# Additional List can be added, but these list need to be included in the All_wells array
All_wells = [Plasmid1_wells, Plasmid2_wells] # Creates an array from the lists of wells. More lists can be declared and added to this array
# By adding in another variable to this section a second list for cells requiring a different plasmid can be used
# A third variable would be needed to house both lists and could be used to iterate through the loops with each smaller list being for each plasmid, biglist = [list1,list2], biglist[0]
#All_Wells = Randomizer(All_wells) # Randomizes the wells, delete the hashtag to allow this randomizer to run. Imported from OT2_Functions
#########################################################################################
#########################################################################################
tempdeck = TempDeck() # Saves the temperature deck into a variable,
temperature = {"temp1": 4, "temp2": 42, "temp3": 37} # Saves the temperatures for the protocol into a dictionary. Dictionaries have keys and values
# The value can be called by the key i.e temperature["temp1"] = 4
if not robot.is_simulating(): # If the robot is inactive and the temperature deck isn't processing a command
tempdeck.connect('/dev/ttyACM0') # Connects to and begins cooling the temperature deck
tempdeck.set_temperature(temperature["temp1"]) # Initialization temperature for cooling
tempdeck.wait_for_temp() # Pauses the protocol until the temperature deck reaches the set temperature
target = All_wells # Adds the array of wells into a variable for easier readability during manipulation
SOB_wells = [well.top(1) for well in target] # well.top moves the pipette to the top of the well, the number specifies the distance in mm
robot.pause() # Opentron command that pauses whatever the robot is doing. The user can remove and centrifuge at this point, if the need is there. resumed via the OT app
# The code below handles distributing plasmid DNA
for i in range(NumberofPlasmids): # Transfers plasmid DNA into competent cell aliquots. The variable NumberofPlasmids controls how many times the loop is carried out, once for each plasmid
P10.distribute( # Presumes same plasmid for all cells, adds all doses to the pipette, wells specified later in the block
PlasmidVolume, # Specifies the volume in ul
DNA(i), # Selects which plasmid to pipette based on it's position on the container declared DNA. I increases with each loop, meaning the next plasmid is selected
target, # Target is the specified wells where the plasmid is then distributed (this will not work if multiple plasmids are being used)
blow_out=True, # Empties the pipette with an extra gust of air to ensure it is fluid free
new_tip='always' # Changes the pipette after every dispense to avoid contamination
class TempDeck(commands.CommandPublisher):
"""
Under development. API subject to change without a version bump
"""
def __init__(self, lw=None, port=None, broker=None):
super().__init__(broker)
self.labware = lw
self._port = port
self._driver = None
self._device_info = None
self._poll_stop_event = None
@commands.publish.both(command=commands.tempdeck_set_temp)
def set_temperature(self, celsius):
"""
Set temperature in degree Celsius
Range: 4 to 95 degree Celsius (QA tested).
The internal temp range is -9 to 99 C, which is limited by the 2-digit
temperature display. Any input outside of this range will be clipped
to the nearest limit
"""
if self._driver and self._driver.is_connected():
self._driver.legacy_set_temperature(celsius)
@commands.publish.both(command=commands.tempdeck_deactivate)
def deactivate(self):
""" Stop heating/cooling and turn off the fan """
if self._driver and self._driver.is_connected():
self._driver.deactivate()
def wait_for_temp(self):
"""
This method exits only if set temperature has reached.Subject to change
"""
if self._driver and self._driver.is_connected():
while self.status != 'holding at target':
pass
@classmethod
def name(cls):
return 'tempdeck'
@classmethod
def display_name(cls):
return 'Temperature Deck'
# TODO: there should be a separate decoupled set of classes that construct
# the http api response entity given the model instance.
def to_dict(self):
return {
'name': self.name(),
'port': self.port,
'serial': self.device_info and self.device_info.get('serial'),
'model': self.device_info and self.device_info.get('model'),
'fwVersion': self.device_info and self.device_info.get('version'),
'displayName': self.display_name(),
**self.live_data
}
@property
def live_data(self):
return {
'status': self.status,
'data': {
'currentTemp': self.temperature,
'targetTemp': self.target
}
}
@property
def port(self):
""" Serial Port """
return self._port
@property
def device_info(self):
"""
Returns a dict:
{ 'serial': 'abc123', 'model': '8675309', 'version': '9001' }
"""
return self._device_info
@property
def temperature(self):
""" Current temperature in degree celsius """
return self._driver.temperature
@property
def target(self):
"""
Target temperature in degree celsius.
Returns None if no target set
"""
return self._driver.target
@property
def status(self):
"""
Returns a string: 'heating'/'cooling'/'holding at target'/'idle'.
NOTE: Depends on _poll_temperature thread to update the temperature to
be used to determine the status
"""
return self._driver and self._driver.status
# Internal Methods
def _poll_temperature(self):
while not self._poll_stop_event.wait(TEMP_POLL_INTERVAL_SECS):
self._driver and self._driver.update_temperature()
def connect(self):
"""
Connect to the 'TempDeck' port
Planned change- will connect to the correct port in case of multiple
TempDecks
"""
if self._port:
if temp_locks.get(self._port):
self._driver = temp_locks[self._port][1]
else:
self._driver = TempDeckDriver()
if not self._driver.is_connected():
self._driver.connect(self._port)
self._device_info = self._driver.get_device_info()
self._poll_stop_event = Event()
Thread(target=self._poll_temperature, daemon=True).start()
else:
# Sanity check Should never happen, because connect should never
# be called without a port on Module
raise MissingDevicePortError(
"TempDeck couldn't connect to port {}".format(self._port))
def disconnect(self):
'''
Disconnect from the serial port
'''
if self._poll_stop_event:
self._poll_stop_event.set()
if self._driver:
if self.status != 'idle':
self.deactivate()
self._driver.disconnect(port=self._port)
Buffers_positions = Buffers.wells(
'A1', length=25
) # Specify the buffer positions, change length=25 to whatever the number
# of buffers you have, eg if 15 buffers length=15
#########################################################################################
#########################################################################################
# BELOW IS CODE FOR THE PROTOCOL
# IF WORKING WITH E. COLI, BELOW IS A OPTIMAL PROTOCOL THAT ONLY REQUIRES 1 WASH STEP
# IF INVESTINGATING DIFFERENT INCUBATION TIMES, ALTER P300 DELAYS
# IF WANTING TO CHANGE TEMPDECK ON CONSTANTLY, REMOVE ALL tempdeck.disengage() AND PLACE BEFORE
# FINAL ROBOT COMMENT
tempdeck = TempDeck() # Connects the Tempdeck module to OT-2
if not robot.is_simulating(): # Cannot use while simulating,
tempdeck.connect('/dev/ttyACM0')
tempdeck.set_temperature(
target_temperature) # Sets the temperature to whats specified above
target1 = Compcells1(Even_wells) # Where your cells are going
robot.home() # turbulent airflow within the OT-2
robot.pause()
robot.comment(
"Make sure that centrifuge has been chilled down to 4*C and all buffers are on ice."
)
robot.comment(
"All plates should be chilled at the beginning and culture should be incubated on ice for 15 minutes before start."
)
robot.comment(
"Once at set temperature, insert culture into slot 6 and plate onto TempDeck, then resume!"