// Arduino code to run a pcr machine with a heating element, a cooling element a

nd a thermistor
//This code is still very much in the editing stage, current as of January 6th 2
010
//Written by Russell Durrett, red272@nyu.edu
const int thermpin = A0;
const int heatpin = 3;
const int coolpin = 9;
const int hot = 40; //these are resistance-based temperatures, not yet calibrate
d for Celsius
const int tm = 20;
const int elongtemp = 30;
const int delaytime = 2000;
const int elongtime = 5000;
int cyclecount = 1;
void setup(){
pinMode(thermpin, INPUT);
pinMode(heatpin, OUTPUT);
pinMode(coolpin, OUTPUT);
analogReference(EXTERNAL);
Serial.begin(9600);
}
void loop(){

int temp = analogRead(thermpin);
do {
//Begin PCR Reaction by heating to 95 degrees;
digitalWrite(heatpin, HIGH);
temp = analogRead(thermpin);
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(", Heating Lamp ON, Temp = ");
Serial.println(temp);

} while (temp < hot);
digitalWrite(heatpin, LOW);
Serial.println("DNA Dissociating");
delay(delaytime);
do {
digitalWrite(coolpin, HIGH);
temp = analogRead(thermpin);
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(", Cooling to Tm, Temp = ");
Serial.println(temp);
} while (temp > tm);
digitalWrite(coolpin, LOW);
Serial.println("Primers Annealing");
delay(delaytime);
do{
digitalWrite(heatpin, HIGH);
temp = analogRead(thermpin);
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.print(", Heating to Extension Temp, Temp = ");
Serial.println(temp);
} while (temp < elongtemp);
digitalWrite(heatpin, LOW);
Serial.print("Cycle #");
Serial.print(cyclecount);
Serial.println(", DNA Elongating");
delay(elongtime);
//strobe bulb to maintain elongtemp?
cyclecount++;
//digitalWrite(cyclespin, cyclesdonecount);



}