The open-source Pacer PCR

[kenny kostenbader]

About 12 months ago I started designing a cheap open-source PCR (I've dubbed it "the Pacer") that would mimic the lightbulb rig that Professor Blais created [1], but with the intention of mass-producing the final product. I've privately developed the basic project framework, and now that the concepts have matured enough, I finally feel comfortable releasing it.

The project has a homepage [2] that gives a simple overview, a Github repository [2] to center development around, and a WePay site [3] to accept donations. I'm going to set up a blog soon because I really need to share my thoughts on some things (like patents), but for now you'll just have to guess what I'm thinking..

The big idea behind the Pacer is to make contributing as simple and enjoyable as possible. I want folks to visit the main website, spend a few minutes getting familiar, and then start tweaking the source code or uploading their sketches of the hardware before they even blink an eye. There are a million ways to streamline this process, but README instructions in the repository should suffice while the project is in its infancy.

Speaking of project infancy, I do not expect this to grow fast. I hope that the open-source model will bless us with a decent and sustainable rate of improvement until we are finally ready to market the product, but no more. The best-case scenario here would be if each person contributing to the project told a few friends about it, and then if those friends told more friends, and so on. Media attention in these early months would be a bad thing.

I'd really like to see you guys creating and testing Pacer prototypes of your own and sharing your innovations, as this is meant to be a distributed initiative. Right now I'm building my first few prototypes and experimenting with the best methods of construction, and by the end of this week I will have some videos to post as 'tutorials' to serve as guidance.

Send me an email at kenny (at) pacerpcr.com the minute you think of a question or possible improvement.

All the best to our collective endeavors,

Kenny

- - -

in case the links don't work, I'll paste them here:

[1] - http://web.bryant.edu/~bblais/pdf/cycler-Feb02.pdf

[2] - http://pacerpcr.com

[3] - https://github.com/svensken/Pacer

[4] - https://www.wepay.com/donate/42218

[kenny kostenbader]

The $30 Arduino is great for prototyping, but a marketable circuit
would require a completely customized $10 - $15 circuit. Similarly,
the hardware could only be mass-produced if it were made of
commonplace, low-price materials, and had a design that wouldn't
require overly-sophisticated manufacturing machinery to produce. With
these concerns, the "shell" finally took the shape of a hollow cube
with one open face (for the door) and vent holes on the top. The
material mimics the robust, light-weight, and insulatve mixture of
cement and perlite that metallurgy hobbyists use in backyard
aluminum-smelting foundries.

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[kenny kostenbader]

aw crap, that last one was an accidental post

pretty silly, but i thought i was emailing that paragraph to myself. didn't see DIYbio in the address field :P

[Dakota Hamill]

New PCR designs are always interesting to look at.  I'm trying to figure out though if this is just a PCR machine, or if you plan on somehow attaching a gel electrophoresis box to the PCR machine  ( or just the same circuit?) to be able to run PCR and gels in the same "box".

 Do you hope to automate the transfer of the PCR product directly into the gel wells, such that PCR ---> completed and stained gel is all done automatically with no manual intervention?

[Cathal Garvey]

>> in case the links don't work, I'll paste them here:
>> [1] - http://web.bryant.edu/~bblais/pdf/cycler-Feb02.pdf
>> [2] - http://pacerpcr.com
>> [3] - https://github.com/svensken/Pacer
>> [4] - https://www.wepay.com/donate/42218

Thanks for that consideration: for encryption to work right, I had to
turn off HTML in Thunderbird. It handles it well and places the URLs
in-line, but it's nice to have them collected neatly.

Will be reading through this work with interest! Thanks for sharing it!

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[Nathan McCorkle]

is it a typo/mistake that under "circuit" at http://www.pacerpcr.com/
that it says it includes "a power-supply controller for the
electrophoresis chamber."?

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[John Griessen]

On 12/11/2011 05:47 PM, Nathan McCorkle wrote:
> is it a typo/mistake that under "circuit" athttp://www.pacerpcr.com/

> that it says it includes "a power-supply controller for the
> electrophoresis chamber."?

electrophoresis and PCR need such different Volt ranges...usually...

But some talk of using 100 Volts for electrophoresis in slow mode.

1 or 2 kV is more like it.

John

[Nathan McCorkle]

Electrophoresis in labs is generally less than 200V

Sent from my mobile Android device, please excuse any typographical errors.

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[Cathal Garvey]

Although bear in mind that electrophoresis itself functions on V/cm; so,
100V in a 5cm rig is twice as powerful as 100V in a 10cm rig.

So, you could probably run electrophoresis at much lower voltages if you
were content with much shorter gels; for routine applications this
mightn't matter at all. If you just want to check the concentration
versus a known reference, or check the coarse size against a ladder, you
can get by with half the length gels are normally cast in.

The width of the gel, then, corresponds to current draw, so if you're
using 9V batteries (which have sweet F-all current to give), you're
better off with narrow gel rigs.

On 12/12/11 01:21, Nathan McCorkle wrote:
> Electrophoresis in labs is generally less than 200V

[Simon Quellen Field]

Um, maybe not.

A nine volt battery can easily put out 10 amps or more into a short circuit.

That probably exceeds the current sourcing of any of your lab power supplies

used to run gels.

Doubling the width of the gel will cut the resistance in half, that part is true.

That will double the current.

But so will doubling the voltage (Ohm's Law applies to gels if you keep the

voltage and current fairly low).

Clipping nine volt batteries together is a cheap and easy way to get high

voltage. I bought a few hundred cheap heavy duty nine volts and clipped

them together in series when I was playing around with homemade Geiger

counters and ionization chambers. At 69 cents each when bought in hundreds,

it's hard to find a more stable high voltage source. No filtering needed, and

for most applications that need 1,000 volts, the current draw is so small that

the battery life is basically the shelf life.

200 volts is just 20 or so batteries (at low current they are 10 volts). They clip

together nicely in series.

I am not an expert at running gels, so I defer to Cathal's experience.

But if a 5 cm run does not get you the resolution you need, you can simply use

twice as many batteries in series to get double the voltage. But instead of

making the gel narrower, why not make it shallower?

Suppose you have a salt solution of 0.25 moles per liter.

It has a resistivity of about 8 ohms centimeter moles per liter.

So a 10 cm long run that is 10 cm wide and 1 cm deep will have a

resistance of about 32 ohms.

At 100 volts, that is about 3 amperes, which, as Cathal would be quick to

point out, is probably a lot to expect from a dozen nine volts in parallel.

But at a millimeter deep, it is only 300 milliamperes, which is easy to do

with batteries. And if we then narrow it (as Cathal suggested) to 5 cm, we

are only drawing 150 milliamperes, and life gets even simpler.

And, of course, if your solution has less than 0.25 moles per liter of salt,

then the resistance is even higher, and the current requirements are even lower.

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[Simon Quellen Field]

Oops.

I meant to say a dozen nine volts in series.

A dozen nine volts in parallel could source close to 100 amps,

and melt all of your wiring.

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[Nathan McCorkle]

I think the problem with open gels at least, is that you need to keep
the gel hydrated, so you run lots of buffer on top of the gel as well.
I think the way to solve this problem is by using some sort of
capillary/closed-system to prevent dehydration. My genomics professor
said his capillary polymer (which is not agarose) can go for weeks of
sequencing before he needs to change it. Glass capillaries, straw
keikei gel, cut double-sided sticky tape sandwiched between glass or
plexiglass, maybe even cast silicone so its easy to clean and reuse.

At the end of any capillary/closed system, you need buffer reservoirs.
You start electrophoresing in your sample, then switch from the DNA
sample chamber at the end of the capillary/gel to the chamber with the
running buffer.

> And, of course, if your solution has less than 0.25 moles per liter of salt,
> then the resistance is even higher, and the current requirements are even
> lower.
>
>
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>
>
>
>
> On Mon, Dec 12, 2011 at 1:21 AM, Cathal Garvey <cathal...@gmail.com>
> wrote:
>>
>> The width of the gel, then, corresponds to current draw, so if you're
>> using 9V batteries (which have sweet F-all current to give), you're
>> better off with narrow gel rigs.
>
>

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[Cathal Garvey]

Forgive my misuse of "current": I was searching for the unit of stored
energy rather than energy rate. Most 9V batteries I see around Ireland
only pack ~200mAh, which is pretty low compared to the capacities of
decent NiMH AA batteries.

Also, my enthusiasm for 9V batteries is considerably lower because they
are literally ten times as expensive in Ireland. For some unfathomable
reason, 9V batteries easily cost �5 each over here. :(

> ohms<https://www.google.com/search?q=8.0645+ohms+centimeter+/+0.25+*+10+centimeters+%2F+10+square+centimeters>

> .
> At 100 volts, that is about 3

> amperes<https://www.google.com/search?q=8.0645+ohms+centimeter+/+0.25+*+10+centimeters+%2F+10+square+centimeters>,

> which, as Cathal would be quick to
> point out, is probably a lot to expect from a dozen nine volts in parallel.
> But at a millimeter deep, it is only 300 milliamperes, which is easy to do
> with batteries. And if we then narrow it (as Cathal suggested) to 5 cm, we
> are only drawing 150 milliamperes, and life gets even simpler.
>
> And, of course, if your solution has less than 0.25 moles per liter of salt,
> then the resistance is even higher, and the current requirements are even
> lower.
>
>
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> Get a free science project every week! "http://scitoys.com/newsletter.html"
>
>
>
>
> On Mon, Dec 12, 2011 at 1:21 AM, Cathal Garvey <cathal...@gmail.com>wrote:
>
>> The width of the gel, then, corresponds to current draw, so if you're
>> using 9V batteries (which have sweet F-all current to give), you're
>> better off with narrow gel rigs.
>>
>