[sudo-discuss] Coming up at CCL!: CCL has a lab robot! Now what?

Wed Jan 27 09:57:42 PST 2016

hi all,

one last thing from CCL - they now have a lab robot!

if you're interested in learning more about this robot and possibly being a
part of its assembly, operation, and programming, come to the protein
modeling meetup this fri 1/29 at 7PM:
http://www.meetup.com/Counter-Culture-Labs/events/228129282/ . in addition
to protein modeling, this meetup will include discussion, plans, and next
steps for the robot.

Forwarded conversation
Subject: [CCL] CCL has a lab robot! Now what?
------------------------

From: *Patrik D'haeseleer* <patrikd at gmail.com>
Date: Mon, Jan 18, 2016 at 9:34 PM
To: "cclmembers at googlegroups.com" <cclmembers at googlegroups.com>, "
counterculturelabs at googlegroups.com" <counterculturelabs at googlegroups.com>,
"cultlabsboard at googlegroups.com" <cultlabsboard at googlegroups.com>

As most of you probably have heard, CCL acquired a large OpenTrons
<http://opentrons.com/>lab robot (pics below), thanks to our friends
at Arcturus
Bio <https://www.arcturus.io/>. Which is awesome, except that we don't
really have space for it, or anyone who knows how to run it at the moment.
:-D

If we are going to keep this beast, we should also put together a core
group of people interested in care and feeding of a lab robot. *PLEASE
REPLY TO THIS EMAIL IF YOU'D LIKE TO BE INVOLVED!* There is a bit of a
community around the OpenTrons platform, and I'm sure we could come up with
some interesting applications.

Unfortunately, the robot was too large to fit in the truck, so it had to be
substantially disassembled to bring it over. So the first thing we should
do it to reassemble it. But before we can do that, we need to *figure out
WHERE to put it.*

Couple of options:

1) Install it on one of the lab benches. This would take up most of a lab
bench, plus some space next to it for the freezer.

2) If we lose the freezer, we should be able to cut down the axes so it
fits on about half a lab bench.

3) We could find some place elsewhere in the building to put it - likely in
the basement.

Welcome to any other suggestions!

Here's some pic of the robot in its full, functioning glory:

And here's its current sorry state, disassembled and taking up way too much
space:

Patrik

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----------
From: *Maureen Muldavin* <muldavin.m at gmail.com>
Date: Mon, Jan 18, 2016 at 10:03 PM
To: Patrik D'haeseleer <patrikd at gmail.com>
Cc: "cclmembers at googlegroups.com" <cclmembers at googlegroups.com>, "
counterculturelabs at googlegroups.com" <counterculturelabs at googlegroups.com>,
"cultlabsboard at googlegroups.com" <cultlabsboard at googlegroups.com>

I'm excited about the robot! I also have robot parts in my car still. It
was raining too hard yesterday to carry them inside.

On Mon, Jan 18, 2016 at 9:34 PM, Patrik D'haeseleer <patrikd at gmail.com>
wrote:

> As most of you probably have heard, CCL acquired a large OpenTrons
> <http://opentrons.com/>lab robot (pics below), thanks to our friends at Arcturus
> Bio <https://www.arcturus.io/>. Which is awesome, except that we don't
> really have space for it, or anyone who knows how to run it at the moment.
> :-D
>
> If we are going to keep this beast, we should also put together a core
> group of people interested in care and feeding of a lab robot. *PLEASE
> REPLY TO THIS EMAIL IF YOU'D LIKE TO BE INVOLVED!* There is a bit of a
> community around the OpenTrons platform, and I'm sure we could come up with
> some interesting applications.
>
> Unfortunately, the robot was too large to fit in the truck, so it had to
> be substantially disassembled to bring it over. So the first thing we
> should do it to reassemble it. But before we can do that, we need to *figure
> out WHERE to put it.*
>
> Couple of options:
>
> 1) Install it on one of the lab benches. This would take up most of a lab
> bench, plus some space next to it for the freezer.
>
> 2) If we lose the freezer, we should be able to cut down the axes so it
> fits on about half a lab bench.
>
> 3) We could find some place elsewhere in the building to put it - likely
> in the basement.
>
> Welcome to any other suggestions!
>
> Here's some pic of the robot in its full, functioning glory:
>
> And here's its current sorry state, disassembled and taking up way too
> much space:
>
> 
> Patrik
>
> --
> You received this message because you are subscribed to the Google Groups
> "CCult Lab's Board" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to CultLabsBoard+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>

----------
From: *Kathy Buehmann* <kathy.buehmann at gmail.com>
Date: Mon, Jan 18, 2016 at 10:30 PM
To: Maureen Muldavin <muldavin.m at gmail.com>
Cc: counterculturelabs at googlegroups.com, cclmembers at googlegroups.com, "
cultlabsboard at googlegroups.com" <cultlabsboard at googlegroups.com>, Patrik
D'haeseleer <patrikd at gmail.com>

I'm interested in helping reassemble the robot and figuring out how to
operate/care for it.

I'll put a sign up on it tmr for those who don't read their email :-P

I'd love to have a group of 4-5 people who are educated on and interested
in caring for the robot, and whose names are written boldly on it somewhere
for when newbies are ready to give it a try.

Real vegan cheese, open insulin, alex n, mary/maureen, and other projects
out there: do you have any foreseeable need for a high thruput liquid
handler in the near-ish future?

Kathy

----------
From: *Maureen Muldavin* <muldavin.m at gmail.com>
Date: Mon, Jan 18, 2016 at 10:39 PM
To: Kathy Buehmann <kathy.buehmann at gmail.com>
Cc: cclabs <counterculturelabs at googlegroups.com>, Counter Culture Labs
Members <cclmembers at googlegroups.com>, "cultlabsboard at googlegroups.com" <
cultlabsboard at googlegroups.com>, Patrik D'haeseleer <patrikd at gmail.com>

I want to plan to have classes in robot operation by May. I think that open
insulin might have some use for the robot at some point, but not sure when.
I'm really interested in learning how to use a liquid handler robot.

I strongly feel that we should keep the robot. I have a feeling that once
Noel's protein software group gets going, we might start to attract more
programmers and engineers into the lab. The robot can be a bridge between
the fields of engineering and biology.

----------
From: *Mary Ward* <maryhbw at gmail.com>
Date: Tue, Jan 19, 2016 at 6:25 AM
To: Kathy Buehmann <kathy.buehmann at gmail.com>
Cc: Maureen Muldavin <muldavin.m at gmail.com>,
counterculturelabs at googlegroups.com, cclmembers at googlegroups.com, "
cultlabsboard at googlegroups.com" <cultlabsboard at googlegroups.com>, Patrik
D'haeseleer <patrikd at gmail.com>

Hi All,

Marc said he was interested in using the robot for assembly of a parts
similar to Biobrick. He said he would be attending next weeks delegate
meeting to request a spot for the robot in the basement because this sucker
is big.

-Mary

Sent from my iPhone

On Jan 18, 2016, at 10:30 PM, Kathy Buehmann <kathy.buehmann at gmail.com>
wrote:

I'm interested in helping reassemble the robot and figuring out how to
operate/care for it.

I'll put a sign up on it tmr for those who don't read their email :-P

I'd love to have a group of 4-5 people who are educated on and interested
in caring for the robot, and whose names are written boldly on it somewhere
for when newbies are ready to give it a try.

Real vegan cheese, open insulin, alex n, mary/maureen, and other projects
out there: do you have any foreseeable need for a high thruput liquid
handler in the near-ish future?

Kathy
On Jan 18, 2016 10:04 PM, "Maureen Muldavin" <muldavin.m at gmail.com> wrote:

> I'm excited about the robot! I also have robot parts in my car still. It
> was raining too hard yesterday to carry them inside.
>
> On Mon, Jan 18, 2016 at 9:34 PM, Patrik D'haeseleer <patrikd at gmail.com>
> wrote:
>
>> As most of you probably have heard, CCL acquired a large OpenTrons
>> <http://opentrons.com/>lab robot (pics below), thanks to our friends at Arcturus
>> Bio <https://www.arcturus.io/>. Which is awesome, except that we don't
>> really have space for it, or anyone who knows how to run it at the moment.
>> :-D
>>
>> If we are going to keep this beast, we should also put together a core
>> group of people interested in care and feeding of a lab robot. *PLEASE
>> REPLY TO THIS EMAIL IF YOU'D LIKE TO BE INVOLVED!* There is a bit of a
>> community around the OpenTrons platform, and I'm sure we could come up with
>> some interesting applications.
>>
>> Unfortunately, the robot was too large to fit in the truck, so it had to
>> be substantially disassembled to bring it over. So the first thing we
>> should do it to reassemble it. But before we can do that, we need to *figure
>> out WHERE to put it.*
>>
>> Couple of options:
>>
>> 1) Install it on one of the lab benches. This would take up most of a lab
>> bench, plus some space next to it for the freezer.
>>
>> 2) If we lose the freezer, we should be able to cut down the axes so it
>> fits on about half a lab bench.
>>
>> 3) We could find some place elsewhere in the building to put it - likely
>> in the basement.
>>
>> Welcome to any other suggestions!
>>
>> Here's some pic of the robot in its full, functioning glory:
>> <20150708_192355.jpg><Last Import - 13 of 30.jpg>
>>
>> And here's its current sorry state, disassembled and taking up way too
>> much space:
>> <20160118_212334.jpg>
>> 
>> Patrik
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "CCult Lab's Board" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to CultLabsBoard+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
> --
> You received this message because you are subscribed to the Google Groups
> "CCult Lab's Board" group.
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> email to CultLabsBoard+unsubscribe at googlegroups.com.
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>
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----------
From: *Noel Carrascal* <noelcarrascal at gmail.com>
Date: Tue, Jan 19, 2016 at 11:12 AM
To: Maureen Muldavin <muldavin.m at gmail.com>
Cc: Kathy Buehmann <kathy.buehmann at gmail.com>, cclabs <
counterculturelabs at googlegroups.com>, Counter Culture Labs Members <
cclmembers at googlegroups.com>, "cultlabsboard at googlegroups.com" <
cultlabsboard at googlegroups.com>, Patrik D'haeseleer <patrikd at gmail.com>

Now that we have a Robot, and a protein software group on the making, and
that my name was mention in a previous email,
I would like to emphasize the importance of volunteers to turn this
equipment and project into something useful to the lab.

I have realized that it takes a lot of work setting up, deploying, testing
and maintaining the software tools for the whole lab to
benefit.  I worked with three new tenure-track faculty during my PhD, and
it took months of installing, scripting and debugging
before the software tools could be put to work on projects, and longer to
turn them  into publications. Outside academia, it should
take less time and work.

At CCL and Biocurious, I have tried to help people with the CRISPR-CAS9 and
Insulin, only to find out that I cannot do this
by myself, even with the know-how. CRISPR-Cas9 is too large a protein to do
much on a personal computer, and I do not
have the required software to build a linker for the insulin project.

So, I would like to take this opportunity to encourage volunteers who want
to work on the robot or computational protein design to
join me for a presentation on January 29th. The meeting is on Protein
Structure, visualization, modeling and design
<http://www.meetup.com/Counter-Culture-Labs/events/228129282/> and it is on
meetup.com. That will be the starting point for organizing volunteer
efforts for the software side of the Counter Culture Labs.
People of all levels of skill are welcome. I will provide papers, book
references and guidance for those who are not experts and want to learn
the fundamentals of the biophysics of protein dynamics and design.

Noel

----------
From: *Maureen Muldavin* <muldavin.m at gmail.com>
Date: Tue, Jan 19, 2016 at 12:37 PM
To: Noel Carrascal <noelcarrascal at gmail.com>
Cc: Kathy Buehmann <kathy.buehmann at gmail.com>, cclabs <
counterculturelabs at googlegroups.com>, Counter Culture Labs Members <
cclmembers at googlegroups.com>, "cultlabsboard at googlegroups.com" <
cultlabsboard at googlegroups.com>, Patrik D'haeseleer <patrikd at gmail.com>

I've announced the meetup and posted it to several biohacker Facebook
groups. I also submitted it to the funcheap website. I'll post it on CCL's
Facebook and start marketing the class over twitter later tonight. I was
planning to do a 2-week class marketing push anyways.

Maureen

----------
From: *Patrik D'haeseleer* <patrikd at gmail.com>
Date: Tue, Jan 19, 2016 at 1:51 PM
To: Maureen Muldavin <muldavin.m at gmail.com>
Cc: Kathy Buehmann <kathy.buehmann at gmail.com>, Noel Carrascal <
noelcarrascal at gmail.com>, "cultlabsboard at googlegroups.com" <
cultlabsboard at googlegroups.com>, cclabs <counterculturelabs at googlegroups.com>,
Counter Culture Labs Members <cclmembers at googlegroups.com>

Excellent - don't forget about the Bay Area Science calendar as well!

We could use some help making the class listing on Meetup a bit more
attractive. I pasted in some images,  but the meetup editor is rather
minimalistic (no image resizing - really? ) I believe you can paste in from
Word or a web page though,  and it'll preserve some of the formatting that
you cannot edit directly in Meetup (sigh)...

Patrik

>>>>>> And here's its current sorry state, disassembled and taking up way
too much space:
>>>>>>
>>>>>> 
>>>>>> Patrik
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
Groups "CCult Lab's Board" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
send an email to CultLabsBoard+unsubscribe at googlegroups.com.
>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>>
>>>>> --
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Groups "CCult Lab's Board" group.
>>>>> To unsubscribe from this group and stop receiving emails from it,
send an email to CultLabsBoard+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>>
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Groups "Counter Culture Labs" group.
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.
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>>
>>
>
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