chore(Release): 2023-09-09

data/data/fields.csv

@@ -338,6 +338,7 @@ diluent_csv,1
 diluent_scheme,1
 diluent_vol,1
 dilution_factor,2
+dilution_plate,1
 dilvol,1
 disp_bottom_clearance,1
 disp_delay,1
@@ -383,6 +384,7 @@ dna_well_plate_tmod,1
 do_cool_samples,1
 do_deactivate_tc,1
 do_dnase_step,1
+do_flash,1
 do_mm_resusp_pause,1
 do_plate_mm,1
 do_premix,1
@@ -469,6 +471,7 @@ final_air_gap,1
 final_asp_speed,1
 final_conc,1
 final_extension_cycles,1
+final_plate,1
 final_plate_slot4,1
 final_temp,3
 final_tubes,1
@@ -1176,6 +1179,7 @@ reagent,1
 reagent1_loadname,1
 reagent2_loadname,1
 reagent_labware,3
+reagent_plate,1
 reagent_scan,5
 reagent_slot_scan,2
 reagent_transfer_vol,2
@@ -1192,6 +1196,7 @@ res12_type,1
 res1_type,1
 res_dead_vol,1
 res_type,20
+reservoir,1
 reservoir12_lname,1
 reservoir_fill_volume,1
 reservoir_height,3

protoBuilds/0b97ae-protocol-3B/README.json

@@ -6,13 +6,13 @@
         ]
     },
     "deck-setup": "\nWater Reservoir (slot 2):\n    Column 1: Nuclease Free Water\n    Column 2: Binding Buffer\n    Column 3 & 4: Ethanol\n    Column 10, 11 & 12: Empty for Supernatent Removal\nDiluted RNA Plate (slot 7 Temperature Module):\n    RNA Samples Starting Plate\nReagent Plate (Slot 10):\n    Column 1: MasterMix\n    Column 2: Magentic Beads",
-    "description": "This is Part 3 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 2 to this protocol is the Fragementation.\nLinks:\n Part 1: Sample Normalization\n Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation\n* Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction",
+    "description": "This is Part 3 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 2 to this protocol is the Fragementation.\nLinks:\n* Part 1: Sample Normalization\n* Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation\n* Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction",
     "internal": "0b97ae-protocol-3B",
     "labware": "\nPerkin Elmer 12 Reservoir 21000 \u00b5L\nApplied Biosystems Enduraplate 96 Aluminum Block 220 \u00b5L\nBio-Rad 96 Well Plate 200 \u00b5L PCR #hsp9601\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nNEST 96 Deepwell Plate 2mL #503001\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\n",
     "markdown": {
         "author": "[Opentrons](https://opentrons.com/)\n\n\n",
         "categories": "* NGS LIBRARY PREP\n\t* QIASeq FastSelect\n\n\n",
-        "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/3F240714-EB34-4978-97F6-5BD0739E874B_1_105_c.jpeg)\nWater Reservoir (slot 2):\n\tColumn 1: Nuclease Free Water\n\tColumn 2: Binding Buffer\n\tColumn 3 & 4: Ethanol\n\tColumn 10, 11 & 12: Empty for Supernatent Removal\nDiluted RNA Plate (slot 7 Temperature Module):\n\tRNA Samples Starting Plate\nReagent Plate (Slot 10):\n\tColumn 1: MasterMix\n\tColumn 2: Magentic Beads\n\n",
+        "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/deck.jpg)\nWater Reservoir (slot 2):\n\tColumn 1: Nuclease Free Water\n\tColumn 2: Binding Buffer\n\tColumn 3 & 4: Ethanol\n\tColumn 10, 11 & 12: Empty for Supernatent Removal\nDiluted RNA Plate (slot 7 Temperature Module):\n\tRNA Samples Starting Plate\nReagent Plate (Slot 10):\n\tColumn 1: MasterMix\n\tColumn 2: Magentic Beads\n\n",
         "description": "This is Part 3 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 2 to this protocol is the Fragementation.\n\nLinks:\n* [Part 1: Sample Normalization](http://protocols.opentrons.com/protocol/0b97ae)\n* [Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation](http://protocols.opentrons.com/protocol/0b97ae-protocol-2B)\n* [Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction](http://protocols.opentrons.com/protocol/0b97ae-protocol-3B)\n\n\n",
         "internal": "0b97ae-protocol-3B\n",
         "labware": "* Perkin Elmer 12 Reservoir 21000 \u00b5L\n* Applied Biosystems Enduraplate 96 Aluminum Block 220 \u00b5L\n* [Bio-Rad 96 Well Plate 200 \u00b5L PCR #hsp9601](http://www.bio-rad.com/en-us/sku/hsp9601-hard-shell-96-well-pcr-plates-low-profile-thin-wall-skirted-white-clear?ID=hsp9601)\n* Opentrons 96 Filter Tip Rack 20 \u00b5L\n* [NEST 96 Deepwell Plate 2mL #503001](http://www.cell-nest.com/page94?product_id=101&_l=en)\n* [Opentrons 96 Tip Rack 300 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L](https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set)\n\n\n",
@@ -21,7 +21,7 @@
         "pipettes": "* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [Opentrons P300 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n\n\n",
         "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit \"Run\".\n\n\n",
         "protocol-steps": "1. Before this protocol the RNA plate should have went through the thermocycler according to FastSelect 5s/16s/23s, Table 3 and placed on a back on the temperature deck on slot 7.\n2. The Reagent plate will be placed on the temperature module on slot 10, which will contain MasterMix in column 1 and magentic beads in column 2.\n3. The reservoir will be placed on slot 2, which will contain Nucleas Free Water in well 1, Binding Buffer in well 2, and Ethanol in wells 3 and 4. Wells 10, 11 and 12 will be used for supernatent removal.\n\n\n\n",
-        "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/part+4/reagen.jpg)\n\n\n",
+        "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/reagents.jpg)\n\n\n",
         "title": "QIAseq FastSelect Extraction"
     },
     "modules": [

protocols/0b97ae-protocol-3B/0b97ae-protocol-3B.ot2.apiv2.py

@@ -53,9 +53,28 @@ def create_thread(ctx, cancel_token):
 def run(ctx: protocol_api.ProtocolContext):
     """PROTOCOLS."""
     [
-     num_samples, vol_dna , flash, bead_timer] = get_values(  # noqa: F821 (<--- DO NOT REMOVE!)
-        "num_samples","vol_dna","flash","bead_timer")
+     num_samples, vol_dna , flash, bead_timer, reservoir, F_Plate, D_Plate, R_Plate] = get_values(  # noqa: F821 (<--- DO NOT REMOVE!)
+        "num_samples","vol_dna","flash","bead_timer","reservoir","final_plate","dilution_plate","reagent_plate")
     num_samples = int(num_samples)
+    if reservoir == 'perkinelmer':
+        res_labware = 'perkinelmer_12_reservoir_21000ul'
+    else:
+        res_labware = 'nest_12_reservoir_15ml'
+
+    if F_Plate == 'Biorad':
+        F_labware = 'opentrons_96_aluminumblock_biorad_wellplate_200ul'
+    else:
+        F_labware = 'appliedbiosystemsenduraplate_96_aluminumblock_220ul'
+
+    if D_Plate == 'Biorad':
+        D_labware = 'opentrons_96_aluminumblock_biorad_wellplate_200ul'
+    else:
+        D_labware = 'appliedbiosystemsenduraplate_96_aluminumblock_220ul'
+
+    if R_Plate == 'Biorad':
+        R_labware = 'biorad_96_wellplate_200ul_pcr'
+    else:
+        R_labware = 'appliedbiosystemsenduraplate_96_aluminumblock_220ul'
 
     'Global variables'
     TEST_MODE = False
@@ -83,13 +102,13 @@ def run(ctx: protocol_api.ProtocolContext):
 
     # load labware
     mag_plate = Mag_mod.load_labware('nest_96_wellplate_2ml_deep','Extraction Plate')
-    final_plate = tempdeck_1.load_labware('opentrons_96_aluminumblock_biorad_wellplate_200ul', #noqa: E501
+    final_plate = tempdeck_1.load_labware(F_labware, #noqa: E501
                                        'Reagent Plate')
-    Diluted_plate = tempdeck_2.load_labware('appliedbiosystemsenduraplate_96_aluminumblock_220ul',  # noqa: E501
+    Diluted_plate = tempdeck_2.load_labware(D_labware,  # noqa: E501
                                             'Diluted RNA plate')
-    water_res = ctx.load_labware('perkinelmer_12_reservoir_21000ul', 2,
+    water_res = ctx.load_labware(res_labware, 2,
                                  'Water reservoir')
-    Reagent_plate = ctx.load_labware('biorad_96_wellplate_200ul_pcr', '1')
+    Reagent_plate = ctx.load_labware(R_labware, '1')
 
     # load tipracks
     tips3 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)

protocols/0b97ae-protocol-3B/README.md

@@ -42,7 +42,7 @@ Links:
 
 
 ### Deck Setup
-![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/3F240714-EB34-4978-97F6-5BD0739E874B_1_105_c.jpeg)
+![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/deck.jpg)
 Water Reservoir (slot 2):
 	Column 1: Nuclease Free Water
 	Column 2: Binding Buffer
@@ -55,7 +55,7 @@ Reagent Plate (Slot 10):
 	Column 2: Magentic Beads
 
 ### Reagent Setup
-![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/part+4/reagen.jpg)
+![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/reagents.jpg)
 
 
 ### Protocol Steps

protocols/0b97ae-protocol-3B/fields.json

@@ -38,5 +38,41 @@
     "label": "Bead Timer?",
     "name": "bead_timer",
     "default": 6
+  },
+  {
+    "type": "dropDown",
+    "label": "Is the Reservoir PerkinElmer or Nest?",
+    "name": "reservoir",
+    "options": [
+      {"label": "perkinelmer", "value": "perkinelmer"},
+      {"label": "nest", "value": "nest"}
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "Is the Final Plate Biorad or AppliedBio?",
+    "name": "final_plate",
+    "options": [
+      {"label": "Biorad", "value": "Biorad"},
+      {"label": "AppliedBio", "value": "AppliedBio"}
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "Is the Diluted DNA Plate Biorad or AppliedBio?",
+    "name": "dilution_plate",
+    "options": [
+      {"label": "Biorad", "value": "Biorad"},
+      {"label": "AppliedBio", "value": "AppliedBio"}
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "Is the Reagent Plate Biorad or AppliedBio?",
+    "name": "reagent_plate",
+    "options": [
+      {"label": "Biorad", "value": "Biorad"},
+      {"label": "AppliedBio", "value": "AppliedBio"}
+    ]
   }
 ]

protocols/gsdx/bacgene.ot2.apiv2.py

@@ -19,22 +19,29 @@
 DO_SET_TEMP = True
 REUSING_LYSIS_BUFFER = True
 OFFSET_Y_LYSIS_BUFFER_LISTERIA = 13.0
-OFFSET_Z_LYSIS_BUFFER_LISTERIA = -5.0
+OFFSET_Z_LYSIS_BUFFER_LISTERIA = -4.5
 OFFSET_Y_LYSIS_BUFFER_SALMONELLA = 11.0  # magnitude (positive number!)
-OFFSET_Z_LYSIS_BUFFER_SALMONELLA = -5.0
+OFFSET_Z_LYSIS_BUFFER_SALMONELLA = -4.5
 OFFSET_X_TUBERACK = 0.5
 P20_MOUNT = 'left'
 P300_MOUNT = 'right'
 
 
 def run(ctx):
 
+    def flash_lights():
+        initial_status = ctx.rail_lights_on
+        for _ in range(19):
+            ctx.set_rail_lights(not ctx.rail_lights_on)
+            ctx.delay(seconds=0.25)
+        ctx.set_rail_lights(initial_status)
+
     [num_samples_listeria, num_samples_salmonella,
      num_samples_listeria_remaining, num_samples_salmonella_remaining,
-     sample_rack_type, salmonella_meat] = get_values(  # noqa: F821
+     sample_rack_type, salmonella_meat, do_flash] = get_values(  # noqa: F821
         'num_samples_listeria', 'num_samples_salmonella',
         'num_samples_listeria_remaining', 'num_samples_salmonella_remaining',
-        'sample_rack_type', 'salmonella_meat')
+        'sample_rack_type', 'salmonella_meat', 'do_flash')
 
     # modules
     tempdeck = ctx.load_module('temperature module gen2', '10')
@@ -190,28 +197,34 @@ def run(ctx):
         num_cols_offset_samples_listeria*8+num_samples_salmonella]
 
     # load liquids
+    vol_sample = 5.0
+
     try:
         if num_samples_listeria > 0:
-            positive_control_l.load_liquid(positive_control_l_liq, volume=10)
+            positive_control_l.load_liquid(
+                positive_control_l_liq, volume=vol_sample)
         if num_samples_salmonella > 0:
-            positive_control_s.load_liquid(positive_control_s_liq, volume=10)
+            positive_control_s.load_liquid(
+                positive_control_s_liq, volume=vol_sample)
         [well.load_liquid(samples_listeria_liq_sample,
-                          volume=30/len(samples_single_listeria))
-         for well in samples_single_listeria]
+                          volume=round(30/len(samples_single_listeria)))
+         for well in samples_single_listeria[
+            :max(0, len(samples_single_listeria)-2)]]
         [well.load_liquid(samples_salmonella_liq_sample,
-                          volume=10/len(samples_single_salmonella))
-         for well in samples_single_salmonella]
+                          volume=round(10/len(samples_single_salmonella)))
+         for well in samples_single_salmonella[
+            :max(0, len(samples_single_salmonella)-2)]]
         [well.load_liquid(samples_listeria_liq_lysis,
-                          volume=30/len(lysis_single_listeria))
+                          volume=round(30/len(lysis_single_listeria)))
          for well in lysis_single_listeria]
         [well.load_liquid(samples_salmonella_liq_lysis,
-                          volume=10/len(lysis_single_salmonella))
+                          volume=round(10/len(lysis_single_salmonella)))
          for well in lysis_single_salmonella]
         [well.load_liquid(samples_listeria_liq_pcr,
-                          volume=30/len(pcr_single_listeria))
+                          volume=round(30/len(pcr_single_listeria)))
          for well in pcr_single_listeria]
         [well.load_liquid(samples_salmonella_liq_pcr,
-                          volume=10/len(pcr_single_salmonella))
+                          volume=round(10/len(pcr_single_salmonella)))
          for well in pcr_single_salmonella]
     except AttributeError:
         pass
@@ -423,7 +436,7 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0):
             num_partial_salmonella_buffers+num_additional_salmonella_buffers]
 
         # load partial liq
-        if num_samples_listeria > 0:
+        if num_samples_salmonella > 0:
             try:
                 [
                     well.load_liquid(
@@ -635,8 +648,6 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0):
         ctx.delay(minutes=10, msg='Incubating for 10 minutes @ 95C.')
         tempdeck.set_temperature(37)
 
-    vol_sample = 5.0
-
     if DO_TRANSFER_SAMPLE_TO_PCR:
         """ transfer samples to PCR plate """
 
@@ -713,3 +724,6 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0):
             drop(m20)
 
     tempdeck.deactivate()
+
+    if do_flash:
+        flash_lights()

protocols/gsdx/fields.json

@@ -1,44 +1,59 @@
 [
-    {
-        "type": "int",
-        "label": "number of listeria wells to run (including +/- controls)",
-        "name": "num_samples_listeria",
-        "default": 48
-    },
-    {
-        "type": "int",
-        "label": "number of salmonella wells to run (including +/- controls)",
-        "name": "num_samples_salmonella",
-        "default": 48
-    },
-    {
-        "type": "int",
-        "label": "number of listeria wells in kit remaining",
-        "name": "num_samples_listeria_remaining",
-        "default": 96
-    },
-    {
-        "type": "int",
-        "label": "number of salmonella wells in kit remaining",
-        "name": "num_samples_salmonella_remaining",
-        "default": 96
-    },
-    {
-        "type": "dropDown",
-        "label": "sample rack format",
-        "name": "sample_rack_type",
-        "options": [
-          {"label": "KingFisher 96 Tube Rack with GoldStandard 1.1 mL", "value": "kingfisher_96_tuberack_1100ul"},
-          {"label": "BIOPlastics BV 96 Aluminum Block 200 µL", "value": "bioplasticsbv_96_aluminumblock_200ul"}
-        ]
-    },
-    {
-        "type": "dropDown",
-        "label": "running salmonella meat",
-        "name": "salmonella_meat",
-        "options": [
-          {"label": "no", "value": false},
-          {"label": "yes", "value": true}
-        ]
-    }
-]
+  {
+    "type": "int",
+    "label": "number of listeria wells to run (including +/- controls)",
+    "name": "num_samples_listeria",
+    "default": 48
+  },
+  {
+    "type": "int",
+    "label": "number of salmonella wells to run (including +/- controls)",
+    "name": "num_samples_salmonella",
+    "default": 48
+  },
+  {
+    "type": "int",
+    "label": "number of listeria wells in kit remaining",
+    "name": "num_samples_listeria_remaining",
+    "default": 96
+  },
+  {
+    "type": "int",
+    "label": "number of salmonella wells in kit remaining",
+    "name": "num_samples_salmonella_remaining",
+    "default": 96
+  },
+  {
+    "type": "dropDown",
+    "label": "sample rack format",
+    "name": "sample_rack_type",
+    "options": [
+      {
+        "label": "KingFisher 96 Tube Rack with GoldStandard 1.1 mL",
+        "value": "kingfisher_96_tuberack_1100ul"
+      },
+      {
+        "label": "BIOPlastics BV 96 Aluminum Block 200 µL",
+        "value": "bioplasticsbv_96_aluminumblock_200ul"
+      }
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "running salmonella meat",
+    "name": "salmonella_meat",
+    "options": [
+      { "label": "no", "value": false },
+      { "label": "yes", "value": true }
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "flash on completion",
+    "name": "do_flash",
+    "options": [
+      { "label": "no", "value": false },
+      { "label": "yes", "value": true }
+    ]
+  }
+]