OpenPCR - open source biotech on your desktop | Hacker News Reader

OpenPCR - open source biotech on your desktop

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51 pointsminouye21 comments

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.

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.

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!

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.

Excluding primers, the cost of those is about $0.8 - $2 per reaction, depending on how you do things.

Provided you have a PCR machine, a small centrifuge and an apparatus to run DNA gels an experiment like the one they are mentioning (finding out the kind of tree you have in the backyard) would cost you something like $50-$100 if you really know what you are doing. Much more if you are not a pro.

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.

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 )

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.

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

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

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

What, back in your day you didn't even have water baths or accurate temperature measurement?

(tongue-in-cheek)

...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?

Gave you $8 and reblogged. http://www.thinkgene.com/openpcr-dna-amplification-for-anyon...

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.

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.

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

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

Tito

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... )

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

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.

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

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

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