logging thermocycler performance

My favourite PhD student (hi, squids!) was having issues with her PCR. She was ending up with empty tubes at the end of her program and was concerned that the machine wasn’t producing the right temperature cycle. As I had an Adafruit MAX6675 thermocouple board on my desk I offered to log the cycle to determine whether this was the case. I used a miniature breadboard to connect the Arduino Nano and MAX6675 breakout. The measurements were output to serial and logged to text file by a PC running my Processing datalogger sketch. Here’s the result:

image

There seems to be some real issues here as the temperatures don’t match the program well at all. There’s meant to be a 55C step immediately before each polymerisation hold at 62C and the sensor gets no where near this. This might be a result of poor heat transfer between the reaction tubes and the thermocouple but I figure that accurately reflects the same process of heat transfer between the block and the liquid in the reaction tubes. 

I’ve run the test again in a different well on the block. I’ll need to validate the thermocouple’s temperatures using another couple of thermometers to make sure its giving accurate temps but just this initial test has revealed a problem worthy of serious investigation. The fun continues another day … . 

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