BioCurious, a hackerspace for bio now open to public | Hacker News Reader

BioCurious, a hackerspace for bio now open to public

biocurious.posterous.com

196 pointsminouye57 comments

Implanting Jellyfish DNA in Bacteria to make them glow is Hello World for Biotech !? Mind = Blown.

Yes, it is. I was involved in this kind of things before dropping my Ph.D. Have a look at biobricks, for example: http://biobricks.org/

Well, kinda... making them glow is just being a bit fancy. And you need a light at a particular wavelength to get them to glow. I assume they inserted Green Fluorescent Protein (GFP).

The traditional "Hello World" that I learned was to insert a functioning lacZ plasmid into a mutant E. coli strain that had their lacZ gene damaged. When you do this, you introduce a functioning lacZ gene into the E. coli, which will cause the colony to turn blue in the presence of X-gal. It is a nice and cheap way to do screens... but it isn't nearly as cool as glowing super-bugs.

http://en.wikipedia.org/wiki/Blue_white_screen

LacZ is definitely Hello World in microbiology. From there you typically scale up with inducible/repressible promoters. Ara comes to mind.

GFP is a fun product to learn hydrophobic column chromatography. I still think it's best to start with nucleic acid separation before protein separation, though.

Aside from yeasts, there's no way you can do Eukaryotic stuff easily. You'd need a laminar flow hood and very sterile incubators.

Gel electorphoresis might be fun as well. At least my first run was fun for me :)

Just be careful with the ethidium bromide.

That what lab assistant usually says. At uni we used some blue florescent dye that apparently got ionically bonded to P group of DNA backbone. It was completely safe(not carcinogenic). I can't remember the name of the dye, but results with EtBr were much clearer.

GelRed is another safe one. It is designed so that it will not cross cell membranes. I don't think it intercalates either.

What about Methylen blue? Do you guys have an idea if this will work? Read it somewhere. But i don't think it is florescent.

If my memory doesn't lie to me, I think its a load dye, which only dyes the DNA sample to visually assist during the loading of the samples into the "wells" of the gel. Otherwise you can't be sure whether you put it inside the well or somewhere into the surrounding buffer.

Depending on what hazmat disposal they have, they'd be better off using something like SYBR Safe, especially with beginners. It's almost as good as EtBr for staining, but not toxic. (Downside: it's much more expensive, EtBr is cheap as hell)

EtBr is cheap as hell, but the hazmat disposal needed to get rid of EtBr gels is very expensive.

Yea, it's super fun, even kids can do the experiment. Here's some pics from our last Glowing Cells class!

http://www.meetup.com/BioCurious/photos/3739322/#61569752

Tito

It may warrant its own 'Ask HN' entry but I will piggy-back on that thread.

What are the books that one should read if one wants to start bio-hacking? Programming and CS books were discussed here many times: K&R, SICP, Corman etc, but what about biotech/life sciences?

I've tried some O'Reilly books like "Perl/Python for bioinformatics" but they are really for biologists trying to program, not the other way around.

I was IBO(International Biology Olympiad) participant during high school, majored in Bioengineering and now a full time web programmer(entrepreneur). Knowing both domains pretty well(better than average person) I have no idea what kind of books should one read, or what kind of approach should one take in order to start biohacking. If any bioprogrammes around here, share some thoughts and recomendation.

If you are a complete newbie, I'd recommend "Cartoon Guide To Genetics". Sadly, it is over a decade old at this point. If anyone has a more contemporary reading list, I would also be interested.

I believe general biology genetics would be more than enough to get into the business. And for an average hacker, those concepts won't be hard to consume. Campbell-Reece Biology book(just the genetics part) might be the right choice.

I'm actually trying to get into bioinformatics myself. Here are some of the resources I've been using:

  - Khan Academy (Biology, Chemistry, Statistics, Probability)
  - Molecular and Cell Biology for Dummies <-- includes overview of lab techniques like PCR and electrophoresis
  - Bioinformatics for Dummies
  - R Cookbook
  - Molecular Biology of the Cell <-- expensive textbook, very detailed

I was pretty surprised to see a lot of stats being used. I'm sure other people can recommend better resources for bio-hacking instead of bioinformatics.

If you are a good programmer you ought to know math and statistic.

I would suggest trying to learn biology or chemistry like anyone going for a degree in either or both. Look into what books and other publications they read. Or just go back to school and add a squishy degree to your CS degree. Or do the equivalent of that on your own.

I would say that is way better than Bioinformatics for Dummies.

NCBI is pretty good (i'd say definitive) resource (and time sink :).

For example http://www.ncbi.nlm.nih.gov/books/NBK20260/ or http://www.ncbi.nlm.nih.gov/education/ or just http://www.ncbi.nlm.nih.gov/

When you're experimenting with bioinformatics (specifically in R), are there sample data sets you can run queries on? What have you been using?

The great thing about bioinformatics is that there's so much data available online for free. Here are some links:

  http://www.ncbi.nlm.nih.gov/ - sequences, papers, and so much more
  http://www.expasy.org/
  http://smd.stanford.edu/ - microarray data
  http://archive.ics.uci.edu/ml/ - not biology related but good data sets to play with R

To navigate NCBI databases and learn file formats, you can read their documentation (http://www.ncbi.nlm.nih.gov/education/) or get any bioinformatics book.

Thanks very much for the helpful links!

I recommend watching Steve Yegge's excellent presentation at O'Reilly's OSCON Data. He points out a number of books in the video, but in general this is an excellent talk about preparing to solve hard problems in bio. http://www.youtube.com/watch?v=vKmQW_Nkfk8

Thank you, I'll look at that once again, although AFAIR he showed covers of some O'Reilly books that, like I mentioned, were not very useful.

You should watch iBioSeminars (www.ibioseminars.org) to become familiar with biology research. These are free online talks given by leading scientists. They contain a general intro to a topic and then go into the research behind it.

Here are links to two genomics lectures: David Botstein (Princeton): http://www.ibioseminars.org/lectures/cell-bio-a-med/david-bo...

and Jonathan Weissman (UCSF): http://ibioseminars.org/lectures/bio-techniques/jonathan-wei...

Good luck!

I highly recommend "Molecular Biology for Computer Scientists" by Lawrence Hunter: www.biostat.wisc.edu/~craven/hunter.pdf

Biology, is MASSIVE. So first question: What aspect would you like to get involved in?

WET LAB: pipette lab coats and playing with chemicals

"LH002" https://github.com/delinquentme/LH001

"biotech temp agency" http://bit.ly/onCmQI

BIOINFORMATICS: probably the quickest route for a programmer

"Best resources to learn molecular biology for a computer scientist." http://bit.ly/p0zKXG

"Bioinformatics for programmers" http://bit.ly/nxWGps

"A Quick Guide for Developing Effective Bioinformatics Programming Skills" http://bit.ly/6hZEUj

MICROFLUIDICS: "lab on a chip"

List of microfluidic companies http://fluidicmems.com/list-of-microfluidics-lab-on-a-chip-a...

Talk to me if you're serious about it ... there is a HUGE community basically waiting to blow open ... I've recently begun working in bioinformatics and bio into my skillset, in this short time the interest has only grown.

If you're into biohacking you should check out http://cofactorbio.com/

They sell a kit that lets you do a 23-and-me style analysis in your own home.

An article in Wired about them and others working on similar efforts: http://www.wired.com/magazine/2011/08/mf_diylab/

For NYC people, there is http://genspace.org/ which has intro courses several times a year. You will also make bacteria glow and smell like bananas!

Bump! I ran into them at the local Maker Faire and got some DNA extracted. Will be taking the synthetic bio class starting tomorrow!

By any chance do you know if there's anything like this in L.A?

L.A. Biohackers. http://www.biohackers.la/ Great people

<3 Genspace

Check out their calendar; on Oct 26th "Advanced Personal Genomics". http://bit.ly/o5rUrT

"...on how to hack your own genomic data, in this hands-on-computer class, where you can use your own 23andMe data (or someone else's) to see which of your biochemical pathways are the most unique, what percentage of the NEanderthal genome you share, and other interesting stuff. Bring your laptop and your 23andMe data, if you have it."

Sweet, sign me up! I've been looking for an opportunity to dive deeper into this data, but being a beginner, it can be a bit overwhelming.

http://biocurious.org/classes/

Hey! I just added a signup on meetup for you -- thanks for reminding me :)

Advanced Personal Genomics (hacker friendly!) http://www.meetup.com/BioCurious/events/37411362/

Tito

If you want to learn more, you might hang out at the DIYbio list - most of the BioCurious folk post there.

http://groups.google.com/group/diybio

We also post heaps more at http://groups.google.com/group/biocurious

Come check us out this Sunday at the East Bay Mini Maker Faire, if you get a chance:

http://www.meetup.com/BioCurious/events/34349702/ https://ebmakerfaire.wordpress.com

We'll be issuing and stamping our own version of Mitch Altman's Hackerspace Passports as well.

Does anyone know what type of equipment they have? What about consumables (enzymes, tubes, etc...). I'd love to try a few things at the bench, but would need to know what to bring.

I'm a bit curious though as to whether or not they should have an IRB or some sort of rules about what types of experiments can go on there...

Hi!

Here's a list of the equipment available today: pipettes, pipette tips, realtime PCR machine, OpenPCR PCR machine, incubator, shaking water bath, vortexers, gel electrophoresis boxes.

If you don't have an experiment in mind, we have lots of awesome classes where you can do things like sequence your own DNA and make glowing cells: http://meetup.com/biocurious

Tito co-founder BioCurious

Hi. Horses are very important animals in where i live(We even have ministry of horses...). So me and one friend of mine tried to isolate DNA from best horse breeds and then make a database, and later mine that database to perform selection predictions by computer... Its a big project and founded by gvt. I am not a part of it, my friend just consults me from time to time, since I am both acquainted with programming and biology. We are stuck with DNA isolation from horse blood right now. Do you think this kind of experiment would be interesting?

Is there a veterinary school near you (Turkmenistan)? If so, this is your best bet. They should have the equipment to do proper DNA isolation from blood. (Something like this will help: Qiagen DNeasy Blood and Tissue kit [1]) What you'll probably want to do is high-throughput DNA sequencing and then map the sequences to the Horse genome [2]. Then you'll be able to compare the variations from various breeds.

But this is a pretty large project.

[1] http://www.qiagen.com/products/genomicdnastabilizationpurifi...

[2] http://www.uky.edu/Ag/Horsemap/ (I think)

Hi, thank you for the info. The project is well funded(equipment is therefor isnt much of an issue), the problem is not with money but with professionals. The guy just finished university, and they ask him to conduct this project. There are not many people here who know this stuff, neither the biological aspect nor the programming. And I guess they don't want to hire foreigners, i am not sure why. You see, horses are so important here, you can even get a sentence for killing one. So maybe it has something to do with foreigners thing.

Making bacteria glow at the BioCurious meetup last month was one of the most fun things I've done, because, well, IT'S SCIENCE!, but also for the curiosity of the participants, the patience and knowledge of the instructors, and the slightly strange feeling I got where, on that particular Saturday afternoon, I doubted you could find another group of people engaged in quite the same pastime on planet Earth!

It's been a while since I did my IRB training but I believe activities here are exempt since there's no federal funding involved. Privately funded research (for instance, the social sciency papers involving human subjects that come out of Microsoft Research) generally don't go through IRB, afaik.

Even if there isn't any federal requirement for an IRB, it probably isn't a bad idea to have some sort of oversight. You don't want someone doing something stupid there. You also need to make sure that there are some safety standards to be followed (autoclaving biohazard waste, or limiting work to BSL-1, for example).

Another example: you don't want someone sequencing a person's genome without approval. (It's probably not as big of a risk here as it would be to a place like 23andme, but they should still probably try to cover themselves).

Edit: It looks like they've had some of these same discussions on their mailing list: http://groups.google.com/group/biocurious/browse_thread/thre...

A play on the phrase bi-curious? Wow.

I was about to comment on that but I thought I would be too down-voted!

"Play" ?? That's what I read it as and I was, like, wow, what is this all about? Got my attention!

Part of our motto is "Experiment with friends!" :-)

Yes, very tongue-in-cheek. If I remember correctly, in one of the videos Eri says something like "I experimented a little in college, but it never really went anywhere". :-D

Weren't they worried about being one letter away from "bicurious"? And to quote Seinfeld, not that there's anything wrong with that.

Apparently not; see the reply from one of them to my top-level comment.

Sure, the first zombie apocalypse will start this way but it is so cool! Big props for starting this.

Yeah I was about to say: nothing can possibligh go wrong... Possibly go wrong. That's the first thing that's ever gone wrong...