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Example data demonstrating the PCR works

Green channel was plotted to compare. Heat conditions:

• 95C 15 seconds
• 60C 30 seconds
• 40 cycles

Samples

1. beta-actin - PCR with taqman probe
2. blank - water control with master mix

Note: after 30 cycles signal was visable

Steps for building a mini thermocycler

Custom Parts:

Off the shelf ($43) + assembled brd is around $20 a unit + pipetters $20:

import time,datetime,os
from datetime import datetime
import json,re
import serial
import subprocess



def timestamp(gg):
 now = datetime.now() # current date and time
 date_time = now.strftime("%m/%d/%Y, %H:%M:%S")
 print("date and time:",date_time)
 gg.write("date and time: " + date_time)

def openport(prt):
  try:
   ser = serial.Serial(prt, 115200, timeout=0.2)
   time.sleep(2)
  except:
   print("its not connecting")
  return ser


def whatstheports():
 try: 
  output = subprocess.check_output("python3 -m serial.tools.list_ports -v", shell=True).decode()
  b = re.split("\n", output)
  if len(b)>1:
      for i in b:
          if re.match('^ ', i):
              pass
          else: 
              try: 
               dada = (re.sub(' .*', '',i))
               if re.match('^.*AMA0.*$', dada):
                pass
               else:
                #ser = serial.Serial('/dev/ttyUSB0', 115200, timeout=0.2)
                ser = serial.Serial(dada, 115200, timeout=0.2)
                time.sleep(2)
                ser.write(b'info\n')
                time.sleep(0.2)
                resp = (ser.readlines()[0].decode())
                ser.close()
                if re.match('^tempcontrol.*', resp):
                    return dada
              except: 
               pass
  else:
     print("You need to plug in the device")
 except:
  print("please plug the device in")


def read():
  port = whatstheports()
  ser = openport(port)
  ser.write(b'readlevel\n')
  b = (ser.readlines())
  temp = float(b[0].decode().rstrip())
  print(temp)



def incubate(stemp):
  print("Beginning to incubate at this temp "+stemp)
  print("To stop, ^c to kill the program")
  port = whatstheports()
  ser = openport(port)
  ser.write(b'settemp '+stemp.encode()+b'\n')
  ser.write(b'readlevel\n')
  time.sleep(0.2)
  b = (ser.readlines())
  temp = float(b[0].decode().rstrip())
  a = 1
  while a >0:
   ser.write(b'readlevel\n')
   time.sleep(0.2)
   b = (ser.readlines())
   temp = float(b[0].decode().rstrip())
   print(temp)


def coolon():
  print("cooling ... ")
  port = whatstheports()
  ser = openport(port)
  ser.write(b'fanon\n')
  time.sleep(0.5)
  ser.write(b'coolon\n')
  time.sleep(0.5)
  ser.write(b'settemp 0\n')
  a = 1
  while a > 0:
   ser.write(b'readlevel\n')
   time.sleep(0.2)
   b = (ser.readlines())
   temp = float(b[0].decode().rstrip())
   print(temp)


def flashon():
  port = whatstheports()
  ser = openport(port)
  ser.write(b'strobmic\n')
  return ser

def flashoff(ser):
  ser.write(b'off\n')
  ser.close()

def runcycle(dtemp,dtemptm,etemp,etemptm,cy):
  print(int(cy))
  ccy = int(cy)
  gg = open("log.txt", "w")
  timestamp(gg)
  gg.write("Thermcycler denature "+dtemp+"C time "+dtemptm+" extend "+etemp+" time "+etemptm+" cycle "+cy+"\n")
  
  print("Thermcycler denature "+dtemp+"C time "+dtemptm+" extend "+etemp+" time "+etemptm+" cycle "+cy)
  print("To stop, ^c to kill the program\n")
  port = whatstheports()
  ser = openport(port)
  time.sleep(1)
  #ser.write(b'setp 300\n')
  for i in range(0,ccy):
   print("cycle "+str(i))
   gg.write("cycle "+str(i)+"\n")
   cycle(dtemp,dtemptm,etemp,etemptm,cy,ser,i,gg)
  print("finished thermocycling")
  timestamp(gg)
  gg.write("finished thermocycling\n")
  gg.close()


def cycle(dtemp,dtemptm,etemp,etemptm,cy,ser,cycle,gg):
  print("Cycle "+str(cycle))
  print("Setting denaturing temperature to "+str(dtemp)+"C")
  gg.write("Cycle "+str(cycle)+"\n")
  gg.write("Setting denaturing temperature to "+str(dtemp)+"C\n")
  ser.write(b'settemp '+dtemp.encode()+b'\n')
  ser.write(b'readlevel\n')
  time.sleep(0.2)
  b = (ser.readlines())
  temp = float(b[0].decode().rstrip())
  while temp < (int(dtemp)+1):
   ser.write(b'readlevel\n')
   time.sleep(0.2)
   b = (ser.readlines())
   temp = float(b[0].decode().rstrip())
   print(temp)
   gg.write(str(temp)+"\n")
   if temp == (int(dtemp)):
       break
  time.sleep(int(dtemptm))
  ser.write(b'settemp 0\n')
  print("Setting extend temperature to "+str(etemp)+"C")
  print("Cooling ... ")
  gg.write("Setting extend temperature to "+str(etemp)+"C\n")
  gg.write("Cooling ... \n")
  ser.write(b'fanon\n')
  time.sleep(0.3)
  ser.write(b'coolon\n')
  time.sleep(0.3)
  ser.write(b'readlevel\n')
  time.sleep(0.2)
  b = (ser.readlines())
  temp = float(b[0].decode().rstrip())
  while temp > (int(etemp)+1):
   ser.write(b'readlevel\n')
   time.sleep(0.2)
   b = (ser.readlines())
   temp = float(b[0].decode().rstrip())
   print(str(cycle) + ' ' + str(temp))
   gg.write(str(cycle) + ' ' + str(temp)+'\n')
   if temp == (int(etemp)):
       break
  ser.write(b'fanoff\n')
  time.sleep(0.3)
  ser.write(b'cooloff\n')
  time.sleep(0.3)
  print("extend temperature begins")
  gg.write("extending \n")
  time.sleep(0.3)
  ser.write(b'settemp '+etemp.encode()+b'\n')
  while temp > (int(etemp)+1):
   ser.write(b'readlevel\n')
   time.sleep(0.2)
   b = (ser.readlines())
   temp = float(b[0].decode().rstrip())
   print(temp)
   gg.write(str(temp)+"\n")
  gg.write("incubating at extend temperaure\n")
  print("incubating at extend temperaure\n")
  time.sleep(int(etemptm))



input_var = input("Thermobock controller [help|h, about|a, incubate|i, cycle|c], read|r, cool, flashon: ")
if re.match("help|h", input_var):
    print("This controller the thermocycler. Here are the available commands")
    print("\thelp[h] - Provides the options")
    print("\tabout[a] - About the program, the product its used for and the developer")
    print("\tincubate[i] - Incubate at specific temperate. The command goes like this -incubate[i]_[your temperature]. So something like this 'i_55' or 'incubate_55' for incubating at 55C")
    print("\tread[r] - Read temperature sensor, it reports in Celcius")
    print("\tcycle - Cycling conditions. Argument goes like this -cycle[c] extent_time_denature_time_cycles. Like cycle_94_30_55_180_40 for 55C for 30 seconds then 55 for 180 seconds")
    print("\tflashon - Turns on LED")
elif re.match("port", input_var):
    whatstheports()
elif re.match("read|r", input_var):
    read()
elif re.match("cool", input_var):
    coolon()
elif re.match("incubate_.*|i_.*", input_var):
    [arg, temp] = re.split('_', input_var)
    incubate(temp)
elif re.match("cycle_.*|c_.*", input_var):
    [arg, dtemp,dtemptm,etemp,etemptm,cy] = re.split('_', input_var)
    runcycle(dtemp,dtemptm,etemp,etemptm,cy)
elif re.match("flashon", input_var):
    ser = flashon()
    floff = input("Press [enter] to turn off")
    flashoff(ser)
else:
    print("command not recognized")