Category Archives: Goals

OpenPCR in the Wild + We need your help!

Around the world!

Hi all, It’s a delight to see OpenPCR on so many desktops! Josh and I spent the past year staring at mostly-disassembled prototypes with wires all over the place. It makes it all worth it to see everyone assembling their kits, posting pictures, and having a blast doing it. At the end of the post there’s several pictures that I thought you would enjoy of OpenPCR around the world!

Here’s a couple examples of what’s going on with OpenPCR 2 weeks after shipping:

  • A high school in Hawaii is testing for genetically modified foods, with plans to upgrade to identifying and tracking non-native species.
  • A college professor in Missouri is booting up her biotech class + gel electrophoresis and has successfully amplified DNA
  • A biotech company in Utah has amplified DNA to successfully test OpenPCR
  • OpenPCR assembled by Singularity University students in Mountainview, California

How you can help

Over the past year we’ve designed, engineered, and shipped our first product. We are now seeking seed funding to take our company to the next level (and build some new awesome stuff). If you know someone who would be interested in investing in OpenPCR, we would love an introduction! Email me (tito@openpcr.org) or send your friends to AngelList (http://angel.co/openpcr).

Also, we’ve raised the price of OpenPCR from $512 to $599. This allows us to get OpenPCR out to distributors around the world — if you’ve got a shop, give us a holler (contact@openpcr.org).

Join the OpenPCR Google group to chat about OpenPCR! We’ve got some great conversations brewing and it would be great to hear from you! http://groups.google.com/group/openpcr

Tito

DNA is now DIY: OpenPCR ships worldwide

OpenPCR PCR machine thermal cyclerHi everyone,

The eagerly awaited OpenPCR kit is now shipping! UPS picked up the first batch of kits and OpenPCRs are on their way to users in 5 continents and 13 countries around the world. For $512, every OpenPCR kit includes all the parts, tools, and beautiful printed instructions – you ONLY need a set of screwdrivers.

A PCR machine is basically a copy machine for DNA. It is essential for most work with DNA, things like exposing fraud at a sushi restaurant, diagnosing diseases including HIV and H1N1, or exploring your own genome. The guy who discovered the PCR process earned a Nobel Prize in 1993, and OpenPCR is now the first open source PCR machine.

The price of a traditional PCR machine is around $3,000. So, do people in garages have great PCR machines? Not really. Howabout high school or middle school teachers? Nope. Howabout smaller medical testing labs or labs in India or China? Nope. Even some big bio labs try their luck on eBay. We set out to change that.

Josh and I prototyped OpenPCR over about 4 months — it was a lot of fun. Last May we unveiled the first OpenPCR prototype to all a bunch of crazy people on Kickstarter, 158 people gave us a total of $12,121. With that we designed and manufactured a repeatable, works-all-the-time device — it took a lot of hard work. Now we’re done and ready to share!

OpenPCR Firsts:

1. First commercially available PCR machine for $512

We get a lot of people who come up to us and say “jumping jillikers, batman! we paid $10,000 for ours and it’s this big (make refrigerator-sized hand motion)!”. While modern PCR machines aren’t fridge sized anymore, we’re proud to say that OpenPCR is the most affordable and most compact PCR machine out there.

2. First Arduino USB storage device:OpenPCR thermal cycler USB Arduino port

This is a big deal for you Arduino hackers out there. A normal Arduino can only talk back and forth over a serial port. This is a pain to set up, and we wanted OpenPCR to just plug-in and go. How does it work? When OpenPCR is plugged in, the Arduino mounts itself as a USB drive called “OpenPCR”. The computer passes love notes to OpenPCR by writing to that file, and Arduino sends love notes back by writing to another file. The implementation was tough, and there are size restrictions due to the size of the chips used by Arduino, but it’s pretty simple to make use of. We also built a cross-platform app for your Mac or PC in Adobe Air so that the we could have a simple computer control interface. Simply plug in your OpenPCR to your computer with USB. No setup besides downloading the OpenPCR app! (Josh and Xia totally pulled off a miracle on this!) If you’ve got questions on this specifically, be sure to post below!

No cutting corners

The clear vision of OpenPCR that made it great was driven by 2 things. First off, Josh is an incredible engineer and we both enjoyed learning a lot of new things over the past year — everything from how to make circuit boards, machine metal parts, laser cutting, Arduino hacking, USB hacking.  I’d say 90% of the success of OpenPCR was lots of hard work. Hard work is great but there are lots of projects where hard work is put in but never “pays off”. How did we stay on course? I think the prototype + showing it off on Kickstarter/Maker Faire had a lot to do with it. We of course had lots of exciting ideas about new functionality and extra things over the past year. The beauty of having built our prototype was we knew if we could just get to that point we would have a hit.

OpenPCR pcr machine guts - thermal cyclerFor example, we designed OpenPCR to be assembled by hand. The printed Build Instructions are a big part of OpenPCR and we did a lot of work to get them right. As we finalized the OpenPCR design a few steps stood out as “hard”. We switched from thermal paste to thermal pads (not messy, no need for gloves), assembled circuit boards (no need for a pro soldering setup), and pre-epoxied the thermistor. The OpenPCR kit is easy to build because of those decisions. We’ve still got to publish the gel pictures showing how great OpenPCR works, but that’s been well tested ourselves. If you’ve got an OpenPCR kit coming your way and would like to post pictures of a gel run afterwards, we would love to see your results too!

The intent of the prototype was simple – we wanted a PCR machine for people like us. That meant a 16 well PCR machine controlled by computer, with a built in screen, good for the lab bench or a workshop/garage. And that’s exactly what OpenPCR is.

Where did the time go?

After Kickstarter started in May, we worked for going on 14 months now. Between Josh and I, I estimate we put about 3,000 hours into OpenPCR, not counting the time leading up to the prototype. We’ve got 57 posts and 600+ comments on the OpenPCR blog, covering a lot of aspects of OpenPCR development. In the past few months we’ve kept our heads down getting everything out the door and we’ve got some stories to share. Short answer is, there’s a lot of blogging to catch up on.

Special thanks to Xia Hong, Eri Gentry, and Will Reinhardt who volunteered lots of their time to help OpenPCR.

OpenPCR PCR machine connected to Mac with Arduino
Just the beginning

OpenPCR is designed for labs, classrooms, and garages. Tell your science-y friends about OpenPCR, “Like” us on Facebook, or write us and tell us that you stopped by! You can also get your own OpenPCR kit!

Do you want to see us develop more breakthrough biotechnology? Along this journey we uncovered a lot of opportunities for PCR and other biological devices. We’re a new company and would love to meet other passionate people. Our hurdles right now are manufacturing (mechanical engineers!), distribution (sales + marketers!), and new hardware (hackers!)/software (hackers!)/bioware (biologists!) + industrial design. If you’re in the Bay Area and want to get in on making all this crazy DNA stuff useful to regular people, send us an email: contact@openpcr.org.

For more information, we’ve gotten a lot of media attention over the past year  including NYTimesGQ FranceBiotechniques, and USA Today.

Ordered a kit and wondering where it is? We have shipped a first batch of kits and emailed out tracking numbers to the recipients. If your kit hasn’t shipped yet, we’re working on shipping a second batch and will keep you updated.

[button color="blue" size="large" href="http://openpcr.org/buy" ]Buy Now[/button]

It Lives

The below is a gel showing PCR reactions from the final OpenPCR prototype that will be used for our kit production. This experiment was done to validate various polymerases rather than test OpenPCR, but thought you may want to see it. Lane 1 at the right is a control with no polymerase. Lanes 2 – 4 show amplification of a ~1kb amplicon with different polymerases/salt concentrations. Lanes 3-4 have a different loading dye, but pay attention to the fluorescent DNA band (imaged with GelGreen / Invitrogen Safe Imager).

OpenPCR PCR machine results

This is just an early glimpse – when we release the final machine kit, we’ll include a gel image with well-by-well results for an identical reaction. That release is thankfully getting closer – over the weekend Tito and I tested a prototype with full mechanical assembly and got excellent results, so we’re just getting the final pieces into production. Stay tuned for the official release date!

Thank you! 202%

Thank you so much for your overwhelming support for the OpenPCR project. We raised 202% of our goal, thanks to the massive support of 158 people that contributed financially and the hundreds of people that helped get the word out on Twitter, Facebook, blogs, and the nightly news!

One point I want to highlight — there are other biotech innovators like Josh and I and they need your support! Josh and I are part of a group called BioCurious, a community biotech lab starting up in San Francisco. BioCurious is trying to raise $30,000 in order to open their doors to dozens of innovators. As a supporter for BioCurious, you will be helping to start a major innovation engine, spurring education, public understanding, and entrepreneurship in biotech. Check out BioCurious at:

www.biocurious.org/kickstarter

And, if you’re in the Bay Area, come by for a meetup: www.meetup.com/biocurious

Best,

Tito and Josh

The Importance of Speed in PCR

The job of a thermocycler is to implement a set of temperature changes in a reaction volume. The biological requirement for PCR is to implement a set of temperature changes such as this:

Repeat 30 times:

  1. Denature at 95 C for 30 seconds
  2. Anneal at 64 C for 45 seconds
  3. Extend at 73 C for 45 seconds

If you add up the times required, the biological requirements of this reaction take 50 minutes. However it also takes time for the PCR machine to transition between each set of temperatures, which is effectively wasted time. Here’s where the speed of the PCR machine comes in. If the PCR machine is capable of changing 2 C/s, then starting from 20 C the above reaction would take 66 minutes. However if it was only capable of changing 0.5 C/s, the above would take nearly twice as long: 114 minutes.

When we sat down to design a low cost thermocycler, we had options that were cheap but slow, such as relying on convection and radiation to cool the heat block. We opted instead to go with a more complex peltier cooling solution so the machine would be faster: our prototype currently ramps at about 2 C/s.

Why did we feel speed was so important? There’s two reasons.

My formal background is in computer science. When writing new software code, I do not write it correctly the first time. I may have a design flaw, or simply have made some mistakes. However I’m able to get rapid feedback, correct the issue, and test it again, so making mistakes is not a problem at all. In software, it’s typically possible to get feedback in a time ranging from seconds for small changes to at most about 10 minutes to run a well designed test suite on a modestly sized application. That rapid feedback cycle not only allows engineering projects to proceed rapidly, but it is also a large part of how the novice developer learns the art of software development.

When I work in biology, my experience is anything but that. Experiments (or design-build-test cycles) run anywhere from hours for simple operations, to days if cells must be grown, to weeks if DNA must be synthesized, to years for long-running clinical trials. Faster PCR cannot solve all of that, but it can do its part for the experiments where it is critical.

For example, I’ve been working to create a SNP genotyping protocol which would allow people to read any SNP of interest from their own DNA. It’s complex and involves DNA extraction, PCR, and a gel run. Currently it takes the better part of a day to complete; reducing it so it could be run twice a day would be a big win, especially considering someone new to biology is likely to make mistakes the first couple times. We should all be thinking about how we can make design-build-test cycles faster when we create tools for biology.

The second reason is a little more technical. The PCR reaction makes use of a “thermostable” polymerase enzyme, which really means that the polymerase doesn’t denature and cease to function right away at the denaturing temperatures of PCR. In actuality the polymerase has a half-life which is reduced as temperature increases. At the end of a 25 cycle PCR run, the majority of the polymerase may in fact be destroyed, which is a limiting factor in the amount of amplification possible.

That can be a problem if you’re starting from a very small amount of DNA, as may be the case in a forensics application. It is also important if your upstream DNA preparation protocol is sub-par. For example, suppose a DIYbio enthusiast was doing sushi DNA barcoding. While they have access to an enormous amount of DNA to begin with, they may use a lower-cost DNA extraction method which doesn’t remove as many PCR inhibitors as a Qiagen extraction kit would. That’s not a problem so long as you’re still able to get enough amplification for sequencing, which you can do by extending the number of PCR cycles so long as you have enough working polymerase left.

So faster PCR can introduce resilience to overcome poorer upstream processing, and if that enables you to get the same results with cheaper reagents, that’s another win for everyone.

Why we built OpenPCR

First off, let me extend a warm welcome to everyone that’s taken an interest in this project. Over the past two months I’ve been extremely busy with the design and testing of the OpenPCR machine and getting a prototype ready to demonstrate at the Maker Faire, so haven’t had the time to blog about it until now.

I wanted to talk a little about why we undertook this project. Building a PCR machine is something that Tito and I first talked about nearly a year and a half ago, but the project only got started in earnest this February, after Tito and I discussed it driving back from the Outlaw Biology symposium in LA. What really made me jump on it was that I had heard from one too many people that this needed to be done, and I certainly thought it was doable, but I hadn’t seen much progress in actually building a thermocycler to date.

There are really two core benefits I see to a machine like OpenPCR. The first is a drastically lower price point. The cheapest commercial unit I’m aware of costs $4000, with other units easily running up to $10,000. There is no reason these machines have to cost so much. While they have to be accurate, the basic technology is quite mature. The high price point has more to do with the traditional biotech market than it does with the complexity of the machine. Academic and industrial labs can afford these high prices, but there is increasing demand from garage biotech companies, labs in developing nations, the DIYbio community, and even high schools for PCR machines, and OpenPCR was designed to serve these new users.

A common objection to this argument is that “thermocyclers can be found on eBay for $100″, so why re-invent the wheel? eBay can be the solution for some people, but it’s far from a solution for everyone. The $100 eBay thermocycler is actually quite elusive, $300 machines are much more common. It can take quite some time to find the better deals. Even then, these machines are commonly sold “as-is”, which frequently means broken. I stopped buying lab equipment from eBay three years ago for this reason. And even if you do get a working machine for $300, it’s an antique unit without modern features such as a heated lid, and the temperature ramp times are often pathetic.

The second core benefit to building OpenPCR was to create a substrate for further hacking. We’d eventually like to add quantitative functionality to OpenPCR, and I know others who would like to develop more automation around it. You have to walk before you can run, so building a working thermocycler gives us all a starting ground for the more ambitious projects to come.

Easy breezy PCRzy

One of our main goals for the OpenPCR project is to enable people to do PCR. With our first prototype we’re getting tools into the hands of people — with off the shelf parts, flexible design, and free control software.

What about enabling people to do PCR after they have the tool? What about helping them actually run their first reaction (does anyone get it right the first time?), their second reaction, or their 50th sample. How do we enable that?

I’ve broken “Make PCR easy” into 3 chunks:

1. Make mistakes!
2. Share mistakes!
3. Learn from mistakes!

Software
Sharing: twitter, facebook, human readable protocols
Troubleshooting: “Help!!” – heres a “troubleshooting” process for both newbies and veterans: http://www.bio.uio.no/bot/ascomycetes/PCR.troubleshooting.html

Other stuff
Since it’s a given that your first few reactions on a new machine won’t work, is there a standard curriculum used to train newbies? A sampler that opens your eyes to several PCR techniques?
Or a “is my PCR machine working correctly” wet/dry test? We are proposing that people build their own PCR machines, which hasn’t been done before.

First light!

Our first run with the OpenPCR machine just kicked off. We’re amplifying a SNP for bitter tasting. 2 samples each from Josh, Xia, and myself. One was made using a plastic swab against the inside of our cheek, the other made by putting a piece of Kim wipe against our cheek.

Kicked it off at 10:10 pm, 30 cycles to go, 94, 68, 84!