
BioCurious, a hackerspace for bio now open to public - minouye
http://biocurious.posterous.com/biocurious-meets-world-the-next-big-thing-to
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tejaswiy
Implanting Jellyfish DNA in Bacteria to make them glow is Hello World for
Biotech !? Mind = Blown.

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mbreese
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>

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

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bedris
Just be careful with the ethidium bromide.

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nazar
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.

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RoyalSWiSH
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.

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nazar
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.

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mynegation
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.

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hbien
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.

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

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hbien
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.

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ndespres
Thanks very much for the helpful links!

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jfarmer
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/>

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akaalias
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!

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

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

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aantix
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/>

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tito
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

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reasonattlm
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>

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

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PatrikD
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.

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mbreese
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...

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tito
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

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nazar
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?

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mbreese
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...](http://www.qiagen.com/products/genomicdnastabilizationpurification/dneasytissuesystem/dneasybloodtissuekit.aspx#Tabs=t0)

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

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nazar
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.

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benatkin
A play on the phrase bi-curious? Wow.

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PatrikD
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

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

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

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

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

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dillona
This looks really great!

Congratulations on the launch.

Does anyone know if anything like this exists in central Florida?

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flipbrad
the london hackspace is trying its hand at PCR and algal biodiesel

