Nucleotides are nice, but codons are capital!

I’ve updated my OpenGL DNA renderer to support amino acids, rather than just single nucleotides. I find these colorful DNA representations oddly aesthetically pleasing, so I’m pursuing it a bit further. It’s always possible I’ll find utility in being able to do some unique sequence rendering. I borrowed the color scheme for amino acids from RasMol software. According to RasMol, the colors were chosen “according to traditional amino acid properties”. This is the same arbitrarily chosen Borrelia plasmid as last time, except since we’re looking at a coding sequence of amino acids (and stop codons in black), there are about 1/3 as many entities to represent (3157 codons), so each one is much clearer. This is a first run, so there may be some artifacts/errors, of course.

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Pronounced Plasmids

Several months ago I posted a maze I generated in C++ with OpenGL. Being pre-occupied with molecular biology lately, I took my old code out and adapted the concept for rendering a bacterial plasmid. Specifically, this little beauty is: Borrelia valaisiana VS116 plasmid VS116_cp9, complete sequence. The generative sequence renders quads around in a spiral, trying to accommodate the 9400+ bases in the sequence in less than 725 lines of resolution. This is a circular plasmid, so the physical reality is that it loops back on itself, but rendeirng this as a circle make it impossible to discern any bases. I think you can almost make out the sequence, where the amino acids A/T/G/C are red/blue/green/yellow. Click image for higher res.

 

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Open Source PCR and electrophoresis roundup

PCR (polymerase chain reaction) and gel electrophoresis are the two building blocks of DNA analysis and they’re going open source! Here’s a quick roundup of some open source efforts that have been incubating.

While you can’t decipher genetic code directly with these technologies, DNA sequencers which pump out the actual discrete code of DNA are built on these two foundational technologies. Alone, PCR and electrophoresis can be used to do meaningful genetic and forensic analysis.

PCR:

OpenPCR raised $12,000 on kickstarter to produce a $600 PCR kit made from a lasercut plywood frame with a 16 well plate and PC based controls. Open source (cad, eagle, source code available).

Coffee cup PCR is an impressive DIY project posted on Instructables that appears to be made by a student research group out of RIT, but I’m not entirely sure. Features PC controls using a proprietary heat controller.

Lighbulb PCR is a project by biohacker Russell Durrett which uses an arduino controlled lightbulb to thermocycle pcr tubes. The housing is made from PVC pipe and air is circuled with a PC fan. Open source.

Gel electrophoresis:

Cheapass gel box is a project by Joseph Elsbernd for a working gel box made for $21. The enclosure appears to be a $2 box.

Mini Gel electrophoresis system is an Instructables project posted by Joanne C. Long which describes a rather nice looking gel box design that can be built for $50-80. The enclosure is a professional looking set of laser-cut acrylic parts.

Open Gel Box 2.0 is a community effort to design an open source gel box. It culminated in kit and assembled gel box offerings from the company Pearl Biotech. Some design files are available.

Low cost DNA gel documentation is an article by Nick Oswald that describes a project to do affordable digital photography of stained gels. A comment left by Dan Rhoads reads “You don’t even need the UV transilluminator. If you’re using sybr Green or sybrSafe, you simply use blue LEDs like a bicycle lamp or a strong torchlight.”

It’s worth mentioning umbrella project OpenWetWare which is a driving force for open source community effort in biotech. If you’re looking for DIY bio stuff, that’s a good place to start. You’ll also want to check out the DIYBIO site and join the global and regional discussion groups (mailing lists).

I’ve almost certainly missed any number of promising DIY projects, so please send them along if you’re aware of any. Happy biohacking!

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Surprising and delightful quote at the end of my biology text.

This delightful quote was discovered on the very last page of my biology text. It so eloquently encapsulates why I participate in the hackerspace movement. There’s some poetry to this being on the page least likely to be read.

We have a civilization based on science and technology, and we’ve cleverly arranged things so that almost nobody understands science and technology. That is as clear a prescription for disaster as you can imagine. While we might get away with this combustible mixture of ignorance and power for a while, sooner or later it’s going to blow up in our faces. The powers of modern technology are so formidable that it’s insufficient just to say, “Well, those in charge, I’m sure, are doing a good job.” This is a democracy, and for us to make sure that the powers of science and technology are used properly and prudently, we ourselves must understand science and technology. We must be involved in the decision-making process.

Carl Sagan

OccupyScience? The full essay by Carl Sagan can be found here.

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The Bodega That Went Vegan

What’s more New York than the corner bodega? I tracked down busy Queens-based vegan entrepreneur Eric Hopf to interview him on his plans to open a cruelty-free and aptly named Vegan Bodega in Manhattan’s Lower East Side. To get your juices flowing here’s a short video introduction, featuring Eric himself.

[Daniel] Obligatory vegan story request. What was it that led you to become a vegan? Give us a little background.

[Eric] I gave up meat when I was 17 and went vegan at 18 but it did not last, due to a lack of understanding of basic nutrition and an aversion to vegetables at the time. Over time my palate has changed and I know how to eat after educating myself.

What do you do with your time when you’re not working on Vegan Bodega?

I am a stay at home dad, I photograph now and then, build websites, and cook for my family.

Tell me about the exact moment you realized Vegan Bodega was going to happen.

Well, the thought had been in my mind for a while, and one day I started to talk about my idea with my significant other. I was explaining the market and how NY vegans were waiting for a place like this. She just looked at me and said, ‘It sounds great, do it!”

What inspired you to start Vegan Bodega? Do you have any vegan entrepreneur heroes or mentors?

The inspiration came from two sources – seeing shops in the Pacific Northwest, and a trip to Orlando, my hometown. When I went to Seattle and Portland over two years ago, I saw functioning money making businesses and thought NYC needed one. I didn’t think I could do it until I found Artichoke Red in Florida. This small shop was surviving in a tiny market for vegans and producing positive cash flow. Seeing that store, I knew this was could work. I can’t name everyone I look up to, but so many vegan business owners have been supportive with their guidance.

Looking back at yourself as a child and young adult, could you have foreseen yourself running a food business? What in your life pushed you towards this path?

Having worked in the restaurant industry since my first real employment, I thought it was just a field I would be in as I went through high school and college. Turns out I love food, sharing my favorites and seeing people really enjoying what they are eating.

Your indiegogo.com campaign site doesn’t mention a potential location, but I read in the Village Voice food column that you’re looking at the Lower East Side. What are your thoughts on location and hours? Delivery?

We feel that the store needs to be close to as many different modes of public transportation as possible, as most customers will be traveling 15-30  minutes or more to visit us. The Lower East Side has that, as well as other vegan shops and a great atmosphere. Hours have not yet been determined. Right now, we are working with the idea of 10AM – 8PM six days a week to start and see how folks like those hours and if people need us open more often. Concerning delivery, we are trying to determine how it will work in regards to a minimum order, maximum radius, and delivery fees. Everything depends on what our shoppers want and request.

What do you think people should be most excited about when shopping at Vegan Bodega? Are there particular items that you find people request often? Do you predict any popular items? Any exclusives?

What, you mean an all vegan store isn’t enough to get you so excited you wet yourself? I think some of the more interesting things will be the vintage 70′s candy machine dispensing vegan and accidentally vegan candies for the kids (both big and small,) the prospect of sliced meat substitutes by the pound and getting most everything you need and want in one go. As with any large community, everyone has their own tastes and we haven’t had a lot of repeated requests, save Upton’s Natural seitan. I think some of the more popular items will be candies, Cavi-Art, and some local food producers we are talking to about carrying their products. I don’t think we will have anything exclusive. But I believe, though I could be wrong, that we will be the only store in the Northeast to carry 2 or 3 kinds of vegan queso.

Will Vegan Bodega have a deli counter that makes sandwiches, or will it be by-the-pound? Any surprises in store? (no pun intended)

Currently, we are looking at having the aforementioned sliced meat alternatives but after the store is up and running, we will investigate if the demand is there for sandwiches. We are also looking at having other non-sliced items to weigh and sell. Chick’n salad, raw cole slaw, and some other items.

Will vegan bodega offer cosmetics and accessories from vegan companies? Tell us what a girlie-girl has to look forward to.

Well, that is a great question. We are planning on stocking toiletries and everyday items like lip balm, hair care products, etc. We are extremely interested in hearing what vegans would like us to carry. Although we are going to be heavily focused on food, we want to have what our customers need, within reason.

I hear you’re into vegan fashion. Can you recommend any designers, stores to vegan new yorkers?

Well, I’m more into fashion as a byproduct of working in photography, where I predominately work on fashion and lifestyle shoots. Most of the designers I know are thanks to my significant other being a compendium of vegan info as well as big into supporting new businesses. Leanne Hilgart of Vaute Couture is fantastic and gave us great business advice, then there is Elizabeth Olsen’s Olsen Haus shoes, Julie and Gina of Cri de Coeur, Joshua Katcher’s small runs of eco-concious fashion, Dan Mims and there are loads of others, but they are all well covered in GGA and other NYC blogs. I’m not so hip that I know of small designers on the verge of breaking big.

What’s your favorite vegan product. Favorite vegan restaurant? Favorite vegan meal?

Product right now is Chris and Dan’s creation, Dun-Well Doughnuts. I don’t have one favorite and when my family really likes a place, we eat there all the time until we find a new one. Favorite meal is still probably the Massaman Curry at Pukk.

Why should non-vegans be excited about a vegan convenience store? Do you think that your store will create some awareness?

I think anything new and interesting is both exciting and scary for some. I think it will serve as a great place for people to take their friends when they are curious or say to them, “Wow, you’re vegan, I could never do that. If you don’t eat meat or cheese, what’s left to live for?”, or a variation of that same old question.


Thanks to Eric Hopf for taking time out of a busy schedule to share the inside scoop on his inspiring Vegan Bodega project. At the time of this writing, the Vegan Bodega fund-raising campaign on indiegogo.com had raised $3,230 of the $15,000 goal. To support the Vegan Bodega fund-raising campaign, visit their indiegogo.com page:

http://www.indiegogo.com/Vegan-Bodega-NYCs-Vegan-Convenience-Store

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  • The Native Inhabitant:

    Web and IT pro turned novice scientist. Currently studying computer science and bioinformatics at Hunter College.

    Here be: dragons, bio + engineering + medicine + ethics, vegan eats and fashion, music and words, gadgets and software, photography, design, DIY/maker/hacker culture, NYC, running/fitness, cyborg anthropology, et cetera.

    dp at danielpacker dot org