

OpenPCR - open source biotech on your desktop - minouye
http://www.kickstarter.com/projects/930368578/openpcr-open-source-biotech-on-your-desktop

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vessenes
I love this idea. Interestingly, they reference Gates and how cheap computers
helped him. All those guys, Gates included, started out working on mainframes
and minis that they stole time from in University labs.

Probably that's what Gates-of-2030 is doing right now; making glowing mice in
the basement of the University of Minnesota, or somewhere similar.

~~~
easp
A fine point, though keep in mind though that Mini-computers were themselves
sort of the PCs of the mainframe era. A story I heard, possibly apocryphal, is
that Ken Olsen named DEC "digital equipment corporation" rather than , say
"Digital Computer Corporation," as a way around IBMs lock on central
purchasing at universities, national labs and corporations for any "computer"
purchases.

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minouye
For those unfamiliar with a PCR box (<http://en.wikipedia.org/wiki/PCR>),
think of it as a photocopier for DNA--by creating copies, the DNA can be
visualized through other tools like a gel box
(<http://en.wikipedia.org/wiki/Gel_electrophoresis>). I saw Tito and Josh's
prototype at Maker Faire and it was truly impressive. Please support them if
you can!

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teamhandley
I am completely behind the spirit of this idea, but I wish they would openly
address the cost of running PCR reactions which take enzymes, nucleotides,
specific phosphate buffers in or to complete. All of these things cost as do
the methods to analyze your final PCR products. I assume this is all covered
under their mentioning 'kits', but these accessory components can rapidly
become more expensive than the instrument itself.

~~~
jperfetto
This is Josh - one of the people behind the OpenPCR project. I agree with you
that reagents can be a huge amount of the cost.

Part of this depends on the quantity of reactions you're doing. Taking the DNA
barcoding of trees example we gave, if you're doing hundreds of reactions the
cost can already be quite low as crocowhile pointed out. If you're just
learning or doing a few reactions, here's where a kit containing small
quantities of the needed reagents and educational information can be more cost
effective.

The other part has to do with the exact reagents you need. Obviously if you
can use an off the shelf master mix you'll pay much less than if you need to
purchase a specialized enzyme and specific reaction buffer. There are cases
where that is needed, but there's also cases where people purchase reagents
more expensive than what they need, simply because they just want their
reaction to work, they've found one way to make it work, and they'd rather
spend more time on their project rather than finding the more cost effective
ways to make it work.

Here there's a lot of opportunity for software or software coupled with
hardware to find the most cost effective way to do a reaction and make it work
better. For example, a PCR machine networked with a UV spec and some software
could quantify template DNA, present recommendations on enzymes, calculate the
best reaction parameters accurately, and tell the user exactly what quantities
to add of primers/enzyme/buffer/water. Many users of PCR are not necessarily
experts at PCR, so there's some opportunity to help people get better results
while saving time and money.

We're thinking about these larger problems, but focusing on getting an
accurate and reliable PCR machine working first. Once we have that, we'll have
the foundation to pursue these other areas.

~~~
epiphany47
Going back to the barcoding of trees, how would you do it? I assume you'd use
some sort of SNP identification or specific DNA primers, but then you've just
got a bunch of DNA in a tube.

The typical way of visualizing DNA is using an electrophoresis gel - most of
the components are cheap/easy to obtain (agarose, electrodes, power supply,
buffer), but how would you visualize your gel? Typical ethidium bromide stains
are probably out of the question, given that ethidium bromide is so
carcinogenic - most people probably don't have access to ethidium bromide.
Maybe use a safer stain? (googling seems to point to invitrogen's SYBR Safe
DNA stain as a possibility).

Then again, you could just use a UV spec to measure concentration, but how
many people have a UV spec?

Looking forward to your results! In the future I think it would be nice to
have open source enzyme starters (kind of like brewers/bakers yeast starter
kits?) so that people could just grow+purify their own enzymes. (after the
open source centrifuge that is =P )

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aheilbut
While this sounds like a fun project, if you want a cheap PCR machine, why not
buy a used one for a few hundred bucks?

Getting molecular biology to work is going to be hard enough without trying to
reinvent the wheel and re-do the relatively uninteresting, but highly
optimized engineering that has gone into these machines over the last 20
years.

~~~
mcantelon
Over and above cost, an open PCR machine design may enable these machines to
develop in unexpected ways.

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bedris
You don't even need a PCR machine. All you _really_ need are three water baths
at the appropriate temperatures!

~~~
surlyadopter
You kids don't know how good you have it. Why back in my day...

~~~
easp
...you had to purify your own DNA polymerase and then add more of it at each
cycle because a thermostable version hasd't been discovered yet?

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rms
Gave you $8 and reblogged. [http://www.thinkgene.com/openpcr-dna-
amplification-for-anyon...](http://www.thinkgene.com/openpcr-dna-
amplification-for-anyone/)

Btw, if anyone reading this wants to upgrade their OpenPCR setup with a nice
PCR hood, I have a beautiful one for sale for $1500.

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easp
Cool! 20 years ago, I tried using PCR quantitatively to study estrogen
receptor gene expression in feline uterine epithelial cells for my senior
thesis. I didn't end up doing much science though, because I spent too much
time hung up on techniques.

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sliverstorm
Instead of pledging money, can I get involved directly, or is this only Tito
and Josh?

~~~
tito
Hey silverstorm -- Awesome, shoot me an email and let us know your interests
-- titojankowski at gmail.com

Tito

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earl
Hey, since you're reading Josh, I have a question: isn't the harder part of
this securing the chemicals / reagents / disposables / tools to actually
perform PCR? I thought you needed special (patent covered) reagents,
96/whatever well plates, seals, pipettes, etc. Sorry, I'm not trying to be
disrespectful of your efforts, but it seems that even if I had a PCR machine,
I'd still be a long way from doing PCR on anything interesting.

In any case, best of luck. I used to work on software that controlled MJ
Research thermocyclers and on a light sensing / real time pcr system software.
It was kind of interesting, but the companies that build these devices move
slowly and charge (in my mind) way too much money. This market is ripe for
disruption. (I worked on a slightly bigger, since discontinued, version of
this: [http://www.bio-
rad.com/prd/en/US/adirect/biorad?ts=1&cmd...](http://www.bio-
rad.com/prd/en/US/adirect/biorad?ts=1&cmd=BRCatgProductDetail&vertical=LSR&catID=dc07e873-5c02-4fd6-bd5e-1aad973eec08)
)

There's actually a used one of the things I worked on for sale for $14K here.
Oof.

<http://www.labx.com/v2/adsearch/detail3.cfm?adnumb=402318>

Also -- if you just want a plain thermocycler, here's one for $20 or so!!!
(these things started at $10K new.)
<http://www.labx.com/v2/adsearch/detail3.cfm?adnumb=415429>

~~~
jperfetto
The supplies and reagents you need are all readily available on the web. For
basic supplies like pipettes and tubes, one of my favorite sources is
<http://www.bio-world.com> . You'll also need a taq polymerase and primers -
both of which tons of companies sell online, just search Google and look at
the ads. Some companies will only ship these reagents to commercial addresses,
but there's more than enough that will ship to residential.

We'll try to get more info on the site in the days to come.

~~~
tito
Hey Earl, MJ Research, cool! I've got one of their PCR machines in my trunk,
all taken apart. We used it as inspiration when we were first starting, it's
got some nice design features. Keep in touch, Tito

~~~
easp
I remember when MJ Research thermocyclers were the bargain option. That was
nearly 20 years ago.

