Category Archives: Other

Update on the OpenPCR project

It’s been way too long since the last post, so wanted to give everyone an update on the project, and where things are going.

First, despite not having a lot of updates on the blog :), I am amazed at the usage growth in OpenPCRs. I think things have gotten to the point where many people are encountering OpenPCRs in other peoples’ labs, hearing that they work, and then wanting their own.

I am also extremely pleased that it is increasingly used in education. For example, Arizona State University used 16 OpenPCRs in a Biomedical Engineering class, where students used them in conjunction with a fluorimeter to amplify and detect DNA. Even better, each group of students then designed and documented their ideas for improvements in the OpenPCR. It was great seeing the open source/kit nature of the OpenPCR being integrated into the class, rather than having a thermalcycler be simply a black box.

One thing we have learned over the course of the OpenPCR project is that despite many of their great attributes, open source projects are not necessarily the best way to manufacture and deliver physical products, and in days past kit orders were plagued with production delays. So I am pleased that Chai has taken on the physical manufacturing and distribution of kits. This has resulted in simple improvements, such as consistent shipping within 1 business day, cheaper international shipping with faster customs clearance (about 50% of OpenPCRs ship internationally), and more reliable sourcing of components. While these details are certainly unglamorous, they are truly important in getting more OpenPCRs into the wild, and thus more users of this project. Chai will also help sponsor and fund further work on the OpenPCR project.

So with the original design complete and kits being delivered, what is the future of the project? Certainly improved version(s) of the machine can be made, and this is likely to happen. But I’d also like for the OpenPCR project to be not just about PCR machine kits, but to more generally be about openness in PCR, including for example protocols, reagents, and open source analysis software. Look for more developments here in the months to come.

Alas! OpenPCR is pre-stocked

After many months of effort, we’ve finally ramped up our manufacturing to the point that OpenPCR is no longer backordered. With our latest weekly shipment, pictured above, all placed orders have finally been fulfilled, and we’re now shipping new orders within 1-2 business days. So no more long waits for your OpenPCR :)

With these delays behind us, we’re now able to concentrate on improving OpenPCR, and will have some exciting software improvements coming soon. Say tuned!

Note that while individual orders will now be fulfilled in 1-2 days, distributors placing bulk orders will continue to receive 4 week shipping quotes, until supply can be built up a bit further.

Ramping up Manufacturing: Now shipping in 1-2 weeks

It’s been no secret that the OpenPCR has been hard to get this past year. Every time we did a manufacturing run, we produced more than the last, but by the time each run was produced, the units of that run had already sold out, resulting in OpenPCR being continuously backordered. Thanks to the great community support we have received, we were able to produce 100 units in our last run, and OpenPCR is now shipping on average 1-2 weeks after being ordered. Our next run will be for 200 units, and we hope that after completed, OpenPCR will finally be pre-stocked, shipping immediately after orders are placed. I want to thank many of your for your patience over the past months as we’ve ramped this up, and hope we don’t have to count on your patience much longer :)

We’ve learned a lot over the past year about manufacturing. Mainly that it’s not much more difficult to produce 50 units instead of 25, or 100 instead of 50. We designed OpenPCR with the philosophy that we should use as many off-the-shelf components as possible, but that has come back to bite us as certain key components became unavailable from our suppliers, necessitating costly re-sourcing. But OpenPCR has grown up a lot this past year as such mistakes are corrected, and scalable manufacturing is now in sight. Stay tuned…

Putting the Open in OpenPCR

OpenPCR PCB

Hi OpenPCR fans!

OpenPCR first came to life last February, and we showed off our first prototype at Maker Faire last May. Those of you following the blog know we designed, refined, and engineered our hearts out. Today, Josh and I are pleased to make the first version of the OpenPCR design docs public. Whether you’re a hardware junkie, circuit board lover, or code addict, we’ve got you covered!

Code, CAD, and Circuits

http://openpcr.org/downloads

  • OpenPCR CAD (SolidWorks 2011) for all 100+ components of OpenPCR
  • Eagle files for the OpenPCR Brains circuit board
  • Arduino control software (still being revised)
  • Adobe Air software interface (still being revised)

Instructions

We also invite you to check out the OpenPCR assembly instructions which come bound and printed with every kit we ship. The cover features beautiful glasswork by Dale Chihuly, and you can read the rest of the story here: http://openpcr.org/instructions/

A question for you — What OpenPCR stories would you like to hear? Any components or topics you would like us to write up in detail? Feel free to reply to this post or email us at contact@openpcr.org

Tito and Josh

DNA Fingerprinting Osama Bin Laden

OpenPCR thermal cyclerThis morning I saw several tweets about DNA testing and Osama Bin Laden:

“All I’m sayin is,if they took DNA samples for bin Laden,who did they match it against,& that was one ruddy fast PCR,can I have your machine?” – upulie

“Did they bring PCR machine on the site to confirm Bin Laden’s death?” – seanjeon

The US military used DNA to identify Osama Bin Laden very quickly after he was killed. How? Although we don’t have intimate knowledge of Osama’s DNA identification, here’s one way that OpenPCR could potentially be used in a similar situation.
Continue reading

OpenPCR Boards Assembled

As we didn’t want to wait for professional PCB assembly, we assembled the first batch of 35 OpenPCR boards ourselves. It took some time but came out decently. The biggest difficulty was soldering the H-Bridge IC, which has three large power connections on the bottom of the package, plus fine pins all around it. We managed that by effectively doing reflow soldering with solder paste and a toaster oven, and then soldering the through-hole components afterwards.

The OpenPCR PCB

The OpenPCR PCB


That's one large Arduino shield

That's one large Arduino shield

As much fun as that was, I’ll let a pick and place robot do it next time. I’ve been looking at Screaming Circuits for PCB assembly in the ~100 unit range, though please feel free to suggest any other companies in the comments.

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.

PCR how fast can aluminum be heated cooled

I checked out the web traffic to our site, looks like a good handful of people are coming by looking for 2 weird things – “importance of the number of wells in a pcr machine” and “pcr how fast can aluminum be heated cooled”.  Well, I wanted to answer both of these questions clearly:

1. Aluminum can be heated and cooled as fast as you can muster! Heating is certainly a lot easier, you just need to heat up. Cooling down is a little bit slower since you have to move the heat “somewhere else” in order to cool the block — like blow it out a side vent in OpenPCR. OpenPCR has a ramp speed of about 2 degrees C per second.

2. The number of wells in a PCR machine is an important point! I’ve used several PCR machines in the past, and all my work took up under 6 tubes (and each tube takes up one well). The minimum you should have when doing an experiment is 2 – a sample and a control, and usually you have more samples and several controls. OpenPCR right now as 16 wells — we thought about a lot of the recent projects people are working on, and they’re really a lot more social. 5 of us got together in a garage and looked at our SNPs, and that’s when we really started using up a bunch of wells. At the same time, having more wells makes the PCR machine’s design more complicated so we didn’t want to have wells that no one would ever use.

(Posting this retroactively)