Category Archives: Testing

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

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!

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!

Case Study: Rapid iteration with hardware

From Eric Reis’ blog, written by Ronald Mannak. (Thanks to Josh Perfetto and Matt Bertram for recommending it!). Excerpt:

The prototypes
The next day we started building the first prototype to see if the sensors actually behaved like they were supposed to, and to see if we could measure the sideway movements. The prototype was crude. Joris taped sensors on his arms with duct tape and started drumming in the air with wooden drum sticks (that did not contain any electronics). We connected the sensors to a seven year old pc with an Arduino-like interface that ran a simple drum program we developed. The results were amazing. It actually worked.

http://www.startuplessonslearned.com/2010/10/case-study-rapid-iteration-with.html

There is certainly a lack of good information on the business of hardware. Hardware sometimes feels like a dark art compared to Software where you can supposedly RentACoder at the drop of a hat, and oh just AB test your way to being a billionaire.

Got a favorite hardware blog? Give them a shout out here, I would love to hear about  them.

Tito

The heated lid

Hi rock stars,

Many thanks to the thoughtful, smart suggestions in Name that component!, from Kyle, David, AdamT, Kyle@otyp, and Ben. All together, we worked through the panini/linkage idea, browsed camera shops to find ball joints, and really set out to get the best design that’s easy to build. That said, it can be impossible to find off the shelf parts to bring a new design to reality. More specifically, I’ll say that my current source for searching (McMasterCarr) has lots of really *big* things, lots of door hinges or refrigerator hinges, but not so much in the *small* side of things. Is there a good source for electronics-sized components that you like? Digikey and Mouser stick to electronics components, what I’m wondering about is a digikey+mcmaster love child. Of course, this will be helped in the near future with the rise of 3D printing and Makerbots, where small batches of custom parts start to make sense. Maybe a Makerbot is in my future.

The best design turned out to be the most simple one, suggested by AdamT — 4 springs pushing down the aluminum plate, the whole assembly floats on 4 bolts. The lid gets locked down into a low position, and the springs/hinge float around as needed. I prototyped it up, showed Josh, and we like it. We’re going to be mounting a heater and really testing it out over the next few weeks.

2 opportunities for improvement are:

  • how to lock the lid in the “down” position (magnets would be great, a bolt with a thumb screw is more realistic).
  • Secondly, the nuts/bolts in the picture are metal and heat up a lot. I’m planning onfinding nylon screws (M3), though their operating temperature is 85C (the lid is heated at 100C to 110C, the melting point of nylon is over double that). Suggestions welcome :)

(Skinny shoulder screws/binding barrels would be nice so that the plate can slide easily up and down except I need 2 nuts on each bolt, one nut to hold the bolt in place at its base, the other nut to keep the aluminum plate/spring on. A bolt with threads at the beginning and end but not the middle would be good.)

Thank you to everyone!

Tito

Bottom view of the heated lid. 4 nuts show where the springs are

Took off the front side of the heated lid so you can see the assembly inside. Springs and bolts hold the aluminum plate in place

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!

Notes to self

Assembling all the nuts bolts and hinges for the first time. Just keeping notes here on my Macbook

1. Drill holes can get ugly with this verneer wood from ponoko. If possible, have holes laser cut. If you do have to drill, drill into the surface that will be visible (i.e. the outer surface)…the wood on the inside will be splintered.

2. Hinge can’t open all the way because the screw heads bump against eachother

3. Need tiny nuts (or a taller lid) for the nut to fit on the bolt for the lid hinge. Otherwise there’s no room for the nuts. Glued in the bolts for now, not a great solution :\

4. Need 1/2″ bolts for the lid. 3/8″ is too short and 1″ is too long.

5. I’m able to mount the heatsink/fan. However, the challenges are that the height of this assembly needs to be somewhat exact, and very stable. Stability is doable if the size of the nuts lines up with expectations for the height. Otherwise you’ll need to find standoffs or just let the heat sink hang from the lid.

6. I’ve mounted the aluminum block. If the heat sink can be mounted securely, then insulation can be used to hold the heat sink in place, at least in the short term. We’ll have to test this out and see if it holds long term. IN the meantime, the search for brackets continues.

First look

I met up with Josh and Xia for some awesome Korean BBQ on Friday. Got my first look at the thermal cycler, which is working!

We spent about an hour making sure that the LCD screen displays the most relevant text in the right places. I also brought a case prototype and we talked about industrial design and how to make the samples the most prominent part of the device. We saw that a good way to make the device more friendly was to isolate the gigantic power supply from the core unit.

We’ve established that a successful project:

1. works (heats up and cools down, able to hit temperature targets of 4C and 100C)

2. can be constructed yourself. for instance, the power supply was chosen because it is cheap and easy to find.

3. has a parts list online.

4. has a software interface

Next steps:
Goal 1. Josh is going through and trying a set of alternative components (i.e. a different fan, different peltiers) to see if any big leaps in performance/design can be made. He expects to be done with this by the end of the week.
Goal 1. Josh will also work on the heating element for the lid. It’s important that this happens soon before trying to build the rest of the casing.
3. Tito now has a good impression about the type of case design that is needed. Overall size, airflow, ease of construction, and lid heating are major concerns.