fix

protocols/cerillo/cerillo.ot2.apiv2.py

@@ -0,0 +1,112 @@
+metadata = {
+    'protocolName': 'Cerillo Plate Reader Protocol',
+    'author': 'Rami Farawi <[email protected]>',
+    'source': 'Custom Protocol Request',
+    'apiLevel': '2.13'
+}
+
+
+def run(ctx):
+
+    [csv_stock, csv_buff, dilute_stock, sol_vol,
+        p300_mount, m300_mount] = get_values(  # noqa: F821
+        "csv_stock", "csv_buff", "dilute_stock", "sol_vol",
+            "p300_mount", "m300_mount")
+
+#     csv_stock = """
+# x,1,2,3,4,5,6,7,8,9,10,11,12
+# A,x,20,20,20,20,20,20,20,20,20,20,20
+# B,X,40,40,40,40,40,40,40,40,40,40,40
+# C,x,29,29,29,29,29,29,29,29,29,29,29
+# D,40,40,40,40,40,40,40,40,40,40,40,40
+# E,29,29,29,29,29,29,29,29,29,29,29,29
+# F,40,40,40,40,40,40,40,40,40,40,40,40
+# G,29,29,29,29,29,29,29,29,29,29,29,29
+# H,40,40,40,40,40,40,40,40,40,40,40,40
+#     """
+#
+#     csv_buff = """
+# x,1,2,3,4,5,6,7,8,9,10,11,12
+# A,20,40,34,20,22,44,89,90,92,29,84,29
+# B,74,29,49,72,49,32,89,29,88,44,22,40
+# C,20,40,34,20,22,44,89,90,92,29,84,29
+# D,74,29,49,72,49,32,89,29,88,44,22,40
+# E,20,40,34,20,22,44,89,90,92,29,84,29
+# F,74,29,49,72,49,32,89,29,88,44,22,40
+# G,20,40,34,20,22,44,89,90,92,29,84,29
+# H,74,29,49,72,49,32,89,29,88,44,22,40
+#     """
+
+    # labware
+    reservoir = ctx.load_labware('nest_12_reservoir_15ml', 5)
+    plate_reader = ctx.load_labware('cerillo_stratus_armadillo_flatbottom_200ul', 1)
+    deepwell = ctx.load_labware('nest_96_wellplate_2ml_deep', 3)
+    tips = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)
+            for slot in [7, 8, 9]]
+
+    # pipettes
+    m300 = ctx.load_instrument('p300_multi_gen2', m300_mount, tip_racks=tips)
+    p300 = ctx.load_instrument('p300_single_gen2', p300_mount, tip_racks=tips)
+
+    csv_lines_stock = [[val.strip() for val in line.split(',')][1:]
+                       for line in csv_stock.splitlines()
+                       if line.split(',')[0].strip()][1:]
+
+    csv_lines_buff = [[val.strip() for val in line.split(',')][1:]
+                      for line in csv_buff.splitlines()
+                      if line.split(',')[0].strip()][1:]
+
+    # mapping
+    stock_solution = reservoir.wells()[0]
+    buffer = reservoir.wells()[1]
+    cells = reservoir.wells()[-1]
+
+    if dilute_stock:
+
+        # protocol
+        ctx.comment('\n---------------ADDING BUFFER TO PLATE--------------\n\n')
+        p300.pick_up_tip()
+        for line, row in zip(csv_lines_buff, deepwell.rows()):
+            for well_vol, well_name in zip(line, row):
+                if well_vol.lower() == 'x':
+                    continue
+                well_vol = int(well_vol)
+                dest_well = well_name
+                p300.aspirate(well_vol, buffer)
+                p300.dispense(well_vol, dest_well)
+        p300.drop_tip()
+
+        ctx.comment('\n---------------ADDING STOCK TO PLATE--------------\n\n')
+        p300.pick_up_tip()
+        for line, row in zip(csv_lines_stock, deepwell.rows()):
+            for well_vol, well_name in zip(line, row):
+                if well_vol.lower() == 'x':
+                    continue
+                well_vol = int(well_vol)
+                dest_well = well_name
+                p300.aspirate(well_vol, stock_solution)
+                p300.dispense(well_vol, dest_well.top())
+        p300.drop_tip()
+
+        ctx.comment('\n-------------Mixing solution and stock------------\n\n')
+        for col in deepwell.rows()[0]:
+            m300.pick_up_tip()
+            m300.mix(5, 50, col)
+            m300.drop_tip()
+
+    m300.pick_up_tip()
+    m300.mix(20, 200, cells)
+
+    ctx.comment('\n-------------Transferring cells to reader-------------\n\n')
+    for col in plate_reader.rows()[0]:
+        m300.aspirate(180, cells)
+        m300.dispense(180, col)
+    m300.drop_tip()
+
+    ctx.comment('\n-------------Transferring cells to reader-------------\n\n')
+    for s, d in zip(deepwell.rows()[0], plate_reader.rows()[0]):
+        m300.pick_up_tip()
+        m300.aspirate(sol_vol, s)
+        m300.dispense(sol_vol, d)
+        m300.mix(3, 150, d)
+        m300.drop_tip()

protocols/cerillo/fields.json

@@ -0,0 +1,52 @@
+[
+  {
+    "type": "textFile",
+    "label": "Stock Solution CSV",
+    "name": "csv_stock",
+    "default": "x,1,2,3,4,5,6,7,8,9,10,11,12,A,x,20,20,20,20,20,20,20,20,20,20,20"
+  },
+  {
+    "type": "textFile",
+    "label": "Buffer Solution CSV",
+    "name": "csv_buff",
+    "default": "x,1,2,3,4,5,6,7,8,9,10,11,12,A,x,20,20,20,20,20,20,20,20,20,20,20"
+  },
+  {
+    "type": "dropDown",
+    "label": "Dilute stock solution? before adding cells?",
+    "name": "pre_mix",
+    "options": [
+      {"label": "Yes, dilute stock solution with csvs", "value": true},
+      {"label": "No, just transfers cells and solution to plate reader", "value": false}
+    ]
+  },
+  {
+    "type": "int",
+    "label": "Transfer volume of diluted stock to plate reader (ul)",
+    "name": "sol_vol",
+    "default": 20
+  },
+
+  {
+    "type": "int",
+    "label": "Pre-mix repetitions",
+    "name": "premix_reps",
+    "default": 3
+  },
+
+  {
+    "type": "float",
+    "label": "Pre-mix Rate",
+    "name": "mix_rate",
+    "default": 1
+  },
+  {
+    "type": "dropDown",
+    "label": "P300 Multi-Channel Mount",
+    "name": "m300_mount",
+    "options": [
+      {"label": "Left", "value": "left"},
+      {"label": "Right", "value": "right"}
+    ]
+  }
+]