wires organized

OpenPCR: Understanding the Final Hold Issues

I’ve been writing about the OpenPCR platform for a couple weeks now and together we’ve had our ups and downs. The most prevalent issue that I’ve had in my tests is a failure to hold. By that I mean, after completing a program, a PCR reaction is usually set to hold at a certain temperature in case the user isn’t around to claim his prize (a complete reaction). I usually set the hold at 4C but discovered OpenPCR can’t handle below ~12C, but I’ve also discovered that in my case (maybe other cases) the machine doesn’t hold at all. It just ends the program and returns to room temp.

So today I investigated…

The short results: I could not consistently get the machine to hold after trying multiple programs. Nor could I get the machine to run the designated program consistently. When the machine did perform a hold in two cases there was a glitch in the LCD, but otherwise reports are ok.

Now for the long answer:

I ran 5 experiments and then gave up. I don’t like admitting that, but after a couple hours of frustrations I think it is warranted noting. Here are all my notes:

  1. I ran the “Simple Experiment” that is pre-programmed into the software. On my first attempt (this is after completing the PCR experiment I posted earlier), the experiment crashed. The software displayed “Done!”, while the machine sat idly. (Get used to that because this will happen a lot in this discussion.) I tried to restart and this time the machine did nothing while the software displayed the time left screen. I turned the machine off and on and tried again. This time the program ran and the machine cooled to hold after completion. While in the hold phase there was a glitch on the LCD that said “Final H” and next to the H was a rectangle and three stacked horizontal lines. (I should have taken a picture of that screen :-( )
  2. I reran the “Simple Experiment.” On my first attempt the machine did nothing while the software displayed the time left screen. I turned off and on the machine. Tried a rerun and this time, the machine held at 20C. It again displayed that weird screen on the LCD.
  3. I created a new program: 1 cycle – 12C (for 30s), 20C (30s), 30C (30s), hold at 12C. On my first attempt, the lid heated and the software said done. Then the program started and the software started the countdown (after saying Done!). The machine got to about 15C and stayed that way for a while (time unknown) and so I stopped it. I tried to run the program again, but changed the lid heating to 0C hoping it would just not activate the lid. This time the program never started and the machine did nothing. I then changed the lid temp to 75C because I noticed it was cooling and thought maybe it needs to reach some temp before the program could start. The machine never started running.
  4. Another new program: 1 cycle – 37C for 30s, hold at 20C. On the first try (yay!) the machine ran, completed, and held. The LCD actually read “Final Hold” too. On a second attempt, the software said “Done!” but the experiment hadn’t started yet. It then ran and completed.
  5. In my last experiment, I did 1 cycle – 16C for 30s, hold at 16C. I tried twice, and both times the machine never started the program.

By that point I had given up and decided to do this write up. If I had to guess I would say there is a glitch whenever the software asks the machine to hold at anything less than 20C. There is definitely a glitch if you want to do two experiments back to back, because a lot of those times is when the machine would not do anything after completing the first of the back-to-back experiments. Other than those observations I have to give a big shoulder shrug and hope that the OpenPCR guys can give me some troubleshooting ideas. Anyone else with the system having any problems?

  • Nhslzt

    Hi Anthony, any news concerning the OpenPCR? Did you get it to work properly?
    I’m trying to convince a few PIs here in Dresden (Germany) to get a machine but if it doesn’t work well there’s not way I’d push for it.
    Would be glad to know how’s it going,
    Nick

    • http://www.iheartanthony.com Anthony Salvagno

      I guess I forgot to write a follow up post. But I worked with Tito and it turned out that there was a file that was missing in the OpenPCR directory. It’s been a while now so I don’t remember the details, I’ll have to look it up and go over it again, but that file was the cause of all the issues. Once I located it (somehow it was there but wasn’t if that’s not confusing enough!) everything worked again. I think what ended up happening was that I needed to use a different computer, because the one that I had installed OpenPCR on was old and very shoddy.

      The OpenPCR machine is a great investment. It’s inexpensive and it works. The temp readings are accurate, based on my tests (see other posts in PCR tag), and you can create your own programs easily. I don’t know how complicated the PCR experiments you are using are but I would say get one. It’s a low risk investment, in my opinion.

      • Nhslzt

         Hi Tony, thx for the clarification! My boss has money to spend on equipment, but before I suggest an OpenPCR I need to be sure it is not a crazy investment. Of course the kit is cheaper but there is a time-investment involved for the assembly. That means paying a PhD student for prob a couplpe of weeks, which is again money. Could you tell me how long it took you to build the machine and get it running?

        • http://www.iheartanthony.com Anthony Salvagno

          The build took no more than 3 hours. The instructions are super detailed and very easy to follow. It is ready to go right after assembly. I had one of the first machines so I ran it through the gamut if tests to make sure everything was up to speed. Just remember to use a more up to date computer.