Python PumpToFlowcell Examples

Example #1

def FirstReadPreparation():
    config.logger.info(u'Start FirstReadPreparation')
    PumpToFlowcell(actPos=8,
                   volume=203)
    SetThermalCyclerTemp(temp=65)
    sleep(60)
    PumpToActuator(actPos=12)
    PumpToFlowcell(actPos=12,
                   volume=203)
    SetThermalCyclerTemp(temp=40)
    sleep(60)
    PumpToFlowcell(actPos=3, volume=311)
    config.logger.info(u'End FirstReadPreparation')
    return

Example #2

def Deblock():
    config.logger.info(u'Start Deblock')
    PumpToFlowcell(actPos=3,
                   volume=311)
    sleep(3.1)
    SetThermalCyclerTemp(temp=60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    PumpToFlowcell(actPos=4,
                   volume=131)
    PumpToFlowcell(actPos=3,
                   volume=48)
    sleep(10)
    config.logger.info(u'End Deblock')
    return

Example #3

def FirstExtension():
    config.logger.info(u'Start FirstExtension')
    SetThermalCyclerTemp(temp=50)
    sleep(30)
    PumpToFlowcell(actPos=5,
                   volume=503,
                   aspirationRate=9)
    sleep(3)
    for i in range(5):
        PumpToFlowcell(actPos=5,
                       volume=24,
                       aspirationRate=9)
    sleep(90)
    config.logger.info(u'End FirstExtension')
    return

Example #4

def AmplificationWash():
    config.logger.info(u'Start AmplificationWash')
    PumpToFlowcell(actPos=3,
                   volume=311)
    SetThermalCyclerTemp(temp=20)
    config.logger.info(u'End AmplificationWash')
    return

Example #5

def Resynthesis():
    config.logger.info(u'Start Resynthesis')
    PumpToFlowcell(actPos=8,
                   volume=90,
                   aspirationRate=9)
    sleep(7.2)
    PumpToFlowcell(actPos=3,
                   volume=90,
                   aspirationRate=9)
    sleep(7.2)
    PumpToFlowcell(actPos=6,
                   volume=196,  # todo проверить объёмы в этом пункте
                   aspirationRate=9)
    sleep(18.7)
    config.logger.info(u'End Resynthesis')
    return

Example #6

def End():
    config.logger.info(u'Start End')
    PumpToFlowcell(actPos=3,
                   volume=311)
    sleep(3.3)
    SetThermalCyclerTemp(temp=60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    PumpToFlowcell(actPos=4,
                   volume=167)
    PumpToFlowcell(actPos=3,
                   volume=48)
    sleep(40)
    PumpToFlowcell(actPos=3,
                   volume=12)
    sleep(35)
    config.logger.info(u'End End')

Example #7

def IndexOnePreparation():
    config.logger.info(u'Start IndexOnePreparation')
    SetThermalCyclerTemp(temp=20)
    sleep(25)
    PumpToFlowcell(actPos=8,
                   volume=203)
    SetThermalCyclerTemp(temp=65)
    sleep(60)
    PumpToActuator(actPos=13)
    PumpToFlowcell(actPos=13,
                   volume=203)
    SetThermalCyclerTemp(temp=40)
    sleep(60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    config.logger.info(u'End IndexOnePreparation')
    return

Example #8

def PreresynthesisTempramp():
    config.logger.info(u'Start PreresynthesisTempramp')
    PumpToActuator(actPos=6)
    PumpToFlowcell(actPos=3,
                   volume=311)
    SetThermalCyclerTemp(temp=50)
    config.logger.info(u'End PreresynthesisTempramp')
    return

Example #9

def PostResynthesisWash():
    config.logger.info(u'Start PostResynthesisWash')
    PumpToFlowcell(actPos=3,
                   volume=311)
    SetThermalCyclerTemp(temp=20)
    sleep(45)
    config.logger.info(u'End PostResynthesisWash')
    return

Example #10

def SecondReadPreparation():
    config.logger.info(u'Start SecondReadPreparation')
    PumpToFlowcell(actPos=8,
                   volume=203,
                   aspirationRate=9)
    SetThermalCyclerTemp(temp=65)
    sleep(60)
    PumpToActuator(actPos=14)
    PumpToFlowcell(actPos=14,
                   volume=203,
                   aspirationRate=9)
    SetThermalCyclerTemp(temp=40)
    sleep(60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    config.logger.info(u'End SecondReadPreparation')
    return

Example #11

def IncorporationWithoutDeblockBefore():
    config.logger.info(u'Start IncorporationWithoutDeblockBefore')
    SetThermalCyclerTemp(temp=60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    PumpToFlowcell(actPos=1,
                   volume=131)
    PumpToFlowcell(actPos=3,
                   volume=48)
    SetThermalCyclerTemp(temp=65)
    sleep(30)
    PumpToFlowcell(actPos=3,
                   volume=12)
    sleep(30)
    SetThermalCyclerTemp(temp=22)
    sleep(60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    PumpToFlowcell(actPos=2,
                   volume=131)
    PumpToFlowcell(actPos=3,
                   volume=48)
    sleep(10)
    config.logger.info(u'End IncorporationWithoutDeblockBefore')
    return

Example #12

def FirstBase():
    config.logger.info(u'Start FirstBase')
    SetThermalCyclerTemp(temp=60)
    PumpToFlowcell(actPos=3,
                   volume=203)
    PumpToFlowcell(actPos=1,
                   volume=131)
    PumpToFlowcell(actPos=3,
                   volume=48)
    SetThermalCyclerTemp(temp=65)
    sleep(30)
    PumpToFlowcell(actPos=3,
                   volume=12)
    sleep(30)
    SetThermalCyclerTemp(temp=22)
    sleep(60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    PumpToFlowcell(actPos=2,
                   volume=131)
    PumpToFlowcell(actPos=3,
                   volume=48)
    sleep(10)
    config.logger.info(u'End FirstBase')
    return

Example #13

def TMPBufferWash():
    config.logger.info(u'Start TMPBufferWash')
    for i in range(15):
        PumpToFlowcell(actPos=3,
                       volume=24,
                       aspirationRate=9)
        sleep(18)
    config.logger.info(u'End TMPBufferWash')
    return

Example #14

def Deprotection():
    config.logger.info(u'Start Deprotection')
    SetThermalCyclerTemp(temp=20)
    sleep(120)
    PumpToActuator(actPos=11)
    PumpToFlowcell(actPos=11,
                   volume=203,
                   aspirationRate=9)
    SetThermalCyclerTemp(temp=38)
    sleep(300)
    PumpToFlowcell(actPos=11,
                   volume=60,
                   aspirationRate=9)
    sleep(300)
    PumpToFlowcell(actPos=3,
                   volume=311)
    config.logger.info(u'End Deprotection')
    return

Example #15

def BridgeAmplification():
    config.logger.info(u'Start BridgeAmplification')
    for i in range(24):
        print("Итерация №" + str(i + 1))
        print("Прокачка реагента №8")
        PumpToFlowcell(actPos=8,
                       volume=90)
        sleep(8)
        print("Прокачка реагента №7")
        PumpToFlowcell(actPos=7,
                       volume=90)
        sleep(8)
        print("Прокачка реагента №5")
        PumpToFlowcell(actPos=5,
                       volume=196)
        sleep(19)
        config.logger.info(u'End BridgeAmplification')
    return

Example #16

def Denaturation():
    config.logger.info(u'Start Denaturation')
    SetThermalCyclerTemp(temp=20)
    sleep(25)
    PumpToFlowcell(actPos=8,
                   volume=203,
                   aspirationRate=9)
    SetThermalCyclerTemp(temp=65)
    sleep(60)
    PumpToFlowcell(actPos=3,
                   volume=743)
    PumpToFlowcell(actPos=3,
                   volume=203)
    SetThermalCyclerTemp(temp=40)
    sleep(60)
    PumpToFlowcell(actPos=3,
                   volume=311)
    config.logger.info(u'End Denaturation')
    return

Example #17

def SBSPrime():
    config.logger.info(u'Start SBSPrime')
    SetThermalCyclerTemp(temp=20)
    PumpToActuator(actPos=1)
    PumpToActuator(actPos=2)
    PumpToActuator(actPos=4)
    PumpToFlowcell(actPos=3,
                   volume=623)
    config.logger.info(u'End SBSPrime')
    return

Example #18

def FirstLinearisation():
    config.logger.info(u'Start FirstLinearisation')
    PumpToActuator(actPos=9)
    PumpToFlowcell(actPos=9,
                   volume=203,
                   aspirationRate=9)
    SetThermalCyclerTemp(temp=46)
    sleep(300)
    PumpToFlowcell(actPos=9,
                   volume=60,
                   aspirationRate=9)
    sleep(300)
    PumpToFlowcell(actPos=9,
                   volume=60,
                   aspirationRate=9)
    sleep(300)
    PumpToFlowcell(actPos=3,
                   volume=311)
    config.logger.info(u'End FirstLinearisation')
    return

Example #19

def InitialPrime():
    config.logger.info(u'Start InitialPrime')
    PumpToActuator(actPos=8)
    SetThermalCyclerTemp(temp=40)
    sleep(30)
    PumpToActuator(actPos=5)
    PumpToActuator(actPos=7)
    PumpToFlowcell(actPos=3,
                   volume=743)
    SetThermalCyclerTemp(temp=75)
    sleep(30)
    PumpToActuator(actPos=17)
    config.logger.info(u'End InitialPrime')
    return

Example #20

sensor = serial.Serial(port=ports.sensors,
                       baudrate=115200,
                       bytesize=serial.EIGHTBITS,
                       parity=serial.PARITY_NONE,
                       stopbits=serial.STOPBITS_ONE)


for i in range(10):
    msg = "FLOWRST\r\n".encode()
    sensor.write(msg)
    logging.info("Xmit Sensor : %s.", msg)
    answer = sensor.readline().decode()
    logging.info("Recv Sensor : %s.", answer)
    if answer.find("error") != -1:
        sensor.write(msg)
        logging.info("Xmit Sensor : %s.", msg)
        answer = sensor.readline().decode()
        logging.info("Recv Sensor : %s.", answer)
    elif answer.find("UNDEFINED"):
        sensor.write(msg)
        logging.info("Xmit Sensor : %s.", msg)
        answer = sensor.readline().decode()
        logging.info("Recv Sensor : %s.", answer)
    rate = 300
    vol = 600
    PumpToFlowcell(actPos=3,
                   volume=vol,
                   aspirationRate=rate,
                   dispenseRate=5800)
    time.sleep(vol/rate + 0.1)

Example #21

print("Заполнение канала номер 8")
PumpToActuator(actPos=8)
print("Заполнение канала номер 9")
PumpToActuator(actPos=9)
print("Заполнение канала номер 12")
PumpToActuator(actPos=12)
print("Заполнение канала номер 17")
PumpToActuator(actPos=17)

print("Выход на температуру 40°C")
SetThermalCyclerTemp(temp=40)
print("Температуры циклера вышла на полку в 40°C")
print("Промывка буфером")
for i in range(10):
    print("Итерация №" + str(i+1))
    PumpToFlowcell(actPos=3, volume=180, aspirationRate=72, dispenseRate=2000)
    sleep(15)

print("Введение и отжиг геномной библиотеки")
print("Введение геномной библиотеки")
PumpToFlowcell(actPos=17, volume=180, aspirationRate=72, dispenseRate=2000)
sleep(15)
SetThermalCyclerTemp(temp=95)

print("Отжиг геномной библиотеки")
SetThermalCyclerTempLowSpeed(startTemp=95, stopTemp=40, timeToGo=1100)
print("Промывка буфером")
for i in range(10):
    print("Итерация №" + str(i+1))
    PumpToFlowcell(actPos=3, volume=180, aspirationRate=72, dispenseRate=2000)
    sleep(15)

Example #22

def BufferWash():
    config.logger.info(u'Start BufferWash')
    PumpToFlowcell(actPos=3,
                   volume=623)
    config.logger.info(u'End BufferWash')
    return

Example #23

def EndRead():
    config.logger.info(u'Start EndRead')
    PumpToFlowcell(actPos=3,
                   volume=311)
    config.logger.info(u'End EndRead')

Example #24

from actuator_lib import TogglePos
from upper_commands import Snap
print("Старт")
n = time.time()
SetStandDown()
time.sleep(7)
print("Установите на рабочее место штатив с реагентами и чип")
h = ''
while h != "work":
    h = input(">>")
    print(h)
SetStandUp()
time.sleep(7)
print("Начало отрабатывания алгоритма")

PumpToFlowcell(actPos=15, volume=743)
PumpToFlowcell(actPos=16, volume=743)
PumpToFlowcell(actPos=3, volume=1823)
for i in range(3):
    AspirateFromBypass(volume=623, aspirationRate=72, dispenseRate=2000)
PumpToFlowcell(actPos=8, aspirationRate=9, volume=623)
SetThermalCyclerTemp(temp=40)
time.sleep(30)
PumpToFlowcell(actPos=5, volume=743)
PumpToFlowcell(actPos=6, volume=743)
PumpToFlowcell(actPos=7, volume=743)
PumpToFlowcell(actPos=3, volume=743)
PumpToFlowcell(actPos=17, volume=743)
SetThermalCyclerTemp(temp=75)
time.sleep(30)
time.sleep(300)

Example #25

import config
from system_commands import PumpToFlowcell
from system_commands import AspirateFromBypass
from system_commands import DispenseToFlowcell
import time

config.logger.info(u'========       Postrun wash is started       '
                   u'========')
n = time.time()
for i in range(3):
    PumpToFlowcell(actPos=3,
                   volume=2400,
                   aspirationRate=500,
                   dispenseRate=2000)
    PumpToFlowcell(actPos=17,
                   volume=3000,
                   aspirationRate=500,
                   dispenseRate=2000)
    PumpToFlowcell(actPos=3,
                   volume=2400,
                   aspirationRate=500,
                   dispenseRate=2000)
    for j in range(8):
        PumpToFlowcell(actPos=3,
                       volume=600,
                       aspirationRate=500,
                       dispenseRate=2000)
        DispenseToFlowcell(actPos=17, volume=600, dispenseRate=500)
for i in range(2):
    for j in range(14):
        if j < 12:

Example #26

File: cyclogram_for_27_11_19.py Project: gelio5/Hydra

conn.set("bubble_need", 1)

print("Заполнение канала номер 3")
PumpToActuator(actPos=3)
print("Заполнение канала номер 4")
PumpToActuator(actPos=4)
print("Заполнение канала номер 8")
PumpToActuator(actPos=8)
print("Заполнение канала номер 19")
PumpToActuator(actPos=19)
print("Заполнение канала номер 20")
PumpToActuator(actPos=20)

SetThermalCyclerTemp(temp=60)
print("Денатурация")
PumpToFlowcell(actPos=8, volume=180, aspirationRate=72, dispenseRate=2000)

print("Промывка буфером")
PumpToFlowcell(actPos=3, volume=180, aspirationRate=72, dispenseRate=2000)
time.sleep(15)

print("Детекция")
h = ''
while h != "work":
    h = input(">>")
    print(h)

SetThermalCyclerTemp(temp=60)

for i in range(5):
    print(str(i + 1) + "итерация для 19 ячейки")

Example #27

PumpToActuator(2)
PumpToActuator(4)
PumpToActuator(3)

# Imaging
print("Imaging")
h = ''
while h != "work":
    h = input(">>")
    print(h)

for i in range(19):
    print("Встраивание " + str(i + 2) + "-й буквы")
    a = time.time()
    SetThermalCyclerTemp(temp=60)
    PumpToFlowcell(actPos=3, volume=331)
    PumpToFlowcell(actPos=4, volume=167)
    PumpToFlowcell(actPos=3, volume=71)
    time.sleep(10)
    PumpToFlowcell(actPos=3, volume=623)
    PumpToFlowcell(actPos=1, volume=131)
    PumpToFlowcell(actPos=3, volume=64)
    SetThermalCyclerTemp(temp=65)
    time.sleep(20)
    PumpToFlowcell(actPos=3, volume=16)
    time.sleep(20)
    SetThermalCyclerTemp(temp=22)
    PumpToFlowcell(actPos=3, volume=311)
    PumpToFlowcell(actPos=2, volume=167)
    PumpToFlowcell(actPos=3, volume=64)
    time.sleep(15)