += volume / (math.pi * (13.5 ** 2))
-            if buffer_height > 75:
-                source = dilution_buffer.bottom(3)
-            else:
-                source = dilution_buffer.top(-buffer_height)
             p1000.transfer(
                 volume,
-                source,
+                dilution_buffer.bottom(z=h_buff),
                 dest.top(-20),
                 new_tip='never')
+
+            adjust_height(volume)
             p1000.blow_out(dest.top())
             p1000.drop_tip()
 

protocols/1464/fields.json

@@ -16,5 +16,11 @@
         "label": "concentration .csv file",
         "name": "concentration_csv",
         "default": "50,500,5000\n10,10000,100000\n100,,\n5,,"
+    },
+    {
+        "type": "int",
+        "label": "Initial volume of buffer (mL)",
+        "name": "init_vol_buff",
+        "default": 45
     }
-]
+]