Re: Meeting times

[Bryan Bishop]

On Thu, Sep 27, 2012 at 8:32 AM, Mitchell N <m.nor...@ymail.com> wrote:
> Don't know if it's been mentioned at all but do we want to register as a
> igem group so we can have access to the parts registry?
> http://partsregistry.org/Main_Page

I thought iGEM doesn't allow DIY groups. This is why DIY folks have to
team up with a university to get accepted as a team. But did this
change? I remember Randy Ruttberg making a fuss about things.. dunno.

- Bryan
http://heybryan.org/
1 512 203 0507

[Cathal Garvey]

Last I'd heard, Randy was still averse to allowing DIY teams, for fear
of having his brand "polluted" by biohacking's popularity.

Oh, also because it would draw attention to the fact that his
widely-called-open repository is anything but.

Oh, and because loads of stuff in the parts registry is patented and
created without a license, but gets away with it as long as it's only
for the Ivory Tower teams.

Oh and..

Essentially, we are better off starting our own parts repository; Cloud
Cultures FTW!

If you haven't heard of the GOODIYbio competition, now's a good time to
familiarise yourself. It's a recently launched open source biology
competition, and there are categories for hardware, software and
wetware, with the "win" tiebreaker being for the most reproducible project.

Wetware projects highly recommended! ;)
http://www.goodiybio.org/

--
www.indiebiotech.com
twitter.com/onetruecathal
joindiaspora.com/u/cathalgarvey
PGP Public Key: http://bit.ly/CathalGKey

[Sebastian S. Cocioba]

Would there be any legal issues with having a cloud culture repository? I had a recent meeting with a nyc fbi agent about lab start-ups and sharing info/material and she was worried about the "wrong kind of people" getting their hands on biostuff and making bionasties. Maybe a biohaking license of sorts with a liability waiver would work? Just to have ppl on record and all action is transparent. Not that we have anything to hide.

Sebastian S Cocioba
CEO & Founder
New York Botanics, LLC

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[Jeswin]

On Mon, Oct 1, 2012 at 1:54 PM, Sebastian S. Cocioba <scoc...@gmail.com> wrote:
> Would there be any legal issues with having a cloud culture repository? I had a recent meeting with a nyc fbi agent about lab start-ups and sharing info/material and she was worried about the "wrong kind of people" getting their hands on

The wrong people can always get their hands on the stuff they need.
They don't care about government or police. Does it make it easier? I
guess so, but it also makes it harder for everyone else who is curious
and trained.

[Sung won Lim]

Just wanted to point out that license for doing amateur biology is a terrible, pointless idea, at least when BSL 1 kind of experiments are concerned.

-sung

[Sebastian S. Cocioba]

But wouldn't a public repo of bioparts like biobricks with no affiliations cause legal trouble?

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

[Cathal Garvey]

I have nothing to hide. But I also have nothing to share.

If I am doing nothing illegal, I will not change my lifestyle or
collaborations to better suit the paranoia of three-letter-agencies, no
matter where they make their home.

If I share legal, harmless DNA to people whom I trust, I have done
nothing illegal. If they happen, exceptionally unlikely as it is in
reality, to do something wrong with said DNA, then it's on them, morally
and legally.

Cloud cultures would be such a social venture; a DHT-style repository of
DNA samples that can be queried to find a contact who has the DNA and is
willing to share. Provided everything is legal, I see no need to
encumber it with licenses, fancy membership cards, or other clutter. The
whole point is an open source repository to rival the closed, jealous one.

[Nathan McCorkle]

If you want legal indemnity host in some country with lax laws, that don't follow/care about any major countries' patent laws.

Making parts more easily searchable is just making access to knowledge easier. It doesn't help a bit with the wet lab work. Sending actual DNA around poses more security risk, for about 2-4 years until gene synthesis hits the desktop.

I would actually worry more about physical DNA being faked or 'malwared', so I'm a propenent of keeping the repo digital. We should start by mirroring the existing registry(s).

[Bryan Bishop]

On Mon, Oct 1, 2012 at 4:51 PM, Nathan McCorkle <nmz...@gmail.com> wrote:

I would actually worry more about physical DNA being faked or 'malwared', so I'm a propenent of keeping the repo digital. We should start by mirroring the existing registry(s).

I am surprised Marc hasn't setup public key signing of the DNA samples from Biofab yet. Hmm. This is a probably a thing that we should do.

[Cathal Garvey]

Key signing and hash verification etc. are all well and good, but they
don't mean anything until you can verify that the hashed-and-signed
digital representation actually matches the DNA.

To meaningfully confirm the content of a DNA strand calls for a DNA
hashing method; DNA barcoding is a step in this direction for whole
species, but a method for smaller molecules that generates useful and
visibly distinct output would be needed to "hash" plasmids.

[Bryan Bishop]

On Mon, Oct 1, 2012 at 5:05 PM, Cathal Garvey <cathal...@gmail.com> wrote:

Key signing and hash verification etc. are all well and good, but they
don't mean anything until you can verify that the hashed-and-signed
digital representation actually matches the DNA.

Huh? What's wrong with using simple checksums?

The other side of the coin, key signing, is more for origin verification.

[Cathal Garvey]

There's nothing wrong with checksums for the sequence. I mean rather
that no number of cryptographic methods *in silico* have any bearing on
the plasmid in front of you in a tube; to verify that, you need to
sequence it.

That's where I'd like to see a "genetic hash"; for easy, rapid
verification of sequence identity. Same niche as cryptographic hashes on
computers; you *could* just verify that your copy of the software
matches a known reference, but then you could end up transferring whole
copies of the file just to verify, so we use hashes instead to get a
quick, dirty, and usually reliable measure of identity. In genetics, a
similar method would be nice for verifying sequence identity rapidly on
receipt of a new bit of DNA from a marginally trusted source.

But this is digressing away from the basics needed for "Cloud Cultures",
which is all in-silico. If it's distributed like a DHT, then yea; you
need hashing and signing, but I imagined simply a modded wordpress site
or something, like Thingiverse but not needlessly closed-source and
centrally managed.

[Bryan Bishop]

On Mon, Oct 1, 2012 at 5:14 PM, Cathal Garvey <cathal...@gmail.com> wrote:

quick, dirty, and usually reliable measure of identity. In genetics, a
similar method would be nice for verifying sequence identity rapidly on
receipt of a new bit of DNA from a marginally trusted source.

Okay, so you are talking about a hash that works on fragments from a tube (which are anywhere from completely lossy to just aggravatingly lossy), rather than fragments you downloaded over the interwebs (which should never be lossy).

Thingiverse wasn't build on wordpress. As I recall, it was some mvc framework on a certain-language-that-will-not-be-mentioned.

[Cathal Garvey]

Huh, I think Bre told me it was wordpress once. Probably in error, as it
wasn't his area I suppose. But yea; as long as the database is regularly
backed up and torrented, there's little reason not to use a simple
central repository for open source DNA designs. If the "man" is going to
clamp down on DNA sequences for fear of the boogieman, he's not going to
start with amateurs' sharing sites; he's going to start with the genome
sequences for deadly pathogens on NCBI. And in the ensuing fallout,
there'll be plenty of time to move to a DHT. ;)

[Nathan McCorkle]

I'm concerned about security of the DNA sequence (not being modified
in transit) whether it's *digital* or *physical*. RFLP could be a good
*physical* DNA hash, Bryan are you saying a checksum of a *digital*
DNA .txt file is sufficient for digital verification?

That 'Cloud Culture' includes the word 'Culture' that seems to mean
live/stable bugs or physical DNA is involved in storage and transit. I
do not think the infrastructure is present yet to support that... ok
there are fridges, but the only DIY suspension culture stuff I've
seen was on E.coli agar stabs. What about the 10s of other strains we
could rattle off a list of that would be cool to have on hand?
Replicating thousands of *physical* parts and distributing them to
multiple peers just seems way too much to do right now... at least
compared to keeping the DNA in *digital* form now.

I expect *digital* DNA to *physical* DNA converters' prices will come
down in the next 2-4 years, I can wait that long.

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--

Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Patrik D'haeseleer]

Heh - I think we'd need something like a set of all 4-nucleotide TAL effector nucleases: pick a random 3-mer TALEN, cut up the target sequence in fragments around 64 bp long, and compare the restriction fragment length pattern against the expected pattern.

In the end, considering that DNA sequencing is orders of magnitude cheaper than synthesis, I assume that sequencing will be our validation of choice. With all the super-high-throughput NGS sequencers these days, I think there's still a real market opportunity for a small and cheap device to do single amplicon sequencing. I'd *love* to have a little desktop device that does a single Sanger sequence at 1/10th the cost.

[Patrik D'haeseleer]

Sorry - meant random 3-nucleotide TALENs, of course. Or maybe 4-mer TALENs for much longer constructs.

[BioGuy]

I heart this post. For a while I thought biobricks and the biological parts database was great! ....that was until I realized there was no possibility of being able to contribute to or use them. But a lot of you are onto something. Develop the same concept on a grassroots level. If the Biological parts database is UNIX then whats stopping a dedicated group from making Linux?

[Dakota]

The idea of a real, "open" parts registry idea comes up every so often
here, and I think a lot of people would like to see it happen, myself
included. On the other hand, and I may be wrong here, I don't think
anyone on this list has a laboratory with the capacity to serve as the
starting point for it. That's not to say it is impossible, or
couldn't be made to happen, perhaps with multiple places starting as a
beginning point working on a few parts at a time. I think an attempt
was made to pick out a handful of parts that people might like to see
in the beginning, so as to get a starting attainable goal of 40 or 50
pieces.

The funny (and really cool) thing about plasmids and these DNA parts
is, once you have them, you theoretically have them forever. As long
as you can do PCR or minipreps you can build up a stock as big as
you'd like.

I spent a few days two months ago reading all about part assembly and
the vector's used, but couldn't really ever find anything on the
licensing or policy concerning using them outside of iGem sanctioned
events. Even on the parts registry main page, nothing is written
under the Privacy Policy of Disclaimer links found at the bottom.

That aside, you can get this BioBricks assembly kit from NEB
http://www.neb.com/nebecomm/products/productE0546.asp which gives you
all the needed restriction enzymes to link parts together as well as
the ligase. I had thought previously (and incorrectly) that it also
came with the main biobrick vector, which it does not.

There are multiple vectors to use for parts assembly though
http://partsregistry.org/Plasmid_backbones/BioBrick_friendly and
http://partsregistry.org/Plasmid_backbones/Assembly

so it's a matter of what suits your needs and what is available.
Getting a BioBrick assembly vector that we could all share could be a
great first step.

If we were to start gathering parts on our own, I believe it would
make sense to continue to use the assembly standards layed out by
iGem, such that in the future, we could submit parts of our own to the
registry, while still maintaining an outside "open" registry, as well
as sharing with iGem teams or using parts we got from iGem teams or
other sources, that all fit into the assembly standard.

http://www.jbioleng.org/content/2/1/5

There is an article to an old paper by Knight going over the design
and thought processes behind the standard assembly vectors, and is
interesting.

Also, there is a decent amount of information on the parts registry
about part design and assembly, as well as on OpenWetWare I believe.
I found the parts registry extremely difficult to read and navigate
around at first, but after some time spent, you manage to get the hang
of it and it has some valuable information.

[Bryan Bishop]

On Thu, Oct 4, 2012 at 8:51 AM, Dakota <dko...@gmail.com> wrote:

I spent a few days two months ago reading all about part assembly and
the vector's used, but couldn't really ever find anything on the
licensing or policy concerning using them outside of iGem sanctioned
events.  Even on the parts registry main page, nothing is written
under the Privacy Policy of Disclaimer links found at the bottom.

Did you try the biobrick public agreement thing?

https://biobricks.org/bpa/

I am not sure which biobricks it presently covers.

[Dakota]

I registered on that website after reading that public agreement, did
an advanced search, and came up with this huge list of available
parts.

http://gyazo.com/2b17236ce442ca23d29a8873ec8bc0a4

[Bryan Bishop]

On Thu, Oct 4, 2012 at 9:25 AM, Dakota <dko...@gmail.com> wrote:

http://gyazo.com/2b17236ce442ca23d29a8873ec8bc0a4

E. coli constitutive promoter with strong ribosome binding site | Joseph H. Davis | BPA Contributor #1

K1-5 transcription system | Drew Endy | BPA Contributor #2

Well that's very disappointing. So much for being open!

[Justin Dormandy]

On the other hand, and I may be wrong here, I don't think
anyone on this list has a laboratory with the capacity to serve as the
starting point for it.

I have been in touch with several scientists in Eugene, OR. They're involved with developing a startup incubator lab space and are very interested in increasing accessibility of biotechnology. They have invited me to participate in their lab and come this winter or spring I'm probably going to move down to Eugene. Once I'm there whatever I choose to pursue is pretty much open ended and my decision. In 3 - 6 months, and if there is enough interest, organization, and people willing to participate, then I can help get this going at the lab.

-Justin
 

[Justin Dormandy]

After I submitted that previous message a question just popped up in my head. Is there no interest from the people at BioCurious, GenSpace, or any of the other well established community bioscience labs to work on developing this?

[Cathal Garvey]

One of the reasons I chose Bacillus subtilis as my
personal-favourite-DIY-microbe was because of sporulation. A culture
collection powered by Bacillus subtilis is trivial to manage; once a
culture is established, you can just leave it sporulate, scrape cells
into a simple buffer and spot onto sterile card, laminate and keep in
pre-stamped envelopes until someone requests one. Shelf life of years.

[Patrik D'haeseleer]

Not speaking for all of BioCurious, but I'd say there is definitely *interest*, yes.

The main problem is that setting up and running a resource like this would be a lot of work, and we're all still unpaid volunteers working on projects in our spare time, just like anyone else on this list. We'd really need someone willing to put a significant amount of time and effort (and some $) into this.

[Cathal Garvey]

I think there are two entirely different models to consider, and they
call for different levels of commitment from participants.

The first is a "traditional" culture collection, where a central
resource manages stocks, orders and dispatching.

The second is a distributed or federated culture collection, where the
culture "collection" is actually just a directory of people with novel
strains or plasmids they are willing to share, which mediates contact
between the requestor/customer and the supplier.

The first would require inordinate work from one small group. The second
would require less work, but more engagement, from a larger group. A
system like this would suck if people offered strains and didn't fulfil
"orders". However, strains would list *all* suppliers, so if I got
plasmid X from Nathan and added myself as a supplier, Bryan could put an
order for either Nathan or I.

Looking at it like this, it becomes a web-dev problem rather than a
freezer-space problem; code a system where requests become tickets that
can be "claimed" by a willing supplier from the available pool, and
where people can add themselves as suppliers for new strains or plasmids
easily.

And, give it a nice interface like Thingiverse, a nice short/concise set
of "Conditions of Use", and a default-open license (don't invite
squabbling about "rights" on a *sharing* platform).

On 05/10/12 19:08, Patrik D'haeseleer wrote:
> Not speaking for all of BioCurious, but I'd say there is definitely *interest*, yes.
>
> The main problem is that setting up and running a resource like this would be a lot of work, and we're all still unpaid volunteers working on projects in our spare time, just like anyone else on this list. We'd really need someone willing to put a significant amount of time and effort (and some $) into this.
>

[Bryan Bishop]

On Mon, Oct 8, 2012 at 4:24 AM, Cathal Garvey <cathal...@gmail.com> wrote:
> Looking at it like this, it becomes a web-dev problem rather than a
> freezer-space problem; code a system where requests become tickets that
> can be "claimed" by a willing supplier from the available pool, and
> where people can add themselves as suppliers for new strains or plasmids
> easily.

Why not just make sure the cultures are maximally distributed between
people willing to have repositories?

[Josiah Zayner]

How about this:
http://www.the-odin.com/ocondb/listings.php?

A centralized database with a decentralized collection. People can charge whatever they want. Shipping is like $2-3 so I was thinking something like $5 is very reasonable. I started listing some things I have, will continue as I have more time.

Sign-up test it out and let me know what you think. Improvements &c.

[Cathal Garvey]

Wowza, where'd that thing come from? :D

On 08/10/12 18:03, Josiah Zayner wrote:
> How about this:
> http://www.the-odin.com/ocondb/listings.php?
>
> A centralized database with a decentralized collection. People can charge
> whatever they want. Shipping is like $2-3 so I was thinking something like
> $5 is very reasonable. I started listing some things I have, will continue
> as I have more time.
>
> Sign-up test it out and let me know what you think. Improvements &c.
>
>
> On Monday, October 8, 2012 9:29:43 AM UTC-5, Bryan Bishop wrote:
>>

>> On Mon, Oct 8, 2012 at 4:24 AM, Cathal Garvey <cathal...@gmail.com<javascript:>>

>> wrote:
>>> Looking at it like this, it becomes a web-dev problem rather than a
>>> freezer-space problem; code a system where requests become tickets that
>>> can be "claimed" by a willing supplier from the available pool, and
>>> where people can add themselves as suppliers for new strains or plasmids
>>> easily.
>>
>> Why not just make sure the cultures are maximally distributed between
>> people willing to have repositories?
>>
>> - Bryan
>> http://heybryan.org/
>> 1 512 203 0507
>>
>

[Nathan McCorkle]

On Mon, Oct 8, 2012 at 3:23 PM, Cathal Garvey <cathal...@gmail.com> wrote:
> Wowza, where'd that thing come from? :D
>
> On 08/10/12 18:03, Josiah Zayner wrote:
>> How about this:
>> http://www.the-odin.com/ocondb/listings.php?

seems alright, how could it be improved, user-experience wise and
library/code wise (Bryan).

[Bryan Bishop]

On Mon, Oct 8, 2012 at 12:03 PM, Josiah Zayner <josiah...@gmail.com> wrote:
> How about this:
> http://www.the-odin.com/ocondb/listings.php?

You have a pretty serious sql injection flaw going on there:

http://www.the-odin.com/ocondb/item_display.php?item_id=7'%20OR%201='1&instance_no=1
http://www.the-odin.com/ocondb/item_display.php?item_id=7'&instance_no=1

just fyi

[Bryan Bishop]

On Mon, Oct 8, 2012 at 2:51 PM, Bryan Bishop <kan...@gmail.com> wrote:
> On Mon, Oct 8, 2012 at 12:03 PM, Josiah Zayner <josiah...@gmail.com> wrote:
>> How about this:
>> http://www.the-odin.com/ocondb/listings.php?
>
> You have a pretty serious sql injection flaw going on there:
>
> http://www.the-odin.com/ocondb/item_display.php?item_id=7'%20OR%201='1&instance_no=1
> http://www.the-odin.com/ocondb/item_display.php?item_id=7'&instance_no=1
>
> just fyi

You can see it in action here:

http://opendb.svn.sourceforge.net/viewvc/opendb/opendb/trunk/item_display.php?revision=973&view=markup&sortby=rev&sortdir=down

(viewvc.cgi is still terrible; why is sourceforge still using it?)

[Josiah Zayner]

Thanks for looking at it.

I don't see the SQL injection you will have to be more obvious I am not very good with this whole coding thing.

Basically I just took (Open Media Collector's Database) OpenDB and hacked it up a teensy bit.