Merge branch 'develop' into 0fdc01

Cookbook.md

@@ -8,6 +8,7 @@ Table of Contents:
 * [Basic Skeleton Protocol](#basic-skeleton-protocol)
 * [Liquid Level Tracking - Simple](#liquid-level-tracking---simple)
 * [Liquid Level Tracking - Complex](#liquid-level-tracking---complex)
+* [Liquid Level Tracking - Complex API level 2.13 and beyond](liquid-level-tracking---complex-versions-after-opentrons_Simulate)
 * [Refill Tips Mid-Protocol](#refill-tips-mid-protocol)
 * [Wash Steps](#wash-steps)
 * [Remove Supernatant](#remove-supernatant)
@@ -157,6 +158,87 @@ def run(ctx):
         transfer(250, source, dest)
     p300.drop_tip()
 ```
+## Liquid Level Tracking - Complex Versions After Opentrons_Simulate
+
+This liquid level tracking employs extension of the Opentrons `Well` class to add custom attributes for current liquid height, current liquid volume, minimum allowable height for aspiration, and a compensation coefficient.These values were moved from well._impl to well.parent, and well._core in APIlevel 2.13. 
+
+The compensation coefficient denotes a multiple that tells the how much "extra" to calculate incrementing or decrementing the liquid level height calculation based on a volume dispensed or aspirated, to account for real-world liquid behavior. This coefficient will likely be higher for viscous liquids, and lower (close to 1.0) for non-viscous liquids.
+
+
+
+```
+from opentrons import protocol_api, types
+from opentrons import APIVersion
+from opentrons.protocol_api.labware import Well
+import math
+
+
+metadata = {
+    'title': 'inheritance',
+    'author': 'Nick Diehl',
+    'apiLevel': '2.13'
+}
+
+
+def run(ctx):
+
+    class WellH(Well):
+        def __init__(self, well, height=0, min_height=5, comp_coeff=1.15,
+                     current_volume=0):
+            # Change one is that we deprecated well._impl
+            super().__init__(well.parent, well._core, APIVersion(2, 13))
+            self.well = well
+            self.height = height
+            self.min_height = min_height
+            self.comp_coeff = comp_coeff
+            self.radius = self.diameter/2
+            self.current_volume = current_volume
+
+        def height_dec(self, vol):
+            dh = (vol/(math.pi*(self.radius**2)))*self.comp_coeff
+            if self.height - dh > self.min_height:
+                self.height = self.height - dh
+            else:
+                self.height = self.min_height
+            if self.current_volume - vol > 0:
+                self.current_volume = self.current_volume - vol
+            else:
+                self.current_volume = 0
+            return(self.well.bottom(self.height))
+
+        def height_inc(self, vol):
+            dh = (vol/(math.pi*(self.radius**2)))*self.comp_coeff
+            if self.height + dh < self.depth:
+                self.height = self.height + dh
+            else:
+                self.height = self.depth
+            self.current_volume += vol
+            return(self.well.bottom(self.height + 20))
+
+    wellrack = ctx.load_labware(
+        'opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', '1')
+    tiprack = ctx.load_labware('opentrons_96_tiprack_300ul', '2')
+    p300 = ctx.load_instrument('p300_single_gen2', 'right',
+                               tip_racks=[tiprack])
+
+    source = WellH(wellrack.wells()[0], height=50, current_volume=7000)
+    dest = WellH(wellrack.wells()[-1], comp_coeff=1.2)
+
+    def transfer(vol, s: WellH, d: WellH, new_tip='never', pip=p300):
+        if new_tip == 'never' and not pip.has_tip:
+            pip.pick_up_tip()
+        pip.transfer(vol, s.height_dec(vol), d.height_inc(vol),
+                     new_tip=new_tip)
+        ctx.comment(f'Source height: {round(s.height, 2)}mm')
+        ctx.comment(f'Destination height: {round(d.height, 2)}mm')
+
+    p300.pick_up_tip()
+    for _ in range(20):
+        transfer(250, source, dest)
+    p300.drop_tip()
+```
+
+
 
 ## Refill Tips Mid-Protocol
 

Makefile

@@ -35,7 +35,6 @@ venvs/ot2:
 	pip install pipenv==2021.5.29 && \
 	pushd $(OT2_MONOREPO_DIR)/api/ && \
 	$(MAKE) setup && \
-	python setup.py install && \
 	popd
 
 .PHONY: parse-errors

data/data/fields.csv

@@ -1,4 +1,4 @@
-_add_water,2
+_add_water,1
 _air_dry,2
 _asp_ht,1
 _csv,3
@@ -231,6 +231,7 @@ component_2_height,1
 component_2_volume,1
 component_3_volume,1
 conc_target,1
+concentration_csv,2
 concentration_template,1
 control_plate,1
 count_mix,1
@@ -367,12 +368,12 @@ dna_volume,5
 dna_well_plate_lname,1
 dna_well_plate_tmod,1
 do_cool_samples,1
-do_day1,1
-do_day2,1
 do_deactivate_tc,1
 do_dnase_step,1
 do_mm_resusp_pause,1
 do_plate_mm,1
+do_premix,1
+do_remove_media,1
 do_sds_step,1
 do_vortex_pause,1
 donor_384_type,1
@@ -455,7 +456,7 @@ final_extension_cycles,1
 final_plate_slot4,1
 final_temp,3
 final_tubes,1
-final_vol,3
+final_vol,4
 first_media_x,1
 flash,32
 flow_rate_asp,1
@@ -494,6 +495,8 @@ height_final,1
 height_intermediate_high,1
 height_intermediate_low,1
 height_intermediate_middle,1
+height_offset_aspirate,1
+height_offset_dispense,1
 height_sample,1
 height_source,1
 hs_rpm,1
@@ -551,7 +554,7 @@ init_vol_dil,2
 init_vols_csv,1
 initial_denaturation_cycles,1
 initial_vol,1
-input_csv,19
+input_csv,18
 input_file,10
 input_file2,6
 input_labware,1
@@ -600,6 +603,7 @@ labware_6,1
 labware_96,1
 labware_96rxnplate,1
 labware_aliquots,1
+labware_child,2
 labware_clinical_samples_1,1
 labware_clinical_samples_2,1
 labware_collect_plate,1
@@ -614,10 +618,11 @@ labware_magneticmodule,5
 labware_mm,1
 labware_mmplate,1
 labware_p300_tips,1
+labware_parent,2
 labware_patient_samples,1
 labware_pcr,1
 labware_pcr_plate,10
-labware_plate,3
+labware_plate,1
 labware_plates,9
 labware_pool,1
 labware_pre_pcr_plate,2
@@ -671,8 +676,11 @@ loc_rnase,1
 loc_tween,1
 lw_checkit,1
 lw_deepwell_plate,3
+lw_deepwell_plate_open,1
 lw_dmso,1
 lw_hplc,1
+lw_media,1
+lw_refill,1
 lw_source,1
 lw_tiprack300,1
 lw_tuberack,1
@@ -682,7 +690,7 @@ lysis_vol,1
 m10_mount,2
 m1k,1
 m20_mount,77
-m300_mount,98
+m300_mount,102
 m300_type,2
 m_mount,1
 mag_bead_mix_resuspend_reps,1
@@ -778,12 +786,12 @@ mntsingle,2
 module_type,1
 mother_plate_type,1
 mount,2
-mount_m20,8
-mount_m300,13
+mount_m20,9
+mount_m300,14
 mount_p1000,2
 mount_p20,11
 mount_p300,9
-mount_pip,1
+mount_pip,2
 mount_side,1
 move_side,2
 move_vol,1
@@ -841,10 +849,12 @@ num_cell_lines,2
 num_col,8
 num_cols,3
 num_columns,1
+num_curves,1
 num_daughter_plates,1
 num_drug_plates,1
 num_extracts,1
 num_gene,1
+num_lw,1
 num_mag_beads_tubes,1
 num_mastermix,3
 num_mixes,1
@@ -863,13 +873,14 @@ num_row,1
 num_rows_a,1
 num_rows_b,1
 num_rxns,1
-num_samp,67
+num_samp,68
 num_samp_p1,1
 num_samp_p2,1
 num_samp_plate1,1
 num_samp_plate2,1
 num_samp_plate3,1
 num_samp_plate4,1
+num_sample_columns,1
 num_samples,172
 num_samples_1,1
 num_samples_2,1
@@ -884,12 +895,14 @@ num_tests,1
 num_tipracks,1
 num_tubes,2
 num_wells,2
+number_of_columns,1
 number_of_dna_samples,1
 number_of_oligo_standards,1
 number_of_plates,4
 number_of_samples,18
 number_of_samples_to_process,5
 number_of_slides_to_process,1
+number_of_standards,2
 numinc,1
 numplates,6
 numpools,1
@@ -931,7 +944,7 @@ p1kmnt,1
 p1n,1
 p1num,1
 p20_blowout_height,1
-p20_mount,126
+p20_mount,127
 p20_multi_mount,3
 p20_rate,2
 p20_reservoir_height,1
@@ -948,7 +961,7 @@ p2num,1
 p300_gen,1
 p300_mixing_height,1
 p300_mnt,3
-p300_mount,146
+p300_mount,148
 p300_mount_1,1
 p300_multi_mount,7
 p300_rate,1
@@ -1067,8 +1080,16 @@ poolvol,1
 post_aspiration_wait,2
 post_size_selection_volume,1
 post_user_sample_volume,1
+pre_dil_facta,1
+pre_dil_factb,1
+pre_dil_factc,1
+pre_dil_factd,1
 pre_dil_factor,1
 pre_dilution,1
+pre_dilutiona,1
+pre_dilutionb,1
+pre_dilutionc,1
+pre_dilutiond,1
 prefill,1
 prepare_mastermix,2
 prepare_standard,2
@@ -1082,6 +1103,7 @@ primer_vol,1
 primer_volume,2
 process,1
 protocol,1
+protocol_selection,1
 protocol_type,1
 prototype,1
 puncture_agar,1
@@ -1169,7 +1191,7 @@ run_number,1
 rxn_bf_volume,1
 rxn_bf_well,1
 rxn_mix_vol_p3,1
-rxn_vol,2
+rxn_vol,3
 s_csv,1
 s_mount,1
 s_pip,1
@@ -1233,6 +1255,10 @@ sep_time_elu,6
 sep_time_wash,6
 serial_boolean,1
 serial_csv,1
+serial_dil_facta,1
+serial_dil_factb,1
+serial_dil_factc,1
+serial_dil_factd,1
 set_tip_max,2
 settling_1,1
 settling_2,1
@@ -1306,6 +1332,7 @@ start_column,1
 start_index_tip,1
 start_tip,1
 start_urea_vol,1
+starting_buffer_volume,1
 starting_conc,2
 starting_diluent_vol,1
 starting_plasma_vol,1
@@ -1374,6 +1401,7 @@ temp_s4_part2,1
 temp_s7_part1,1
 temp_s7_part2,1
 temp_set_reservoir,1
+temp_setting,1
 tempblock,1
 tempdeck_gen,1
 tempdeck_name,1
@@ -1432,6 +1460,7 @@ tipwell_start,1
 tmod_1_lname,1
 tmod_2_lname,1
 total_mixing_volume,2
+total_plate,4
 total_samples,5
 touch_radius,1
 touch_tip,2
@@ -1503,8 +1532,10 @@ tubetype,1
 tvol,1
 twb_rate,1
 twelve_well_resv_lname,1
-type_pip,1
+type_matrix,1
+type_pip,2
 type_pipette_small,1
+type_tc,1
 udi_start_col,1
 uploaded_csv,18
 uploaded_csv_mastermix,1
@@ -1521,7 +1552,7 @@ use_tuberack_b,1
 user_enzyme_volume,1
 user_enzyme_well,1
 using_magdeck,1
-using_tempdeck,3
+using_tempdeck,4
 v_0_tube,1
 v_0_tube1,2
 v_0_tube2,1
@@ -1569,6 +1600,7 @@ vol_peptide2,1
 vol_peptide3,1
 vol_pma_ca,1
 vol_reagent,1
+vol_refill,1
 vol_removal,1
 vol_sample,7
 vol_sample_redissolved,1
@@ -1587,7 +1619,7 @@ vol_tube3,1
 vol_wash,1
 vol_water,3
 vol_xp1,1
-volume,4
+volume,5
 volume_csv,1
 volume_eb_in_ul,2
 volume_final_elution_in_ul,2

protoBuilds/0045f1/README.json

@@ -6,7 +6,7 @@
         ]
     },
     "deck-setup": "\n",
-    "description": "This protocol spots up to 6 slides with antibody. Each slide has 8 wells, to which the protocol will spot with 8 dots for wells 2-7. The user has the ability to manipulate the spacing between the dots, as well as the volume of the dispenses. The user can also specify the number of slides spotted. Please see below for the order in which slides are spotted.\nExplanation of complex parameters below:\n* Number of tubes: Specify the number of tubes this protocol will run.\n* Number of Slides: Specify the number of slides for this run (1-6).\n* Spot Spacing: Specify the spacing between dots on the slide wells.\n* Spot Volume: Specify the volume of each dot.\n* Aspiration Flow Rate: Specify the aspiration rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* Dispense Flow Rate: Specify the dispense rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* P20 Single-Channel Mount: Specify which mount (left or right) to host the P20 single-channel pipette.\n",
+    "description": "This protocol spots up to 6 slides with antibody. Each slide has 8 wells, to which the protocol will spot with 8 dots for wells 2-7. The user has the ability to manipulate the spacing between the dots, as well as the volume of the dispenses. The user can also specify the number of slides spotted. Please see below for the order in which slides are spotted.\nExplanation of complex parameters below:\n Number of tubes: Specify the number of tubes this protocol will run.\n Number of Slides: Specify the number of slides for this run (1-6).\n Spot Spacing: Specify the spacing between dots on the slide wells.\n Spot Volume: Specify the volume of each dot.\n Aspiration Flow Rate: Specify the aspiration rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n Dispense Flow Rate: Specify the dispense rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* P20 Single-Channel Mount: Specify which mount (left or right) to host the P20 single-channel pipette.\n",
     "internal": "0045f1",
     "labware": "\nOpentrons 10ul filter tips\nOpentrons 4-in-1 tube rack with Eppendorf 1.5mL safelock snapcap\nCustom slide plate\n",
     "markdown": {