Fwd: OpenPCR ships worldwide, 512 USD PCR machine
Bryan Bishop
From: Eugen Leitl <eu...@leitl.org>
Date: Thu, Jul 7, 2011 at 6:32 AM
Subject: [biomed] OpenPCR ships worldwide, 512 USD PCR machine
To: bio...@postbiota.org
http://openpcr.org/2011/07/dna-is-now-diy-openpcr-ships-worldwide/
DNA is now DIY: OpenPCR ships worldwide
06 Jul 2011 | Posted by tito | 3 Comments.
OpenPCR PCR machine thermal cycler
Hi 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 of 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: con...@openpcr.org.
For more information, we’ve gotten a lot of media attention over the past
year including NYTimes, GQ France, Biotechniques, 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.
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Nathan McCorkle
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Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
Cathal Garvey
twitter.com/onetruecathal
http://www.indiebiotech.com
Nathan McCorkle
ruphos
Uhh, Flash doesn't work so great on linux, are you sure about Air?
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-- Friedrich Nietzsche
Josh Perfetto
native program to read a status file the PCR machine, and we've
included Mac and Win binaries for that initially. We can incorporate a
Linux binary shortly.
-Josh
Cathal Garvey
twitter.com/onetruecathal
http://www.indiebiotech.com
Phil
programmable 48-well cycler often available on ebay for under $100?
eg
http://cgi.ebay.com/Perkin-Elmer-480-Cetus-PCR-DNA-Thermal-Cycler-a-/360373858661
leaking pen
Jordan Miller
jordan
Nathan McCorkle
has ever seen a wooden-boxed PCR cycler
On Fri, Jul 8, 2011 at 1:31 PM, Phil <phil...@gmail.com> wrote:
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Cory Tobin
> has ever seen a wooden-boxed PCR cycler
Yeah, all the models before peltiers became common had refrigeration
units in them. So they basically weighed as much a mini frig and were
quite large.
-cory
Bryan Bishop
I've been seeing the strangest ads lately.. for mp3-playing
thermocyclers. But a mini fridge thermocycler sounds more enticing.
Grab a cold one while you wait for it to cycle up?
Mackenzie Cowell
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John Griessen
> I've been seeing the strangest ads lately.. for mp3-playing
> thermocyclers. But a mini fridge thermocycler sounds more enticing.
> Grab a cold one while you wait for it to cycle up?
And those SPAM mails about getting a degree...get one
of those while you wait also...
and the PCR could do yogurt culturing duty with it's hot side
when not busy with a PCR order...
John
John Griessen
> Anybody interested in hacking one of these little dry-block heaters to do closed-loop PCR?
>
> http://www.quasarinstruments.com/p-16654-myblock-mini-dry-bath-heat-blocks.aspx
>
> Mac
It's the right size. Maybe reusing some of their plastic would jump start a prototype.
I'm partial to reusing just the idea of a clear plastic open ended box as
an insulating cover, and the rest from scratch. It's not good looking enough
to want to copy. A readout on a PCR could show a graphic status bar and
some label related to the batch -- it would need to be more than a one liner though.
John
BTW emails to you from jo...@industromatic.com do not get a response. Could they be trapped by a filter?
Josh Perfetto
-Josh
Mackenzie Cowell
JonathanCline
> Seriously, it's cheaper than anything else on the market right now.
The aluminum block is listed as $79, is that right?
How on earth can an aluminum block cost $40 to machine? (Assuming
50% markup)
Dimensions (of entire unit): 4.4 x 5.9 x 4 in/ 11 x 15 x 10 cm
Block, 2 x 50ml centrifuge tubes Price: $98.00
Block, 15 x 1.5ml or 2.0ml centrifuge tubes (conical) Price: $74.00
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
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John Griessen
> [MyBlock™ Mini Dry Bath Heat Block]
There's no absolute need for a massive block to even
out temperature. Stirred air can do just as well,
then you skip machining and go straight to the advantage of 3D
printing for low volume, and step up in tooling costs
when you want mid volumes of something molded.
MyFan™ MySauna™ MyConvectionOven™ etc.
Mackenzie Cowell
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Cory Tobin
> overkill, and an airflow-based convection heater could be better (and
> cheaper).
I'm guessing the ramp rate would be horrible though, since air has
such a low thermal conductivity compared to aluminum ( air = 0.025
W/(m*K) vs aluminum = 230 W/(m*K) ).
-cory
Dakota Hamill
Cathal Garvey
Hm. I wonder to what extent that affected my success (or lack thereof) with CyclerCan. The sensor readily detected fantastic air temp ramp rates but the heat transfer to the tubes may have lagged significantly.
Then again, the program was stupidly redundant: one minute at each step. I'll be sure to repeat any successful OpenPCR reactions with CyclerCan and see how it runs.
John Griessen
> Is it easy to measure the temperature of the air + tubes in a convection thermocycler?
> It's obviously easy to measure the temperature of a metal block.
Yes, a heat sink gives you a single point to measure, and thermal delay, as it increases
what you have to heat up, and increases time to heat or cool. That can be simplifying.
Especially if you are trapped in the 1950's controlling with a bi-metal strip thermostat.
But do you want to measure a block? No. You'd like to know the temperature of a vial,
so what you can do is build in a thermocouple surrounded by some typical vial plastic
to physically model the identical vials to control temp. of and be more accurate.
Engineering is balancing cost and performance, and cost up front in design effort
gets spread out over the first production batches, and returned in early selling prices.
It's very legit to spend a little more up front to get lower selling prices with the
same profit (or costs to produce), depending on your viewpoint. Especially
if you can get more performance.
> I believe metal blocks are common because they are a relatively simple way to provide precision
> temperatures.
Precise temperature is possible with a rapidly stirred zone of air having very low mass,
but the low mass means you need smooth, responsive control as well as precision in measuring, or
the temperature might oscillate around the set-point. This is all old old school from
before I learned engineering in the 70's 80's. It's now very easy to do with cheap micros,
cheap analog chips, and aided by slightly more expensive micros, you
can even do the programs in high level language (HLL) instead of C or assembler.
Both responsive control and HLLs are good goals for scientific open hardware, since the
openness lets a module design be reused, and the researcher end users will some of them want
to tweak their gear to become something else. Then the gear makers, like me,
will take that open hardware upgrade and create a new standard instrument or system from
it super-rapido.
> But I agree, they seem like overkill, and an airflow-based convection
> heater could be better (and cheaper).
Much cheaper. The electronics bill of materials for such a module is just $17
including fan and heater. TE coolers could be more, but as far as I've read,
desirable temps for PCR soak cycles are all a good bit above 26
deg C lab room temperature, so the responsive control plus a little robo-actuated-door
to the room ambient air can get you the rapid cool down ramp. The Blocks™
just Block™ you from rapidly ramping temperature. Think about it...
The Blocks™ were just there because the controls used were assuming
no great amount of convection.
On 07/09/2011 01:14 PM, Cory Tobin wrote:
> I'm guessing the ramp rate would be horrible though, since air has
> such a low thermal conductivity compared to aluminum ( air = 0.025
> W/(m*K) vs aluminum = 230 W/(m*K) ).
The aluminum block is not what needs to get hot though - a plastic vial is.
Plastic has low conductivity compared to aluminum. Plastic has some
high heat capacity also, but luckily it is in thin vials. The aluminum is
just another material interface with bad transfer in and out, that is
in the way. I say simplify by reducing the chain of transfer of
heat by one link. Lose the aluminum block.
The "hotter" heat flow chain can be:
heater --> convection forced air --> vial --> solution being processed.
The "colder" heat flow chain can be:
ambient air door --> convection forced air --> vial --> solution being processed.
On 07/09/2011 02:00 PM, Dakota Hamill wrote:
> What about throwing a Peltier cooler on the top as a lid?
Instead you can design air flow around the tops of the vials and insulate the lid well.
Lose the multiple points of control by stirring. Stirring is an old successful way to
even out temperature. The spatial arrangement of vials in the zone of stirred air
can also be designed to let the heat flow in and out of them all at about the same time
by not bunching a lot of them close, and having an edge that is different than the middle.
Space from vial to vial has to be even so air can flow between them and all at once, so not
across rows of them, but from bottom to top -- the lid will be more of a toroidal chimney
returning air to the heater zone, then swirling back under the vials and up through them.
The system case could be a split ring. Split so you twist to open it, rotate back to close
and go. That would be a good approach for 100 vials. For 6 vials, I would use a carousel
to rotate them and be the fan at the same time, and later allow some liquid handling
simplicity. Neither of these fan-based designs need be fast/loud to get the equilibrating needed.
On 07/09/2011 02:52 PM, Mackenzie Cowell wrote:
> In the electroformed copper foil, tight fitting of the sample holder, and uniform and
> controlled thickness is ensured.
This concept of a thin copper heat exchanger for vials is a good one. Using it with
standard vials with no special gluing on prep time is more what I think most people
want though. I bet a one per vial design of copper heat sink could be made that is cheap
and good. They mentioned keeping the thickness exactly the same helped with even heat flow
right at the vials. All that's needed for a one-per-vial heat exchanger design
is how to attach -- some kind of clip is how I think.
John Griessen
Mackenzie Cowell
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Nathan McCorkle
two to a microcontroller? I could probably get some Taq samples and
DNA w/ primers to test against if I could throw something together
fast.
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Cathal Garvey
A solid state AC relay wired into the plug socket. I can't recall the number but I gave the part is mentioned in the code for cyclercan.
John Griessen
> whats the best, cheapest, quickest way to fit together a hair drier or
> two to a microcontroller?
For a hair dryer you would use a SSR. But that is not the best matched sized way
for such a small load as PCR temperatures -- hair dryers
can easily be hair burners, after all, with 1000 Watts.
If you're serious I'll mail you one big enough for a hair dryer, but
it's not a good development path for an open hardware, manufactured tool.
John
Simon Quellen Field
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Nathan McCorkle
Harbor Freight also has these:
http://www.harborfreight.com/12-volt-rubberized-heater-with-fan-96144.html
Which I used earlier this year with a custom cardboard manifold to
de-fog a tube with water dripping inside it... I was just varying the
voltage with a knob on a power supply though.
So what is the dev path, John? With Simon's idea, I could tune the
duty-cycle of a hair-drier to find what the max wattage/CFM that a
tube can handle before it starts to melt, right? Is that the right
unit that I want?
>> John
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Cathal Garvey
Excellent suggestion. Amusingly, that's apparently all an AC ssr is anyway, a case-enclosed photocell with an LED on the logic pins.
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JonathanCline
>
> For a hair dryer you would use a SSR. But that is not the best matched sized way
> for such a small load as PCR temperatures -- hair dryers
> can easily be hair burners, after all, with 1000 Watts.
require both overtemp switches and limit heat (specifically at
some temp below combustion of hair...) -- regardless of stated
power rating. So in effect, a hair dryer is pretty safe. Perhaps
the high wattage is used to decrease ramp rate or air velocity,
if it isn't just a marketing tactic. If anything, it is too safe and
won't get hot enough -- it will shut down first -- unless the safety
control is bypassed.
Quote from web:
"Dryers contain a safety cut off switch that prevents
the temperature of the drier from exceeding 140°F (60°C)."
There might be some variation in this max, so using one
would require checking the specs first.. otherwise could
turn into a waste of effort.
The other thing to look at is using a 12V version (for
autos typically) instead of A/C.
Or alternatively just get nichrome coils of the proper
gauge and connect them directly.
Cathal Garvey
Art store heat guns are handier for this application. They often come with stands too. Just avoid using flammable materials.