challenging-interlab-growth-curve.py

"""
http://2018.igem.org/wiki/images/0/09/2018_InterLab_Plate_Reader_Protocol.pdf
"""
import json
from urllib.parse import quote

import sbol3
from tyto import OM

import labop
import uml
from labop.execution.execution_engine import ExecutionEngine
from labop_convert.markdown.markdown_specialization import MarkdownSpecialization

doc = sbol3.Document()
sbol3.set_namespace("http://igem.org/engineering/")

#############################################
# Import the primitive libraries
print("Importing libraries")
labop.import_library("liquid_handling")
print("... Imported liquid handling")
labop.import_library("plate_handling")
# print('... Imported plate handling')
labop.import_library("spectrophotometry")
print("... Imported spectrophotometry")
labop.import_library("sample_arrays")
print("... Imported sample arrays")
labop.import_library("culturing")
#############################################


# create the materials to be provisioned
dh5alpha = sbol3.Component(
    "dh5alpha", "https://identifiers.org/pubchem.substance:24901740"
)
dh5alpha.name = "_E. coli_ DH5 alpha"
doc.add(dh5alpha)

lb_cam = sbol3.Component("lb_cam", "https://identifiers.org/pubchem.substance:24901740")
lb_cam.name = "LB Broth+chloramphenicol"
doc.add(lb_cam)

chloramphenicol = sbol3.Component(
    "chloramphenicol", "https://identifiers.org/pubchem.substance:24901740"
)
chloramphenicol.name = "chloramphenicol"
doc.add(chloramphenicol)


neg_control_plasmid = sbol3.Component("neg_control_plasmid", sbol3.SBO_DNA)
neg_control_plasmid.name = "Negative control"
neg_control_plasmid.description = "BBa_R0040 Kit Plate 7 Well 2D"

pos_control_plasmid = sbol3.Component("pos_control_plasmid", sbol3.SBO_DNA)
pos_control_plasmid.name = "Positive control"
pos_control_plasmid.description = "BBa_I20270 Kit Plate 7 Well 2B"

test_device1 = sbol3.Component("test_device1", sbol3.SBO_DNA)
test_device1.name = "Test Device 1"
test_device1.description = "BBa_J364000 Kit Plate 7 Well 2F"

test_device2 = sbol3.Component("test_device2", sbol3.SBO_DNA)
test_device2.name = "Test Device 2"
test_device2.description = "BBa_J364001 Kit Plate 7 Well 2H"

test_device3 = sbol3.Component("test_device3", sbol3.SBO_DNA)
test_device3.name = "Test Device 3"
test_device3.description = "BBa_J364002 Kit Plate 7 Well 2J"

test_device4 = sbol3.Component("test_device4", sbol3.SBO_DNA)
test_device4.name = "Test Device 4"
test_device4.description = "BBa_J364007 Kit Plate 7 Well 2L"

test_device5 = sbol3.Component("test_device5", sbol3.SBO_DNA)
test_device5.name = "Test Device 5"
test_device5.description = "BBa_J364008 Kit Plate 7 Well 2N"

test_device6 = sbol3.Component("test_device6", sbol3.SBO_DNA)
test_device6.name = "Test Device 6"
test_device6.description = "BBa_J364009 Kit Plate 7 Well 2P"

doc.add(neg_control_plasmid)
doc.add(pos_control_plasmid)
doc.add(test_device1)
doc.add(test_device2)
doc.add(test_device3)
doc.add(test_device4)
doc.add(test_device5)
doc.add(test_device6)


activity = labop.Protocol("interlab")
activity.name = "Cell measurement protocol (Challenging)"
activity.description = """
This is a more challenging version of the cell calibration protocol for time-interval measurement. At each time point 0-hour, 2-hour, 4-hour and 6-hour, you will take a sample from each of the eight devices, two colonies per device, three falcon tubes per colony → total 48 tubes."""
activity.version = "1.0b"
doc.add(activity)

plasmids = [
    neg_control_plasmid,
    pos_control_plasmid,
    test_device1,
    test_device2,
    test_device3,
    test_device4,
    test_device5,
    test_device6,
]

# Day 1: Transformation
transformation = activity.primitive_step(
    f"Transform", host=dh5alpha, dna=plasmids, selection_medium=lb_cam
)

# Day 2: Pick colonies and culture overnight
culture_container_day1 = activity.primitive_step(
    "ContainerSet",
    quantity=2 * len(plasmids),
    specification=labop.ContainerSpec(
        name=f"culture (day 1)",
        queryString="cont:CultureTube",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)

overnight_culture = activity.primitive_step(
    "Culture",
    inoculum=transformation.output_pin("transformants"),
    replicates=2,
    growth_medium=lb_cam,
    volume=sbol3.Measure(5, OM.millilitre),  # Actually 5-10 ml in the written protocol
    duration=sbol3.Measure(16, OM.hour),  # Actually 16-18 hours
    orbital_shake_speed=sbol3.Measure(220, None),  # No unit for RPM or inverse minutes
    temperature=sbol3.Measure(37, OM.degree_Celsius),
    container=culture_container_day1.output_pin("samples"),
)

# Day 3 culture
culture_container_day2 = activity.primitive_step(
    "ContainerSet",
    quantity=2 * len(plasmids),
    specification=labop.ContainerSpec(
        name=f"culture (day 2)",
        queryString="cont:CultureTube",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)


back_dilution = activity.primitive_step(
    "Dilute",
    source=culture_container_day1.output_pin("samples"),
    destination=culture_container_day2.output_pin("samples"),
    replicates=2,
    diluent=lb_cam,
    amount=sbol3.Measure(5.0, OM.millilitre),
    dilution_factor=uml.LiteralInteger(value=10),
)

baseline_absorbance = activity.primitive_step(
    "MeasureAbsorbance",
    samples=culture_container_day2.output_pin("samples"),
    wavelength=sbol3.Measure(600, OM.nanometer),
)
baseline_absorbance.name = "baseline absorbance"

parent_conical_tube = activity.primitive_step(
    "ContainerSet",
    quantity=2 * len(plasmids),
    specification=labop.ContainerSpec(
        name=f"back-diluted culture",
        queryString="cont:50mlConicalTube",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)

dilution = activity.primitive_step(
    "DiluteToTargetOD",
    source=culture_container_day2.output_pin("samples"),
    destination=parent_conical_tube.output_pin("samples"),
    diluent=lb_cam,
    amount=sbol3.Measure(40, OM.millilitre),
    target_od=sbol3.Measure(0.2, None),
)  # Dilute to a target OD of 0.2, opaque container
dilution.description = (
    "(Reliability of the dilution upon Abs600 measurement: should stay between 0.1-0.9)"
)

# Further subdivision into triplicates
conical_tubes = activity.primitive_step(
    "ContainerSet",
    quantity=2 * len(plasmids),
    replicates=3,
    specification=labop.ContainerSpec(
        name=f"replicate subcultures",
        queryString="cont:50mlConicalTube",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)
conical_tubes.description = (
    "The conical tubes should be opaque, amber-colored, or covered with foil."
)

transfer = activity.primitive_step(
    "Transfer",
    source=parent_conical_tube.output_pin("samples"),
    replicates=3,
    destination=conical_tubes.output_pin("samples"),
    amount=sbol3.Measure(12, OM.milliliter),
)

embedded_image = activity.primitive_step(
    "EmbeddedImage",
    image="/Users/bbartley/Dev/git/sd2/labop/fig3_cell_calibration.png",
)


# Transfer cultures to a microplate baseline measurement and outgrowth
timepoint_0hrs = activity.primitive_step(
    "ContainerSet",
    quantity=2 * len(plasmids) * 3,
    specification=labop.ContainerSpec(
        name="cultures (0 hr timepoint)",
        queryString="cont:MicrofugeTube",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)
# Hold on ice
hold = activity.primitive_step(
    "Hold",
    location=timepoint_0hrs.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)
hold.description = "This will prevent cell growth while transferring samples."

transfer = activity.primitive_step(
    "Transfer",
    source=conical_tubes.output_pin("samples"),
    destination=timepoint_0hrs.output_pin("samples"),
    amount=sbol3.Measure(1, OM.milliliter),
)

# Plate cultures
plate1 = activity.primitive_step(
    "EmptyContainer",
    specification=labop.ContainerSpec(
        name="plate 1",
        queryString="cont:Plate96Well",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)
plate2 = activity.primitive_step(
    "EmptyContainer",
    specification=labop.ContainerSpec(
        name="plate 2",
        queryString="cont:Plate96Well",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)
plate3 = activity.primitive_step(
    "EmptyContainer",
    specification=labop.ContainerSpec(
        name="plate 3",
        queryString="cont:Plate96Well",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)


hold = activity.primitive_step(
    "Hold",
    location=plate1.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)

hold = activity.primitive_step(
    "Hold",
    location=plate2.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)

hold = activity.primitive_step(
    "Hold",
    location=plate3.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)


transfer_map = quote(
    json.dumps(
        {
            "1": "A2:D2",
            "2": "E2:H2",
            "3": "A3:D3",
            "4": "E3:H3",
            "5": "A4:D4",
            "6": "E4:H4",
            "7": "A5:D5",
            "8": "E5:H5",
            "9": "A7:D7",
            "10": "E7:H7",
            "11": "A8:D8",
            "12": "E8:H8",
            "13": "A9:D9",
            "14": "E9:H9",
            "15": "A10:D10",
            "16": "E10:H10",
            "17": "A2:D2",
            "18": "E2:H2",
            "19": "A3:D3",
            "20": "E3:H3",
            "21": "A4:D4",
            "22": "E4:H4",
            "23": "A5:D5",
            "24": "E5:H5",
            "25": "A7:D7",
            "26": "E7:H7",
            "27": "A8:D8",
            "28": "E8:H8",
            "29": "A9:D9",
            "30": "E9:H9",
            "31": "A10:D10",
            "32": "E10:H10",
            "33": "A2:D2",
            "34": "E2:H2",
            "35": "A3:D3",
            "36": "E3:H3",
            "37": "A4:D4",
            "38": "E4:H4",
            "39": "A5:D5",
            "40": "E5:H5",
            "41": "A7:D7",
            "42": "E7:H7",
            "43": "A8:D8",
            "44": "E8:H8",
            "45": "A9:D9",
            "46": "E9:H9",
            "47": "A10:D10",
            "48": "E10:H10",
        }
    )
)


plan = labop.SampleData(values=transfer_map)
transfer = activity.primitive_step(
    "TransferByMap",
    source=timepoint_0hrs.output_pin("samples"),
    destination=plate1.output_pin("samples"),
    amount=sbol3.Measure(100, OM.microliter),
    plan=plan,
)
transfer.description = "See the plate layout below."

plan = labop.SampleData(values=transfer_map)

transfer = activity.primitive_step(
    "TransferByMap",
    source=timepoint_0hrs.output_pin("samples"),
    destination=plate2.output_pin("samples"),
    amount=sbol3.Measure(100, OM.microliter),
    plan=plan,
)
plan = labop.SampleData(values=transfer_map)

transfer = activity.primitive_step(
    "TransferByMap",
    source=timepoint_0hrs.output_pin("samples"),
    destination=plate3.output_pin("samples"),
    amount=sbol3.Measure(100, OM.microliter),
    plan=plan,
)


plate_blanks = activity.primitive_step(
    "Transfer",
    source=[lb_cam],
    destination=plate1.output_pin("samples"),
    coordinates="A1:H1, A10:H10, A12:H12",
    amount=sbol3.Measure(100, OM.microliter),
)
plate_blanks.description = "These samples are blanks."

embedded_image = activity.primitive_step(
    "EmbeddedImage",
    image="/Users/bbartley/Dev/git/sd2/labop/fig2_cell_calibration.png",
)


# Possibly display map here
absorbance_0hrs_plate1 = activity.primitive_step(
    "MeasureAbsorbance",
    samples=plate1.output_pin("samples"),
    wavelength=sbol3.Measure(600, OM.nanometer),
)
absorbance_0hrs_plate1.name = "0 hr absorbance timepoint"

fluorescence_0hrs_plate1 = activity.primitive_step(
    "MeasureFluorescence",
    samples=plate1.output_pin("samples"),
    excitationWavelength=sbol3.Measure(485, OM.nanometer),
    emissionWavelength=sbol3.Measure(530, OM.nanometer),
    emissionBandpassWidth=sbol3.Measure(30, OM.nanometer),
)
fluorescence_0hrs_plate1.name = "0 hr fluorescence timepoint"

absorbance_0hrs_plate2 = activity.primitive_step(
    "MeasureAbsorbance",
    samples=plate2.output_pin("samples"),
    wavelength=sbol3.Measure(600, OM.nanometer),
)
absorbance_0hrs_plate2.name = "0 hr absorbance timepoint"
fluorescence_0hrs_plate2 = activity.primitive_step(
    "MeasureFluorescence",
    samples=plate2.output_pin("samples"),
    excitationWavelength=sbol3.Measure(485, OM.nanometer),
    emissionWavelength=sbol3.Measure(530, OM.nanometer),
    emissionBandpassWidth=sbol3.Measure(30, OM.nanometer),
)
fluorescence_0hrs_plate2.name = "0 hr fluorescence timepoint"

absorbance_0hrs_plate3 = activity.primitive_step(
    "MeasureAbsorbance",
    samples=plate3.output_pin("samples"),
    wavelength=sbol3.Measure(600, OM.nanometer),
)
absorbance_0hrs_plate3.name = "0 hr absorbance timepoint"
fluorescence_0hrs_plate3 = activity.primitive_step(
    "MeasureFluorescence",
    samples=plate3.output_pin("samples"),
    excitationWavelength=sbol3.Measure(485, OM.nanometer),
    emissionWavelength=sbol3.Measure(530, OM.nanometer),
    emissionBandpassWidth=sbol3.Measure(30, OM.nanometer),
)
fluorescence_0hrs_plate3.name = "0 hr fluorescence timepoint"

## Cover plate
seal = activity.primitive_step(
    "EvaporativeSeal", location=plate1.output_pin("samples"), type="foo"
)
seal = activity.primitive_step(
    "EvaporativeSeal", location=plate2.output_pin("samples"), type="foo"
)
seal = activity.primitive_step(
    "EvaporativeSeal", location=plate3.output_pin("samples"), type="foo"
)


## Begin outgrowth
incubate = activity.primitive_step(
    "Incubate",
    location=conical_tubes.output_pin("samples"),
    duration=sbol3.Measure(2, OM.hour),
    temperature=sbol3.Measure(37, OM.degree_Celsius),
    shakingFrequency=sbol3.Measure(220, None),
)

incubate = activity.primitive_step(
    "Incubate",
    location=plate1.output_pin("samples"),
    duration=sbol3.Measure(2, OM.hour),
    temperature=sbol3.Measure(37, OM.degree_Celsius),
    shakingFrequency=sbol3.Measure(220, None),
)
incubate = activity.primitive_step(
    "Incubate",
    location=plate2.output_pin("samples"),
    duration=sbol3.Measure(4, OM.hour),
    temperature=sbol3.Measure(37, OM.degree_Celsius),
    shakingFrequency=sbol3.Measure(220, None),
)
incubate = activity.primitive_step(
    "Incubate",
    location=plate1.output_pin("samples"),
    duration=sbol3.Measure(6, OM.hour),
    temperature=sbol3.Measure(37, OM.degree_Celsius),
    shakingFrequency=sbol3.Measure(220, None),
)

# Hold on ice to inhibit cell growth
hold = activity.primitive_step(
    "Hold",
    location=conical_tubes.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)
hold.description = (
    "This will inhibit cell growth during the subsequent pipetting steps."
)

hold = activity.primitive_step(
    "Hold",
    location=plate1.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)
hold.description = (
    "This will inhibit cell growth during the subsequent pipetting steps."
)

# Transfer cultures to a microplate baseline measurement and outgrowth
timepoint_2hrs = activity.primitive_step(
    "ContainerSet",
    quantity=2 * len(plasmids) * 3,
    specification=labop.ContainerSpec(
        name="cultures (0 hr timepoint)",
        queryString="cont:MicrofugeTube",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)

# Hold on ice
hold = activity.primitive_step(
    "Hold",
    location=timepoint_2hrs.output_pin("samples"),
    temperature=sbol3.Measure(4, OM.degree_Celsius),
)
hold.description = "This will prevent cell growth while transferring samples."

transfer = activity.primitive_step(
    "Transfer",
    source=conical_tubes.output_pin("samples"),
    destination=timepoint_2hrs.output_pin("samples"),
    amount=sbol3.Measure(1, OM.milliliter),
)

plate4 = activity.primitive_step(
    "EmptyContainer",
    specification=labop.ContainerSpec(
        name="plate 4",
        queryString="cont:Plate96Well",
        prefixMap={"cont": "https://sift.net/container-ontology/container-ontology#"},
    ),
)

plan = labop.SampleData(values=transfer_map)
transfer = activity.primitive_step(
    "TransferByMap",
    source=timepoint_2hrs.output_pin("samples"),
    destination=plate4.output_pin("samples"),
    amount=sbol3.Measure(100, OM.microliter),
    plan=plan,
)
# Plate the blanks
plate_blanks = activity.primitive_step(
    "Transfer",
    source=[lb_cam],
    destination=plate4.output_pin("samples"),
    coordinates="A1:H1, A10:H10, A12:H12",
    amount=sbol3.Measure(100, OM.microliter),
)
plate_blanks.description = "These are the blanks."


quick_spin = activity.primitive_step("QuickSpin", location=plate1.output_pin("samples"))
quick_spin.description = "This will prevent cross-contamination when removing the seal."

remove_seal = activity.primitive_step("Unseal", location=plate1.output_pin("samples"))

absorbance_2hrs_plate1 = activity.primitive_step(
    "MeasureAbsorbance",
    samples=plate1.output_pin("samples"),
    wavelength=sbol3.Measure(600, OM.nanometer),
)
absorbance_2hrs_plate1.name = "2 hr absorbance timepoint"
fluorescence_2hrs_plate1 = activity.primitive_step(
    "MeasureFluorescence",
    samples=plate1.output_pin("samples"),
    excitationWavelength=sbol3.Measure(485, OM.nanometer),
    emissionWavelength=sbol3.Measure(530, OM.nanometer),
    emissionBandpassWidth=sbol3.Measure(30, OM.nanometer),
)
fluorescence_2hrs_plate1.name = "2 hr fluorescence timepoint"

absorbance_2hrs_plate4 = activity.primitive_step(
    "MeasureAbsorbance",
    samples=plate4.output_pin("samples"),
    wavelength=sbol3.Measure(600, OM.nanometer),
)
absorbance_2hrs_plate4.name = "2 hr absorbance timepoint"
fluorescence_2hrs_plate4 = activity.primitive_step(
    "MeasureFluorescence",
    samples=plate4.output_pin("samples"),
    excitationWavelength=sbol3.Measure(485, OM.nanometer),
    emissionWavelength=sbol3.Measure(530, OM.nanometer),
    emissionBandpassWidth=sbol3.Measure(30, OM.nanometer),
)
fluorescence_2hrs_plate4.name = "2 hr fluorescence timepoint"

# endpoint_fluorescence_plate1 = protocol.primitive_step('MeasureFluorescence',
#                                                       samples=plate4.output_pin('samples'),
#                                                       excitationWavelength=sbol3.Measure(485, OM.nanometer),
#                                                       emissionWavelength=sbol3.Measure(530, OM.nanometer),
#                                                       emissionBandpassWidth=sbol3.Measure(30, OM.nanometer))
#
# endpoint_absorbance_plate2 = protocol.primitive_step('MeasureAbsorbance',
#                                                     samples=plate2.output_pin('samples'),
#                                                     wavelength=sbol3.Measure(600, OM.nanometer))
#
# endpoint_fluorescence_plate2 = protocol.primitive_step('MeasureFluorescence',
#                                                       samples=plate2.output_pin('samples'),
#                                                       excitationWavelength=sbol3.Measure(485, OM.nanometer),
#                                                       emissionWavelength=sbol3.Measure(530, OM.nanometer),
#                                                       emissionBandpassWidth=sbol3.Measure(30, OM.nanometer))
#
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=baseline_absorbance.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=absorbance_0hrs_plate1.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=absorbance_0hrs_plate2.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=absorbance_0hrs_plate3.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=fluorescence_0hrs_plate1.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=fluorescence_0hrs_plate2.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=fluorescence_0hrs_plate3.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=absorbance_2hrs_plate1.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=absorbance_2hrs_plate4.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=fluorescence_2hrs_plate1.output_pin("measurements"),
)
activity.designate_output(
    "measurements",
    "http://bioprotocols.org/labop#SampleData",
    source=fluorescence_2hrs_plate4.output_pin("measurements"),
)


# protocol.designate_output('measurements', 'http://bioprotocols.org/labop#SampleData', source=absorbance_plate1.output_pin('measurements'))
# protocol.designate_output('measurements', 'http://bioprotocols.org/labop#SampleData', source=fluorescence_plate1.output_pin('measurements'))
#
# protocol.designate_output('measurements', 'http://bioprotocols.org/labop#SampleData', source=endpoint_absorbance_plate1.output_pin('measurements'))
# protocol.designate_output('measurements', 'http://bioprotocols.org/labop#SampleData', source=endpoint_fluorescence_plate1.output_pin('measurements'))
#
# protocol.designate_output('measurements', 'http://bioprotocols.org/labop#SampleData', source=endpoint_absorbance_plate2.output_pin('measurements'))
# protocol.designate_output('measurements', 'http://bioprotocols.org/labop#SampleData', source=endpoint_fluorescence_plate2.output_pin('measurements'))
#

agent = sbol3.Agent("test_agent")
ee = ExecutionEngine(specializations=[MarkdownSpecialization("test_LUDOX_markdown.md")])
execution = ee.execute(activity, agent, id="test_execution", parameter_values=[])
print(ee.specializations[0].markdown)
ee.specializations[0].markdown = ee.specializations[0].markdown.replace(
    "`_E. coli_", "_`E. coli`_ `"
)
with open("example.md", "w", encoding="utf-8") as f:
    f.write(ee.specializations[0].markdown)