First OpenPCR kit assembled

It’s no secret that we’re fast approaching the shipment of our Kickstarter and pre-order OpenPCR kits. But today marked a new milestone: the first assembly of an OpenPCR by someone other than Tito or myself. Eri Gentry was kind enough to spend the day assembling an OpenPCR and giving feedback on our instructions, which we’ll role into the final printing. Here she shows off the completed unit, which will be housed at the BioCurious hackerspace:

The boxes you see in the background are OpenPCR components for the first kits. We’re just awaiting one more shipment from China (expected next week), and making some final software changes, and then these boxes are out the door.

Sexy: OpenPCR in GQ France (updated in English)

We’re featured in the March edition of GQ: France! What’s hot? Josh Perfetto, Russ Durrett, Joe Jackson, Eri Gentry, OpenPCR, and Tito Jankowski: “Dans L’antre Des Biohackers”. Read on for the full article. English translation below, thanks to OpenPCR Fan Max Gleeson! (he includes the translation with a warning: it’s rough at the best, completely incorrect at the worst.)

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Freakonomics: For Biology

Have you read the book Freakonomics? Readers gushed over the logical beauties presented in Freakonomics; tying “broken windows and buildings left in disarray” to a rise in “gang violence”, and other examples tying together two otherwise un-connected events. I hear a similar tune in the following article. How might an effort to treat sick livestock cause $24,000,000,000 ($24 bln) in damage and killing 48,0000 people?

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How Species Save Our Lives

We are coming to an age when technologies for quickly and quantitatively identifying a new species will be in the reach of many more people. Technologies like OpenPCR, DNA barcoding, mail-order DNA sequencing, and DNA barcoding. But technology is useless without people putting it to use. ”Why” might someone like you want to identify new species? I came across a few answers this morning in the New York Times. According to the article, we have new species to thank (and the people who stumbled across them) for the following…

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Help Fund the Synthetic Bio Documentary

Sam Gaty and George Costakis have been shooting footage for a Synthetic Biology documentary over the past year or so, interviewing everyone in this emerging field, including leading synthetic biology researchers as well as DIYbio practitioners. They’ve now started a Kickstarter project to get their film edited in time for submission to Sundance 2012. Check it out, and see the great preview at the end of their Kickstarter video.

Happy Birthday OpenPCR!

Hey everybody!
Last year, February 5th, 2010 marked the day that OpenPCR first came to life. Here’s a picture of our very first prototype, when we were first wondering “can it be done?”.

OpenPCR prototype PCR Machine v 0.000001, sitting atop a spool of solder to help with airflow.

What a successful year. Last February we assembled our first OpenPCR prototype. Right after that, we made a mad rush for Maker Faire in San Mateo, California. By that time we had a beautiful laser cut case (sponsored by Ponoko) and a machine that worked. Hundreds of people support OpenPCR on Kickstarter, doubling our $6,000 goal for the first crowd-funded biotech project in history. OpenPCR featured in Nature Magazine (excellent photo taken by Josh) (link) and the New York Times (link), among others.

Congratulations to all! Josh and I have learned an incredible amount in the past year. Everything from h-bridges, power supply design, and PCB fabrication, to peltiers, thermistors, CNC machining, and USB control. It is great to be working together!

Yesterday we celebrated while out sailing in the San Francisco Bay! Also thanks to Eri for writing us up on the BioCurious blog (link).

Josh and I aboard an Olson 25', on a 5 hour sail around Angel Island in the San Francisco Bay. Thanks to Eri Gentry for the picture!

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).

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!

OpenPCR at the Grenswerk Art Festival (Enschede, the Netherlands)

A while back, we mentioned the excitement of sending an OpenPCR off to the Presidential Commission on Bioethics. After all that hard work, you might think our prototype would come home for some R&R. Instead, it headed onto Amsterdam, the Netherlands, where it was featured in an art show in Enschede by the Joris Laarman Lab, along with lots of other cool experimental devices. Congrats to the Lab, and Anita and Nora for their hard work. Here’s a few shots from the exhibit. Enjoy!

The Exhibit - check out the cool images painted on the walls!

I recognize those pictures from the DIYbio flickr stream

Microbial Fuel Cell

Spiker Box

OpenPCR and the Pearl Gel Box

OpenPCR in the NYTimes

OpenPCR was featured in the New York Times today, in an article on “Home Labs on the Rise for the Fun of Science” (link)

Not everyone is content to fill their labs with centuries-old technology. Samara Rubenstein, the manager of the Sackler Educational Laboratory for Comparative Genomics and Human Origins at the American Museum of Natural History, said home scientists could extract their DNA by rinsing their mouth with salt water, breaking apart the sloughed-off cheek cells with dish detergent, and then rinsing out the DNA with rubbing alcohol. “It’s really cool,” she said.

Other experiments for home labs can be found at Ology, a corner of the museum’s Web site.

After the DNA is extracted, more options are becoming available for identifying the organism using a technique known as PCR, or polymerase chain reaction. A new project, OpenPCR, is designing new home tools for DNA analysis. Tito Jankowski, who founded the project with Josh Perfetto, said the kit would give anyone the chance to analyze DNA.

Mr. Jankowski said one possible experiment for home scientists would be to test for their reactions to certain food. Only some people, for instance, taste the bitterness in brussels sprouts, a trait that has been linked to a part of our genome that the kit can identify.

Eri Gentry, an entrepreneur in San Francisco, said she had already tested herself for this gene, using a $200 kit from Carolina Biological Supply, which sells to school science labs.

“Some of these things you do not because it’s the quickest way to do it, but because you learn a lot,” she said.

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!