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bdev:minithermocycler

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bdev:minithermocycler [2020/11/18 15:20]
richard 		bdev:minithermocycler [2021/08/16 22:22] (current)
Line 3: Line 3:
  
  
-{{ :bdev:pcr_bactin_example.png?200 |}}+ 
 +{{ :bdev:timestamp_95_8_60_15.png?400 |}} 
 + 
 + 
 + 
 +{{ :bdev:timestamp_95_15_60_30.png?600 |}} 
 + 
 + 
 + 
 +{{ :bdev:thermocycling_comparison.png?600 |}} 
 + 
 +Green channel was plotted to compare.  
 +Heat conditions: 
 +  * 95C 15 seconds 
 +  * 60C 30 seconds 
 +  * 40 cycles 
 + 
 +Samples 
 +  - beta-actin - PCR with taqman probe 
 +  - blank - water control with master mix 
 + 
 + 
 +Note: after 30 cycles signal was visable 
 + 
 + 
 +{{ :bdev:pcr_bactin_example.png?400 |}}
  
  
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-Custom Parts:+Custom Parts:{{ :bdev:thermoblock_holder_1inch_half.stl |}}
  
 |1. Milling thermoblock. It costs $100 to make this.  {{ :bdev:thermoblock_holder_1inch_half.stl |}}|{{ :bdev:image_52_.png?200 |}}| |1. Milling thermoblock. It costs $100 to make this.  {{ :bdev:thermoblock_holder_1inch_half.stl |}}|{{ :bdev:image_52_.png?200 |}}|
 |2. Lid with 2 3mm set screws {{ :bdev:drillblock_1inch_lid_half.stl |}}| {{ :bdev:image_55_.png?200 |}}| |2. Lid with 2 3mm set screws {{ :bdev:drillblock_1inch_lid_half.stl |}}| {{ :bdev:image_55_.png?200 |}}|
-|3. Block holder {{ :bdev:thermoblock_holder_1inch_half_1_.stl |}}|{{ :bdev:image_56_.png?200 |}}|+|3. Block holder {{ :bdev:hermoblock_holder_1inch_half.stl |}}|{{ :bdev:image_56_.png?200 |}}|
 |4. Extrusion connects {{ :bdev:tslot_hinge_thermalblock.stl |}} | {{ :bdev:image_57_.png?200 |}}| |4. Extrusion connects {{ :bdev:tslot_hinge_thermalblock.stl |}} | {{ :bdev:image_57_.png?200 |}}|
 |5. Brd base {{ :bdev:thermocycle_brd.stl |}}| {{ :bdev:image_58_.png?200 |}}| |5. Brd base {{ :bdev:thermocycle_brd.stl |}}| {{ :bdev:image_58_.png?200 |}}|
 |6. PCB board {{ :bdev:pcbs_thermominiblock.zip |}} Parts: {{ :bdev:gerberfiles_parts.zip |}}| {{ :bdev:above_view.png?200 |}} {{ :bdev:bottom_view.png?200 |}}| |6. PCB board {{ :bdev:pcbs_thermominiblock.zip |}} Parts: {{ :bdev:gerberfiles_parts.zip |}}| {{ :bdev:above_view.png?200 |}} {{ :bdev:bottom_view.png?200 |}}|
 +|7. Single tip imager {{ :bdev:singletip_imager.stl |}}|{{ :bdev:singletip_imager.png?200 |}}|
  
  
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 else: else:
     print("command not recognized")     print("command not recognized")
 +</code>
 +
 +
 +
 +----
 +
 +
 +<code>
 +#include <Servo.h>
 +#include <PID_v1.h>
 +//#include <FastPID.h>
 +Servo myservo;  // create servo object to control a servo
 +
 +#include <Wire.h>
 +#include <SoftwareSerial.h>
 +
 +
 +#define THERMISTOR_PIN A7
 +#define TEMPCONTROL 3
 +#define FANPIN 5
 +#define THERMOELECTRIC_COOL 6
 +#define LED 9 
 +
 +//Define the aggressive and conservative Tuning Parameters
 +
 +double aggKp=150, aggKi=0.5, aggKd=0;
 +
 +
 +int thermoelectricval = 255;
 +int ledval = 255;
 +int tempcontrol = 3;
 +String command;
 +float currpos;
 +int celsius;
 +int levelstreamon;
 +double settemp = 0;
 +double Setpoint, Input, Output;
 +int tme = 250;
 +
 +//Specify the links and initial tuning parameters
 +//PID myPID(&Input, &Output, &Setpoint, consKp, consKi, consKd, DIRECT);
 +PID myPID(&Input, &Output, &Setpoint, aggKp, aggKi, aggKd, DIRECT);
 +
 +#define NUMTEMPS 20
 +short temptable[NUMTEMPS][2] = {
 +   {1, 841},
 +   {54, 255},
 +   {107, 209},
 +   {160, 184},
 +   {213, 166},
 +   {266, 153},
 +   {319, 142},
 +   {372, 132},
 +   {425, 124},
 +   {478, 116},
 +   {531, 108},
 +   {584, 101},
 +   {637, 93},
 +   {690, 86},
 +   {743, 78},
 +   {796, 70},
 +   {849, 61},
 +   {902, 50},
 +   {955, 34},
 +   {1008, 3}
 +};
 +
 +
 +void setup() {
 +  // put your setup code here, to run once:
 +  Serial.begin(115200);
 +  analogWrite(TEMPCONTROL, 0); 
 +  analogWrite(FANPIN, 0); 
 +
 +  Setpoint = settemp;
 +  //turn the PID on
 +  myPID.SetMode(AUTOMATIC);
 +  analogWrite(THERMOELECTRIC_COOL,0);
 +  analogWrite(LED,0);
 +}
 +
 +void loop() {
 +   Input = read_temp();
 +   
 +   double gap = abs(Setpoint-Input); //distance away from setpoint
 +   myPID.SetTunings(aggKp, aggKi, aggKd);
 +   myPID.Compute();
 +   analogWrite(TEMPCONTROL,Output);
 +   int rawvalue = analogRead(THERMISTOR_PIN);
 +   float celsius = read_temp();
 +   int fahrenheit = (((celsius * 9) / 5) + 32);
 +
 +  if (levelstreamon == 1) {
 +   Serial.println(celsius);
 +   delay(500);
 +  }
 +
 + if(Serial.available())
 + {
 +    char c = Serial.read();
 +    if (c== '\n')
 +    {
 +      parseCommand(command);
 +      command = "";
 +    }
 +    else 
 +    {
 +      command +=c;
 +    }
 + }
 + delay(1);
 +}
 +
 +float parseCommand(String com)
 +{
 +
 +  if(com.equalsIgnoreCase("info")){
 +    Serial.println("tempcontrol");
 +  }
 +  else if(com.equalsIgnoreCase("levelstreamon")){
 +   levelstreamon = 1;
 +  }  
 +  else if(com.equalsIgnoreCase("defaultpid")){
 +    double aggKp=19.56, aggKi=0.71, aggKd=134.26;
 +  }
 +  else if (com.substring(0,4) == "setp") {
 +    aggKp = com.substring(5).toDouble();
 +  }
 +  else if (com.substring(0,4) == "seti") {
 +    aggKi = com.substring(5).toDouble();
 +  }
 +  else if (com.substring(0,4) == "setd") {
 +    aggKd = com.substring(5).toDouble();
 +  }
 +  else if(com.equalsIgnoreCase("coolon")){
 +   analogWrite(THERMOELECTRIC_COOL,thermoelectricval);
 +  }
 +  else if(com.equalsIgnoreCase("cooloff")){
 +   analogWrite(THERMOELECTRIC_COOL,0);
 +  }  
 +   else if (com.substring(0,10) == "setledval") {
 +    ledval = com.substring(11).toInt();
 +  }
 +  else if(com.equalsIgnoreCase("levelstreamoff")){
 +   levelstreamon = 0;
 +  } 
 +  else if(com.equalsIgnoreCase("fanon")){
 +   analogWrite(FANPIN, 255);
 +  } 
 +  else if(com.equalsIgnoreCase("fanoff")){
 +   analogWrite(FANPIN, 0);
 +  } 
 +  else if(com.equalsIgnoreCase("readlevel")){
 +     int rawvalue = analogRead(THERMISTOR_PIN);
 +     float celsius = read_temp();
 +     Serial.println(celsius);
 +  }
 +  else if (com.substring(0,12) == "setthermoval") {
 +    //Serial.println("setting temperature");
 +    thermoelectricval = com.substring(13).toInt();
 +    //Serial.println(settemp);
 +  }
 +  else if (com.substring(0,7) == "settemp") {
 +    //Serial.println("setting temperature");
 +    settemp = com.substring(8).toInt();
 +    //Serial.println(settemp);
 +    Setpoint = settemp;
 +  }
 +  else if(com.equalsIgnoreCase("strobmic")){
 +    strobingmic(ledval, tme);
 +    delay(10);
 +  }
 +}
 +
 +float read_temp()
 +{
 +   int rawtemp = analogRead(THERMISTOR_PIN);
 +   float current_celsius = 0;
 +
 +   byte i;
 +   for (i=1; i<NUMTEMPS; i++)
 +   {
 +      if (temptable[i][0] > rawtemp)
 +      {
 +         float realtemp  = temptable[i-1][1] + (rawtemp - temptable[i-1][0]) * (temptable[i][1] - temptable[i-1][1]) / (temptable[i][0] - temptable[i-1][0]);
 +
 +         if (realtemp > 255)
 +            realtemp = 255; 
 +
 +         current_celsius = realtemp;
 +
 +         break;
 +      }
 +   }
 +
 +   // Overflow: We just clamp to 0 degrees celsius
 +   if (i == NUMTEMPS)
 +   current_celsius = 0;
 +
 +   return current_celsius;
 +}
 +void strobingmic(int ledval, int tme){
 + int strobtimer = 1;
 + while (strobtimer > 0 && Serial.available() == 0){
 +  analogWrite(LED, ledval);
 +  delayMicroseconds(tme);
 +  analogWrite(LED, 0);
 +  delayMicroseconds(tme);
 +  strobtimer++;
 + }
 + analogWrite(LED, 0);
 +}
 +
 </code> </code>
  
bdev/minithermocycler.1605712829.txt.gz · Last modified: 2021/08/16 22:21 (external edit)

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