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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]

November Design Update

We’ve made a lot of changes recently as we near our release, so I wanted to give a quick update on where things stand.

We’ve moved to using a silicone/kapton (pending testing) heater with an integrated thermistor for the heated lid so as to increase the ease of assembly & reliability. We’ve selected a copper heat block for the wells which has excellent thermal properties (high thermal conductivity and low specific heat), and is plated in chrome to protect the copper. We’ve placed the thermistor which measures heat block temperature inside the block to more accurately measure the block temperature, which has improved the thermal control dramatically. We’ve also optimized the air flow through the case/power supply to cool the heat sink more rapidly, thus improving cooling performance.

We’ve made a few changes to aid ease of assembly of our kits. We’ll be including an ATX power supply which has all cables other than the 24 pin motherboard connector removed to save room in the case. Due to the amount of surface mount components on our board which can be tricky to solder, we’ll be including pre-assembled circuit boards as part of our kit. We’ve also moved to the newer Arduino Uno, and are currently researching how we might leverage the new USB capabilities that it provides.

Tito and I are hard at work sourcing all the materials for our kit, which we plan on shipping mid-December. We have large lead times on some of the more custom or hard-to-find components, so our priority right now is getting our orders in. As such, some tasks such as documenting the design & assembly instructions have taken a back seat for the moment, but rest assured that when we begin shipping kits, there will be complete open source designs/bill of materials on our website for those of you that want to hack on your own. We’ve also started accepting pre-orders for our kits if you want to be assured of getting one of the first batch of units. Kits will include all the parts you need to build your own OpenPCR – you’ll just need some basic tools like screwdrivers.

We have plans for some great new things once we finally get past our OpenPCR ship date — stay tuned!

OpenPCR in Nature magazine

OpenPCR PCR Machine
Hi everybody,
Just a tiny little teensy weensy update for you. A sexy picture of OpenPCR is featured this month in a little magazine called Nature. Maybe you’ve heard of it? It’s one of THE MOST IMPORTANT PUBLICATIONS IN THE SCIENCE WORLD. BOOM!
Our wonderful Kickstarter backers were mentioned too, as well as lots of our friends in the biotech scene!
“Other biohackers have also come up with creative ways to fund their projects. Several have used websites such as Kickstarter, which allows inventors to post their projects and funding targets online. Visitors to the site make donations, usually small ones, but the hope is that enough visitors making tiny contributions will add up. Two California garage biohackers, Tito Jankowski and Josh Perfetto, used Kickstarter to fund the development of a small, low-cost PCR machine known as OpenPCR. They reached their fundraising goal of $6,000 in ten days. By the time their Kickstarter listing closed 20 days later, they had doubled that figure. Another group of biohackers used Kickstarter to raise funds for a hackerspace called BioCurious, based in Silicon Valley, California. They raised more than $35,000.”
Read the full article: OpenPCR in Nature
Congrats to all!
Tito

Treat your machine shop professionally

While searching for machine shops — quoted from: http://www.omwcorp.com/how-to-design-machined-parts.html

If you want the best out of your machine shop, it’s important to treat them well. People like to do business with people they like, and it stands to reason that favorite customers get special attention. Here are a few do’s and don’ts regarding machine shop proprieties:

DO communicate regularly with your shop, call them if you perceive a problem. Don’t let problems simmer. Do work with them to resolve issues fairly. Cutting metal to high tolerances is an extremely difficult art, and some mistakes are bound to happen.

DO consult with your shop on design issues. Unless you’ve spent years of your life working as a machinist, don’t assume you know more about manufacturing issues than they do. Virtually all professional machinists have many years of training. Many have advanced degrees. Treat them as peers, not as subordinates.

DO pay your bills on time. Nearly all shops pay close attention to this. There is no question that fast paying customers get treated better.

DON’T use your shop as a free quoting service to scope out the cost of proposed projects. Quotes are expensive for a shop. Only request quotes for jobs the shop has a fair chance to getting. Don’t quote out jobs to more than 2 or 3 shops. Don’t expect a shop to continue to quote multiple jobs without winning some work.

DON’T try to beat a shop down on part costs. Do ask design advice on how part costs can be reduced. Treat your shop as part of your manufacturing team, and foster communication between design and manufacturing.

– PS, to the machine shops we’ve worked with already, thank you!

Update: 9/25/2010

A clarification. I want to point out that this element is important and it can be challenging to do! If you can’t meet in person, it’s tougher to build repertoire over email or telephone no matter how charismatic you are. And, though I’m usually close to my email, people in shops are on tools and machines most of the time. A phone call is a lot quicker and more personal, but conversations on the phone often lead to miscommunications and frustration. What’s worked for me is talking on the phone, and then summarizing in a follow-up email immediately afterwards. Other points of friction I’ve found are in file formats (I was in Bangalore, India, bouncing between coffee shops and I just couldn’t get the right program in order) and computer use  (for instance a shop that insists on 2D drawings of a nice CAD file you struggled to put together…).

Experience says: lavishly praise shops you come across when everything goes smoothly.

Right now: I’m working with an shop called OharaRP (out of Dayton, Ohio) on a PCB board and they kick ass!

Tito

Laser cutting – Acrylic and Wood

This week I designed and sent off requests for new laser cut cases — one wood sheet from Ponoko, and an acrylic sheet from Pololu.

Material: One surprise for me — I made a slightly bigger case, and adding on 1″ to each dimension roughly doubles the material. For instance, take a 4″ square, that’s 16 square inches of material. A 5″ square is 25 inches of material. This can get out of hand pretty quickly!

Speed: On the recommendation of a friend, I browsed onto Pololu.com, which offers custom laser cutting services. Pololu doesn’t have plywood or bamboo in stock, but they do have 1/4″ acrylic and promise a 3 day turnaround time vs Ponoko’s 11-15 day turn time. Of course, I pay extra for the speed but for prototyping it’s well worth it. I placed my Pololu order on Thursday afternoon and it shipped Friday!

Prototyping: Designing laser cut cases sure can be a pain in the butt. I spent all day on July 4th simply designing a bigger OpenPCR case with bolted edges rather than teethed edges. My workflow goes from the overall design in Google Sketchup, adding features like teeth, bolt holes, nodes, and radii. Then importing that into Illustrator, adding additional teeth, and the submitting it to be cut.

This is fine if you’re putting together a one-off design, but for prototyping, changing, and updating designs I certainly could use some better tools. A good friend of mine has the same issues. If you have any suggestions or experience in converting Sketchup designs to Illustrator for Ponoko/laser cutting, let us know!

PCR Machine Patents are Dead

One of the goals of the OpenPCR project is “4. A basic understanding of PCR patents and how they affect this project“. When Josh and I were first discussing OpenPCR back in March, I looked into the original PCR patents and found that they were expired as of March 2005 (US) and March 2006 (Worldwide). These patents have been expired for a little over 4 years now. This was covered somewhat by the media, in articles from Frost (2005) and PatentBarista (2006). There are other articles, but they are not freely accessible — email us PDFs if you like and we may share them.

If you’re interested in reading the original patents that were fought over for years:

USPTO 4965188
USPTO 4683202
USPTO 4683195

What’s also interesting is that “expired PCR patents” doesn’t seem to be common knowledge — lots and lots of people know *about* the patents on PCR, but not too many know they expired. Staying current is really important for those of you who want to innovate. The landscape is quickly changing. In the early 2000s, the question was “Can the human genome really be sequenced?”, the answer was YES, DEFINITELY — and we must move on to bigger and better questions. Current questions are “Can a community biotech lab be a source of innovation?“, ”Will every home want a DNA barcode reader and biotech engineering tools before 2025″? We’ll need to answer them and move on. The hurdles in front of us will soon be behind us.

One area that we want to shed light on for future projects is patents around the qPCR process (update – 7/18, also add Gradient PCR to the list, I’m not sure what the patents around that technology are). qPCR is an important tool as it allows you to easily quantify (q) the DNA in your sample. In many cases this can save a lot of time and shorten the “test cycle” of biotech. Imagine if every iGEM team and community lab had not just an OpenPCR, but a qPCR machine at their fingertips!

Are these questions interesting to you?

  1. Is there any reason to think the basic PCR patents aren’t expired? Lawyers, scientists want to help clarify?
  2. Looking forwards — What are the existing patents on qPCR and other advanced processes?
  3. Looking back — Did the patent for PCR help to encourage innovation and proliferation of PCR?

Thanks to Adam Braithwaite for inspiring this post.