1. #include <OneWire.h>
#include <DallasTemperature.h>
// Arduino code to run a pcr machine with a heating element, a cooling element and a ​DS18B20
t​emperature probe. Based upon designs from ​Brian Blais
(​http://citizensciencequarterly.com/2011/04/the­light­bulb­pcr­machine/​) and Russell Durrett
(http://russelldurrett.com/lightbulbpcr.html)
//code requires libraries http://www.pjrc.com/teensy/td_libs_OneWire.html
http://milesburton.com/Dallas_Temperature_Control_Library
//Last edited 2015 Sept 20.
//Based on code written by Russell Durrett, red272@nyu.edu
// Data wire is plugged into port 2 on the Arduino
#define ONE_WIRE_BUS 10 //Use this for Temperature probe
//const int thermpin = A0;//Use this for the thermistor
const int heatpin = 3;
const int coolpin = 9;
// Setup a oneWire instance to communicate with any OneWire devices (not just Maxim/Dallas
temperature ICs)
OneWire oneWire(ONE_WIRE_BUS);
// Pass our oneWire reference to Dallas Temperature.
DallasTemperature sensors(&oneWire);
const int hot = 95; // 95C
const int tm = 55; // 55C
const int elongtemp = 72; //72
const int initialdenaturetime = 15; //value in sec
const int denaturetime = 15; //value in sec
const int annealtime = 60; //value in sec
const int elongtime = 60; //value in sec
const int finalelongtime = 600; //value in sec
const int cycles = 20; //number of cycles
int cyclecount = 1;
void setup(){
//pinMode(thermpin, INPUT); //use this for thermistor
pinMode(heatpin, OUTPUT);
pinMode(coolpin, OUTPUT);
analogReference(EXTERNAL);
Serial.begin(9600);

2. // Start up the library
sensors.begin();
}
void loop(){
sensors.requestTemperatures(); // Send the command to get temperatures
int temp = (sensors.getTempCByIndex(0));
//initial denaturing step
do {
//Begin PCR Reaction by heating to 95 degrees;
digitalWrite(heatpin, HIGH);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", Heating Lamp ON. Target temp = ");
Serial.println(hot);
} while (temp < hot);
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);
//strobe bulb to maintain hot
for (int count = 0; count < initialdenaturetime; count = count +1){
delay(1000);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
if (temp < hot){
digitalWrite(heatpin, HIGH);
}
else {//(temp < hot)
digitalWrite(heatpin, LOW);
}
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);

3. Serial.print(", DNA Denaturing, Target temp = ");
Serial.println(hot);
}
digitalWrite(heatpin, LOW);
//main program
do {
//denaturing step
do {
//Begin PCR Reaction by heating to 95 degrees;
digitalWrite(heatpin, HIGH);
digitalWrite(coolpin, LOW);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", Heating Lamp ON. Target temp = ");
Serial.println(hot);
}while (temp < hot);
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);
//strobe bulb to maintain hot
for (int count = 0; count < denaturetime; count = count +1){
delay(1000);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
if (temp < hot)
{
digitalWrite(heatpin, HIGH);
}
else
{
digitalWrite(heatpin, LOW);
}
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);

4. Serial.print(", DNA Denaturing. Target temp = ");
Serial.println(hot);
}
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);
//Anealing step
do {
//cooling to Tm
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, HIGH);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", Cooling to Tm. Target temp = ");
Serial.println(tm);
}while (temp > tm);
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);
//strobe bulb to maintain tm
for (int count = 0; count < annealtime; count = count +1){
delay(1000);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
if (temp < tm)
{
digitalWrite(heatpin, HIGH);
}
else
{
digitalWrite(heatpin, LOW);
}
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", DNA Annealing. Target temp = ");

5. Serial.println(tm);
}
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);
//elongation step
do {
//heating to extension temp
digitalWrite(heatpin, HIGH);
digitalWrite(coolpin, LOW);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", Heating to Extension. Target temp = ");
Serial.println(elongtemp);
}while (temp < elongtemp);
//pulse to maintain extension temp
for (int count = 0; count < elongtime; count = count +1){
delay(1000);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
if (temp < elongtemp)
{
digitalWrite(heatpin, HIGH);
}
else
{
digitalWrite(heatpin, LOW);
}
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", DNA Extending. Target temp = ");
Serial.println(elongtemp);
}
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);

6.
cyclecount++;
//digitalWrite(cyclespin, cyclesdonecount);
}while (cyclecount < cycles);
//final extension step
do {
//heating to extension temp
digitalWrite(heatpin, HIGH);
digitalWrite(coolpin, LOW);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
Serial.print("FINAL Cycle");
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", Heating to Extension. Target temp = ");
Serial.println(elongtemp);
}while (temp < elongtemp);
//pulse to maintain extension temp
for (int count = 0; count < finalelongtime; count = count +1){
delay(1000);
sensors.requestTemperatures(); // Send the command to get temperatures
temp = (sensors.getTempCByIndex(0));
if (temp < elongtemp)
{
digitalWrite(heatpin, HIGH);
}
else
{
digitalWrite(heatpin, LOW);
}
Serial.print("FINAL Cycle");
Serial.print(" Temp = ");
Serial.print(temp);
Serial.print(", DNA Extending. Target temp = ");
Serial.println(elongtemp);
}
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);

7.
Serial.print("Completed ");
Serial.print(cycles);
Serial.print("Run completed");
do{
digitalWrite(heatpin, LOW);
digitalWrite(coolpin, LOW);
}while (!(cyclecount < cycles));
}