PocketPCR - low cost, USB powered, open source PCR

[gaudi]

Hi GOSH
With all the experience from openPCR, gaudiPCR, PicoPCR, miniPCR I spent the last 6 months developing the PocketPCR, a simpler, smaller and more affordable thermocycler ( PocketPCR – The thermocycler for the rest of us ) . The whole design is optimized for low cost and desk top mass production. It runs from a regular USB port, power adapter or battery pack. I produced a small batch of kits that I sell at 99 euro on GaudiShop (PocketPCR Kit – GaudiShop) - free shipping worldwide. And of course it is open source science hardware, all files available on GitHub ( GitHub - GaudiLabs/PocketPCR: Pocket size USB powered PCR Thermo Cycler ).

After the launch I was overwhelmed with the positive adoption by the community (134 likes, 45 comments and 61 shares on facebook). And I am now in talks with Alessandro Yaw Crimi about bringing 1000 PocketPCR to Ghana, with Yanwu Guo about bringing it to schools in China and with Josiah Zayner about offering the PocketPCR through The ODIN.

Let me know what you think and how to develop the project further.

Best,
Urs

[szroboman_opentrons]

Congrat. let me know if u need any help.
Chiu
Co-founder Opentrons

[gaudi]

Thank you Chiu. Appreciate a lot. Thinking about coming back to Shenzhen .
Urs

[vektor]

Oh wow! Looks great!

Already ordered one

[asprakash]

Hi Gaudi. I come to know about this great project recently during this corona epidemic. I am an electronics engineer. Can this pocketpcr used for corona virus test?. I imagine a portable pocket pcr to conduct corona virus test instantly at the spot. I may be wrong. But trying to help our local government during this emergency.

TIA

[jcm80]

Welcome to the GOSH Forum @asprakash - great to have you here
@gaudi gave a very useful summary of Pocket PCR and COVID detection on the Pocket PCR website: FAQ – PocketPCR

Can the PocketPCR be used to test for corona virus at home? No. Why:

• Handling Coronavirus (COVID-19) material requires a bio safety lab (BSL2)
• Even trained people need some effort to go though this process and the sample preparation properly.
• The PocketPCR has no quantitative or real-time fluorescence reading needed for reliable testing
• Tests to diagnose diseases with clinical significance need official approval (testing and government approval). Any false test results can have severe consequences.

[amchagas]

A little shout out from our side, with the first result using pocket PCR here in Brighton UK

[hpy]

Very exciting @amchagas! On that note is there open source hardware for gel electrophoresis and taking pictures of it? I know this is a very basic question, but despite my experience running countless PCRs I still don’t know if there is a full open source hardware toolchain for it!

[amchagas]

I think @MakerTobey developed a parametric electrophoresis chamber and @ffederici had a LED array/matrix?

[MakerTobey]

Hey, thanks for flagging it. Yes, there is a full open source toolchain

IORodeo Sells open source high-voltage supplies, gel-chambers and transilluminators: https://iorodeo.com/collections/gel-electrophoresis-and-imaging

Beyond that, as @amchagas pointed out, there is a parametric gel-box designed by me (can be adjusted to any size you want, some day I should make a “pocket sized” version ) here on DocuBricks with instructions how to modify the design: https://www.docubricks.com/viewer.jsp?id=3540694571097352192 Has been replicated by several people in Europe, Australia, Africa.

And the transilluminator from @ffederici @Tim and team, also on DocuBricks: https://www.docubricks.com/viewer.jsp?id=7449430440606889984,
published here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187163
The main advantage of this system is the rasperi pi camera integration for digital picture taking and the capability to use many fluorescent stains in parallel, not just one blue-to-orange filter set.

[ffederici]

Awesome, thanks for sharing @amchagas, we are about to start a course that involves practical work at home based on:

1. RT-PCR of RNA: with pocketPCR + OBL/FreeGenes/ReClone home-made enzymes (pfu, MMLV)
2. LAMP of genomic DNA: with GMO detective kits from Guy Aidelberg, (hopefully, also with some other reactions using locally produced BstLF enzyme) and low cost blue/orange visualization.

For imaging the RT-PCR products on gels, we are thinking on adaptations of @MakerTobey gel elec. system, minipcr gel system (not open) and some combinations of the above with the acrylic filters from IOrodeo that we used in FluoPI. Since acrylic suppliers have changed over the years (and orange/blue filter combinations really matters), we collected some notes:

McMaster is no longer making the Amber acrylic, we have been advised by IOrodeo that the new amber McMaster sells doesn´t work that well.1/8" thick amber # 2422 should work well (it has been recommended by IOrodeo). As it is standardized, you can buy it directly online or from a local supplier.

Here is the characterization performed by IO rodeo:

GMOdetective projects uses this amber filter, we havent tried it but it looks good.

The Blue filter was 5C028 GT from ACRYLITE

But ACRYLITE no longer produces this item in low volume (only available as a make to order of 3-5 pallets). We have been advised to get the #2424 blue that it seems to be the same as the 5C028 blue we originally used from ACRYLITE.

We added a chart for acrylics from ACRYLITE here

More notes about LEDs, diffuser (important) and other follow up uses (e.g. ELISA) here

[ffederici]

Hi, some advances on how PocketPCR (+ Open Bioeconomy Lab off-patent enzymes, GMOdetective and others) enabled us to teach RT-PCR, RNA, ADN, LAMP, etc in the form of at-home labs during lockdown. Here, an OSF site with all links to code, 3D designs, enzyme production protocols, sequences, credits to collabs, etc (currently in Spanish but working on an ENG version…soon)

Briefly, the challenge was to teach:

1. RNA and RT-PCR; —> we used pocketPCR + in-house produced MMLV & pfu-sso7d from the Open Bioeconomy Lab + a short RNA fragment as synthetic target. The enzymes were produced in the lab and shipped in glycerol, being stable at room temp for at least 10 days. PocketPCR was great, it worked really really well. We 'd like to explore the use of an in-house produced Taq (with 5-3 nuclease activity) + taqman-like probes + fluor reading in pocketPCR for real-time measurements. Or pfu + mmlv +intercalatin dyes. @gaudi are you working on something like this for the pocketPCR? like a qPocketPCR?

2. DNA extraction and LAMP, —> we used hot water + the GMOdetective reactions from Guy Aidelberg: w/QUASR reporter + 470nmLEDs + lee filters (GMOdetective device). This worked really great (thanks to Guy!). We also made 3D printed version on openscad since we dont have laser cutting machine to make more devices (file in GMO repo). We are now working on replacing the commercial Bst2.0 with our in-house produced BstLF from ReClone/OBL (QUASR primer seq designed and available from Guy).

3. enzyme kinetics; —> we used jupyter notebooks/google colab with simulated data for that (big thanks to Ale Aravena).

HELP. We would like to add/work on:
1- OSH gel electrophoresis tanks and IOrodeo-like transilluminators to replace the only not-OSH device in our course (ie the minipcr gel electrophoresis tank, which saved us on time in the middle of the pandemic but it is not open ; just low-to-mid cost).
2- make a device for enzyme kinetics experiments (instead of simulating data for the jupyter notebooks). One option would be sucrose experiments using an in-house produced invertase? diy polarimeters? low cost glucometers? The other option would be using colorimetric enzymatic reaction and colorimeters,…ideas are very welcome

Saludos

[gaudi]

Great work @ffederici . Guess everyone would love to work with these at-home labs. Happy to hear PocketPCR does it’s job. And yes, let’s look into qPocketPCR :-). I shared you post with the PocketPCR communtiy - Community – PocketPCR

[Tom]

Edit: Problem has been solved by this thread: can't connect via arduino/usb c · Issue #8 · GaudiLabs/PocketPCR · GitHub
It turns out I tried to upload to the wrong board I needed to get the Adafruit FeatherM0 board spec (to do that - need to edit preferences and add https://adafruit.github.io/arduino-board-index/package_adafruit_index.json to Additional Boards Manager URLs), then had to connect processor pins 52 and 33 twice to reset the board. After that, I was able to upload the code. Lucky that post was there. I’d never have figured that out myself.

Hi. I bought a PocketPCR from Gaudishop several months ago and am very impressed with it. It’s a marvelous little innovation. However, I wanted to modify the program to allow me to do a “step down” PCR with an RT step up front, so I looked at the processor and made possibly a bad assumption: I assumed that I could upload the Arduino program code to the PocketPCR device via the Arduino IDE assuming an Arduino MKR1000 board. The device immediately became unresponsive and unable to be recognized in either Windows or Linux. Do you know if there is any way to recover communication to the board and upload the code? Alternatively, if I buy another one, is there any instruction anywhere for how to upload the .ino code (what is the proper board specification, for example?).

[scientist]

Hi Urs,

What is the RAMP rate of the heating and cooling of PocketPCR?

[gaudi]

Hi
Ramp rate is about 1.2 degree per second.
Urs

[scientist]

@gaudi

1.2

Thanks for letting me know.

[jbrennerFIT]

@Gaudi @Tom @ffederici

I am configuring my PocketPCR for the first time, have added the appropriate AdaFruit libraries, and am now getting an error I can’t figure out.

Within the FlashStorage.cpp file you call, I got an error at

NVMCTRL->ADDR.reg

I did find that there is a newer version of the FlashStorage.cpp file, but the newer version makes no difference with regard to this error.

Is there a workaround for this that I can’t find.

I did look on the Internet.

I think that the problem is that under Tools, I need to set the board to something other than an Arduino Uno, but I don’t know what to set it to.

Under PocketPCR - low cost, USB powered, open source PCR - #13 by gaudi, I found the following comment:

PocketPCR - low cost, USB powered, open source PCR

Great work @ffederici . Guess everyone would love to work with these at-home labs. Happy to hear PocketPCR does it’s job. And yes, let’s look into qPocketPCR :-). I shared you post with the PocketPCR communtiy - Community – PocketPCR

forum.openhardware.science



“It turns out I tried to upload to the wrong board I needed to get the Adafruit FeatherM0 board spec (to do that - need to edit preferences and add https://adafruit.github.io/arduino-board-index/package_adafruit_index.json to Additional Boards Manager URLs), …”. I put the .json file under Preferences.

“Tom” then says that he had to connect processor pins 52 and 33 twice to reset the board. I don’t know where such pins are. I am going to have my students build the other two PocketPCRs that I bought from you to see if I have the same issue.

I am not seeing the Adafruit FeatherM0 board option. Arduino is pre-set to Arduino Uno, and this is probably the problem.

Please help,

Jim Brenner

[Tom]

I have a list of instructions for what worked for me in the ReadMe for a Windows program I wrote for a custom serial-based controller for a programmable PocketPCR modification:

GitHub - thalljiscience/PocketPCR_Programmable: Open-ended, programmable version...

It also describes how to find the two pins that must be connected to reset the Adafruit board. If the board is recognized as connected to a COM port on your computer, however, it should not need to be reset. The fourth post down in the following thread also shows a diagram of the chip: https://github.com/GaudiLabs/PocketPCR/issues/8

[Tom]

Note: You can follow the first part of the instructions, numbers 1-7, and then load the original “PocketPCR_V2_quite_dev_i_disp.ino” from GaudiLabs via the Arduino IDE if you don’t want extensions allowing open-ended programming and multi-program storage.