DIYBio meetup 2: 7:00 - 9:00 Thursday, 12 June 2008 @ BetaHouse

[Mackenzie Cowell]

Hi DIYBioers,

Here's the rough agenda for the upcoming Meetup this week (Note location change!):

DIYbio Cambridge MeetUp #2 @ BetaHouse
7:00pm - 9:00pm Thursday 12 June 2008
13 Magazine st, apt. 2, Cambridge, MA 02139

BetaHouse is a co-working space that I work at and that has graciously agreed to host the event.  It will work better than Asgard because we're going to be getting our hands dirty:

= AGENDA =

== 7:00 - 8:00 DNA Extraction in the Kitchen ==
* Read the attached protocol: MAKE vol 07 - Kitchen Counter DNA Lab
* The only thing you'll need is to bring your favorite organic material (tuna, banana, cow heart... but keep it safe, please)

== 8:00 - 9:00 - DIYbio Hackathon ==
* list and tag all DIYbio protocols and resources known to the interwebs
* Bring your laptops
* add them to del.icio.us: consensus tag "DIYbio" + "protocol", "equipment", "tools" etc.
* feel free to get started early
* p.s. bryan bishop: we want to produce a high-quality, highly-granular collection of links, not a gigantic disorganized grab-bag

I'll get some pizza for us all (we'll eat while discussing the DNA extraction), so please RSVP so I can get a good headcount.

See you all thursday!
Mac

[Mackenzie Cowell]

Also:

DIYbio Meetup 2 on Upcoming: http://upcoming.yahoo.com/event/778635/

DIYbio Meetup 2 wiki:  http://openwetware.org/wiki/DIYbio:Meeting-June_2008

See you there.  Spread the word.

Mac

[Bryan Bishop]

On Monday 09 June 2008, Mackenzie Cowell wrote:
> == 8:00 - 9:00 - DIYbio Hackathon ==
> * list and tag all DIYbio protocols and resources known to the
> interwebs * Bring your laptops
> * add them to del.icio.us: consensus tag "DIYbio" + "protocol",
> "equipment", "tools" etc.
> * feel free to get started early
> * p.s. bryan bishop: we want to produce a high-quality,
> highly-granular collection of links, not a gigantic disorganized
> grab-bag

Hey now, that's not quite fair. :) If you have any constructive
suggestions on the grab bag, be my guest -- I've been lacking creative
insights into organizing something like that. A collection of links
versus a collection of links plus the actual content has little
difference. :-/ I'm wondering where I can dump my 12,000 bookmarks re:
protocols (that are relevant - maybe 1/12th) to this little 'hackathon'
on del.icio.us or whatever it is. Here is my ADR file:

http://heybryan.org/bookmarks/2008-06-09_opera6.adr

So if you want to play with that, it might be a good place to start.

An older copy in HTML form:
http://heybryan.org/bookmarks/bookmarks-old2/toc.html#3-top

Yeah, that HTML version is very, very old. So, have fun. :)

- Bryan
________________________________________
http://heybryan.org/

[benjamin...@gmail.com]

Photos:

http://www.flickr.com/photos/worldpeace/

[Mackenzie Cowell]

Howdy Garagistas,

Thanks to everyone who came out last night to the second meetup - the energy and excitement you all brought was fantastic and I think we are off to a solid start.  Besides precipitating DNA from oatmeal, apple, and human saliva, we had a great time tentatively planning out the next couple of months and establishing a draft mission statement and roadmap with milestones:

DIYbio.org Mission (draft!): To enable enthusiastic amatuers to do iGEM-level work in a responsible, safe way.  This involves producing educational content, developing successful DIY biotech protocols, developing a larger "process" for conducting diybio work in a safe & open way, and perhaps eventually producing kits and materials.

Over the next month we will put together a comprehensive list of DIY resources that already exist online - protocols, equipment instructions, educational material - and test out some of the most promising experimental techniques, publishing our progress under the auspices of diybio.org.  We picked out 3 milestones to work towards:

1. Identify the DIYbio model organism. 
* It needs to be safe, forgiving, interesting, and available
* Candidates include yeast (humanity has a long history of engineering it, and it's commonly available), moss (p. patens?), E. coli (good because it's well understood, bad because it could be pathogenic)

2. Conduct and informally publish a reproducable "$100 transformation", inserting something like GFP into the model organism, or a similar experiment that would be trivial in an academic lab.

3. Form a 2009 DIYbio iGEM team.

I tentatively propose another informal meetup next thursday at 7:00, here at BetaHouse again.

I added photos to a new DIYbio flickr group: http://flickr.com/groups/diybio/.  Join it and add your stuff.

I've never been on a list that had too little traffic - so please don't be afraid to use this one.  Bring on the emails.  Ask questions.  Don't feel stupid.  Feel like we are establishing an interesting and educational public record simply by sending emails to one another:) 


See you on the list!
Mac

[Topher Cyll]

I could make next Thursday.

I wonder, is there a better way for us to handle picking meeting
times/rsvping? I hate to spam everyone with these "me too" emails...

Toph

[Jason Bobe]

RSVP Here:
http://spreadsheets.google.com/viewform?key=pLE3-SQpKAYAWOKMCHoTPLg&email=true

Or fill out this html form (may not be viewable in all email clients):

<iframe src="http://spreadsheets.google.com/embeddedform?key=pLE3-SQpKAYAWOKMCHoTPLg&hl=en" width="300" height="497" frameborder="0" marginheight="0" marginwidth="0">Loading...</iframe>


Best,
Jason Bobe

[Jason Bobe]

I'll try that one more time:

The next DIYbio meeting is Thursday June 19th 7pm @ BetaHouse in Cambridge MA.

If you plan on attending, please RSVP by providing a few details below:
        

If you cannot view this form properly, you can fill it out here:
http://spreadsheets.google.com/viewform?key=pLE3-SQpKAYAWOKMCHoTPLg&email=true

Name

Email

Comments

[Mackenzie Cowell]

Here's the public published version of that spreadsheet, for posterity: http://spreadsheets.google.com/pub?key=pLE3-SQpKAYAWOKMCHoTPLg

On Fri, Jun 13, 2008 at 3:20 PM, Jason Bobe <jaso...@gmail.com> wrote:

I'll try that one more time:

The next DIYbio meeting is Thursday June 19th 7pm @ BetaHouse in Cambridge MA.

If you plan on attending, please RSVP by providing a few details below:
        

If you cannot view this form properly, you can fill it out here:

http://spreadsheets.google.com/viewform?key=pLE3-SQpKAYAWOKMCHoTPLg&email=true

Name

Email

Comments

[William Heath]

Hi All,

I am soooo jealous of what your doing!!!!  I wish you could like broadcast the meeting on the internet live so I could be there in a cyber way :(  Anyone want to do that?  Its completely amazing what your doing!

-Tim

P.S.

I am in Palo Alto, CA and would love to startup a DIY bio group out here, let me know if you have ideas or contacts for me to do this.

[Bryan Bishop]

On Friday 13 June 2008, Mackenzie Cowell wrote:
> DIYbio.org Mission (draft!): To enable enthusiastic amatuers to do
> iGEM-level work in a responsible, safe way.  This involves producing
> educational content, developing successful DIY biotech protocols,
> developing a larger "process" for conducting diybio work in a safe &
> open way, and perhaps eventually producing kits and materials.

So, one of the ideas I was having for the do-it-yourself biotech kits is
the bioreactor that I mentioned on this mailing list a few weeks ago. I
don't know why nobody has brought it up, but it's a pretty useful idea
for modularizing all of these components and protocols down into
something more usable for the amateur and so on. Instead of requiring
big, bulky setups for typical benchwork, let's reconceptualize it and
integrate the functionality into cells themselves. For example, there's
the in vitro DNA synthesizer:

http://heybryan.org/mediawiki/index.php/In_vitro_DNA_synthesizer
http://heybryan.org/mediawiki/index.php/Bioreactors

The idea there would be that we could use simple input into a biological
system to synthesize DNA in vitro. Hopefully in vivo. That would be
even better. But again we come across the purification issues that we
were discussing earlier. There's also another problem that I have been
running into in the design of the system, mostly the polymerase that
would be necessary, but I've been routing around this particular set
back by investigating the integration of phosphodiester chemistry into
biosynthetic pathways (DTD, for starters, looks proteotoxic, so that's
not a good start).

So that larger process, again, can be on the same scale as debian using
the same general software infrastructure, such as with content
repositories and automated tools, since the majority of biological
informatics out there on the internet is already digital it's made all
that much more easy.

> Over the next month we will put together a comprehensive list of DIY
> resources that already exist online - protocols, equipment
> instructions, educational material - and test out some of the most
> promising experimental techniques, publishing our progress under the
> auspices of diybio.org.  We picked out 3 milestones to work towards:

I'll volunteer for those massive reviews. ;-)

> 1. Identify the DIYbio model organism.

There can be more than one.

> * It needs to be safe, forgiving, interesting, and available
> * Candidates include yeast (humanity has a long history of
> engineering it, and it's commonly available), moss (p. patens?), E.
> coli (good because it's well understood, bad because it could be
> pathogenic)

All good options.

> 2. Conduct and informally publish a reproducable "$100
> transformation", inserting something like GFP into the model
> organism, or a similar experiment that would be trivial in an
> academic lab.

So, what I remember from transformation protocols, there's a lot of
proprietary chemicals involved, but that should be abstractable away
from the system anyway. I would prefer a $0, where all of the materials
are biologically produced and purified, or at least a strategy to
eventually come to that, and then the $100 version being one where
we're "almost there" (and by almost I mean, "well, we have a map").

> 3. Form a 2009 DIYbio iGEM team.

:) I'd like to go.

[Bryan Bishop]

On Friday 13 June 2008, William Heath wrote:
> I am soooo jealous of what your doing!!!!  I wish you could like
> broadcast the meeting on the internet live so I could be there in a
> cyber way :( Anyone want to do that?  Its completely amazing what
> your doing!

Since it's Boston I'm sure there's enough local people who know how to
set up live streaming video from a web cam. There are also many servers
that would be willing to broadcast the stream freely.

[Sean Hobin]

Hey guys,

Sorry I wasn't able to make yesterday's meeting.  As I've been going through the process of setting up an iGem team of my own, I'm intrigued about the idea of a DIYbio iGem team.  How would that work?  iGem has really been marketed as an undergraduate competition.  Of course HS teams have also been welcome.  Does that mean only certain people from the DIYbio group would be able to participate?

Sean

[Bryan Bishop]

On Friday 13 June 2008, Sean Hobin wrote:
> Sorry I wasn't able to make yesterday's meeting.  As I've been going
> through the process of setting up an iGem team of my own, I'm
> intrigued about the idea of a DIYbio iGem team.  How would that work?
>  iGem has really been marketed as an undergraduate competition.  Of
> course HS teams have also been welcome.  Does that mean only certain
> people from the DIYbio group would be able to participate?

I would think that if you're able to show up in Hong Kong in August,
then that you would be allowed to participate. Why not? Let's put
everybody's name on the team. That's the idea of collaboration, right?
As for actually arranging transportation, that might be a personal
means issue, or maybe some of us in educational institutions can go
poke some advisors for the money to attend, etc.

[Mario Raya]

First i will say hi. Hi!

Thanks to everyone who came out last night to the second meetup - the energy and excitement you all brought was fantastic and I think we are off to a solid start.  Besides precipitating DNA from oatmeal, apple, and human saliva, we had a great time tentatively planning out the next couple of months and establishing a draft mission statement and roadmap with milestones:

I wish i could go to the meetings but i have class on Thursdays until July 4th

 

...

1. Identify the DIYbio model organism. 
* It needs to be safe, forgiving, interesting, and available
* Candidates include yeast (humanity has a long history of engineering it, and it's commonly available), moss (p. patens?), E. coli (good because it's well understood, bad because it could be pathogenic)

It may be possible to work with a cryophile, everyone has a fridge and this would take out the pathogenic factor.

 

2. Conduct and informally publish a reproducable "$100 transformation", inserting something like GFP into the model organism, or a similar experiment that would be trivial in an academic lab.

BioRad has a protocol and kit for bacterial transformation, this is of course proprietary material but it can be used as a base for the work, it is sold for educational purposes at $88.

[Jason Morrison]

Hi Tim,

Fantastic!  It would be great to start DIYbio interest groups in more cities.  All you really need is a few interested folks, a place to meet up, and a loose agenda.  The two projects at http://openwetware.org/wiki/DIYbio (kit reviews, model organism research) are both excellent candidates for distributed work and have relatively low barriers to entry, so it may be very fruitful to center discussions on those; perhaps hold mini "kit review jamborees" or "model organism research parties."

Not sure on finding the folks or the space, but I imagine you can make great connections for both of these with folks at http://pimm.wordpress.com/2008/06/04/biobarcamp-august-6-7-the-institute-for-the-future-palo-alto/

Cheers,

Jason

--
Jason Morrison
jason.p....@gmail.com
http://jayunit.net
(585) 216-5657

[Jason Morrison]

BioRad has a protocol and kit for bacterial transformation, this is of course proprietary material but it can be used as a base for the work, it is sold for educational purposes at $88.

Mario, this sounds great - do you have a link?  Might you be able to post it to del.icio.us/tag/diybio or this list?

Thanks!

Jason 

[James Gagnon]

hello,

sorry i couldn't make the meeting, i had a quick details question about your DNA prep.  after running through the MAKE protocol, did you by chance run it on a gel to see quality?  run it on a spec to see purity?

thanks,

-jamie

On Fri, Jun 13, 2008 at 2:56 PM, Mackenzie Cowell <maco...@gmail.com> wrote:

[Mario Raya]

The kit is part of their Explorers project, intended for high school and college educators, here is the link (a little long):

http://www.biorad.com/B2B/BioRad/product/br_category.jsp?BV_SessionID=@@@@1989018550.1213715730@@@@&BV_EngineID=ccceadeeghhdijdcfngcfkmdhkkdflm.0&categoryPath=%2fCatalogs%2fLife+Science+Education%2fClassroom+Kits%2fpGLO+Bacterial+Transformation+Kit&catLevel=4&divName=Corporate&loggedIn=false&lang=English&country=HQ&catOID=-18873&isPA=false&serviceLevel=Lit+Request

They have plenty of experiments that are intended to high schools, some require specialized equipment, some not so much, is worthy to look.

[Jason Bobe]

This is fantastic, thanks Mario.

Jason Bobe