temperature

Illumina HiSeq 2500 System :: ARM9 CHEM

Uses commands found on hackteria

Example:

#Create ARM9 Chemistry object
import pyseq
temp = pyseq.temperature.Temperature('COM8')
#Initialize ARM Chemistry
temperature.initialize()
# Get temperature of flowcell A
temp.get_fc_T('A')
# Set temperature of flowcell A
temp.set_fc_T('A', 55.0)
# Set temperature of flowcell A and block until temperature is reached
temp.wait_fc_T('A'), 55.0

Temperatures of flowcells A and B can be independently controlled. The min temperature is 20 °C and the max temperature is 60 °C.

Classes

Temperature(com_port[, baudrate, logger])

HiSeq 2500 System :: Stage & Chiller Temperature Control (ARM9 CHEM)
class pyseq.temperature.Temperature(com_port, baudrate=115200, logger=None)

HiSeq 2500 System :: Stage & Chiller Temperature Control (ARM9 CHEM)

Attributes

  • serial_port: IO wrapper around serial port

  • suffix: Suffix to send commands

  • logger (logger): Logger used for messaging

  • version (str): Controller version.

  • T_fc [float, float]: Set temperature of flowcell in °C.

  • T_chiller [float, float, float]: Set temperature of chillers in °C.

  • min_fc_T (float): Minimum flowcell temperature in °C.

  • max_fc_T (float): Maximum flowcell temperature in °C.

  • min_chiller_T (float): Minimum chiller temperature in °C.

  • max_chiller_T (float): Maximum flowcell temperature in °C.

  • fc_PIDSF0: Flowcell A Temperature servo-loop parameters

  • fc_PIDSF1: Flowcell B Temperature servo-loop parameters

  • tec_PIDSF0: Chiller 0 Temperature servo-loop parameters

  • tec_PIDSF1: Chiller 1 Temperature servo-loop parameters

  • tec_PIDSF2: Chiller 2 Temperature servo-loop parameters

  • p_: servo-loop parameters = Servo_Proportional, Servo_Integral, Servo_Derivative, Feed_Frw_StepSize, Feed_frw_Threshold

  • delay (int): Delay time in querying temperature.

command(text)

Send a serial command to the ARM9 CHEM and return the response.

Parameters:

  • text (str): A command to send to the ystage.

Returns:

  • str: The response from the ystage.

fc_off(fc)

Turn off temperature control for flowcell fc.

fc_on(fc)

Turn on temperature control for flowcell fc.

get_chiller_T()

Return temperature of chiller in °C.

NOTE: There are 3 TEC blocks cooling the chiller. I’m not sure if all 3 cool chiller. I think the 3rd one cools something else because the control parameters are different. - Kunal

get_fc_T(fc)

Return temperature of flowcell in °C.

get_fc_index(fc)

Return flowcell index.

initialize()

Initialize the ARM9 CHEM

reset_ARM9()

Reset ARM9 controller.

set_chiller_T(T, i)

Return temperature of chiller in °C.

set_fc_T(fc, T)

Set temperature of flowcell in °C.

Parameters:

  • fc (str or int): Flowcell position either A or 0, or B or 1

  • T (float): Temperature in °C.

Returns:

  • (float): Current temperature in °C.

wait_fc_T(fc, T)

Set and wait for flowcell to reach temperature in °C.

Parameters:

  • fc (str or int): Flowcell position either A or 0, or B or 1

  • T (float): Temperature in °C.

Returns:

  • (float): Current temperature in °C.

write_log(*args)

Write messages to the log.