[sudo-discuss] [CCLmembers] Re: New OpenTrons OT-2 in Sudo/CCL!

[Jenny Ryan]

A sudoer mentioned that the OpenTrons folks may have some excess shelving
they're looking to get rid of?

It's highly needed in The Village's donation dropoff area next to CCL's
spot in the basement at the base of the stairs. Any leads/donations
appreciated!

<3
Jenny

Help open a professional kitchen at the Omni Commons in Oakland!
https://omnicommons.org/kitchen

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"Technology is the campfire around which we tell our stories."
-Laurie Anderson

"Storytelling reveals meaning without committing the error of defining it."
 -Hannah Arendt

"To define is to kill. To suggest is to create."
-Stéphane Mallarmé

"Anything done for the first time unleashes a demon."
--Dave Sim, "Cerebus the Aardvark"
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On Sat, Oct 6, 2018 at 8:25 PM Tim Dobbs <timdobbs at gmail.com> wrote:

> I stand corrected - here's a link to the hardware repo:
> https://github.com/Opentrons/ot2
>
> I found some wiring schematics and EAGLE PCB design files for the pipette.
> Nothing as far as 3D models that I could see, but there may be something in
> there somewhere.
>
> -Tim
>
> On Sat, Oct 6, 2018, 12:26 PM Tim Dobbs <timdobbs at gmail.com> wrote:
>
>> As near as I can tell, the OT-2 is not open source. All of OpenTrons's
>> open source stuff seems built around the OT-One. The electronic pipette
>> from the OT-2 runs on a stepper motor, so we could probably rig something
>> up (once we get around authentication), but it would be a hack more than
>> plug-and-play.
>>
>> I sent OpenTrons a note to confirm.
>>
>> -Tim
>>
>> On Thu, Oct 4, 2018 at 5:25 PM Patrik D'haeseleer <patrikd at gmail.com>
>> wrote:
>>
>>> Do you know if the OT-2 hardware is still Open Source, and if so, where
>>> to find the design files for the pipettes, for example? Would be great if
>>> we could adapt existing pipettes instead...
>>>
>>> For the mushrooms, Alan uses a little disposable hard plastic pestle
>>> that's just the same shape as the bottom of an Eppy tube (and then he
>>> thoroughly cleans and autoclaves the pestles for reuse). Disposable "pellet
>>> pestles" are around $1 a piece, and Sigma sells a cordless motor
>>> <https://www.sigmaaldrich.com/catalog/product/sigma/z359971> for them -
>>> not sure if it has an eject button though. If we can automatically insert
>>> and eject disposable pestles, they shouldn't really pose any more
>>> cross-contamination issue as pipette tips do...
>>>
>>> Alternatively, looks like there are some enzymatic DNA extraction
>>> protocols for fungi using chitinase - it would be great if we could find
>>> one that didn't require mechanical grinding to release the DNA.
>>>
>>> Patrik
>>>
>>> Patrik
>>>
>>> On Thu, Oct 4, 2018 at 10:27 AM Keoni Gandall <koeng101 at gmail.com>
>>> wrote:
>>>
>>>> Hey Patrik,
>>>>
>>>> I have a single p10 and a broken multichannel 300ul that I'll bring
>>>> over (I bet you may be able to fix the multichannel 300ul).
>>>>
>>>> I'll also think of a good way to automate maceration of mushrooms. I
>>>> feel like it may be a bit difficult due to cross-contamination issues.
>>>>
>>>> Keoni
>>>>
>>>> On Thu, Oct 4, 2018 at 3:58 AM Patrik D'haeseleer <patrikd at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Keoni - do you have any pipettes for the OT-2?
>>>>>
>>>>> We installed it right on the boundary between CCL and Sudo for now.
>>>>> Once we start doing real experiments, we should move it into the wetlab
>>>>> though.
>>>>>
>>>>> We also happen to have a Biometra TRobot, which is essentially a
>>>>> thermocycler with an automated lid, so it can be easily incorporated into a
>>>>> liquid handling robot. That should give us an ideal platform for PCR
>>>>> applications on the Opentrons...
>>>>>
>>>>> DNA barcoding of mushroom species is probably our #1 killer app for
>>>>> this robot. When Alan Rockefeller comes back from his current outing
>>>>> throughout Mexico, he will likely bring several hundred mushroom samples
>>>>> with him, all of which will need to be submitted to PCR amplification and
>>>>> Sanger sequencing. Alan usually mashes each sample with a little plastic
>>>>> pestle in an Eppendorf tube - not sure how to replicate that on the robot,
>>>>> but we could brainstorm a little device to macerate mushroom samples...
>>>>>
>>>>> Patrik
>>>>>
>>>>> On Sun, Sep 30, 2018 at 6:42 PM Keoni Gandall <koeng101 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> The hardware issue should be easily solved with a little hack that
>>>>>> deactivates OpenTrons pipette-verification (it worked before a certain
>>>>>> software update).
>>>>>>
>>>>>> The hope is that the robot can help bridge the gap between the
>>>>>> software folks at SudoRoom and wetware folks in CCL.
>>>>>>
>>>>>> I'll at hands on workshop as well - come find me in the red polo if
>>>>>> you'd like to talk about the machine!
>>>>>>
>>>>>> On Sun, Sep 30, 2018 at 6:34 PM Patrik D'haeseleer <patrikd at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> You may have noticed that Keoni Gandall dropped of a brand new (ish) OpenTrons
>>>>>>> OT-2 liquid handling robot <http://opentrons.com/ot-2>recently!
>>>>>>> This is the much smaller and newer sibling to the giant 5'x5' robot CCL has
>>>>>>> in the basement. It is currently sitting in SudoRoom, and may or may not
>>>>>>> have a hardware or electrical issue to be diagnosed first.
>>>>>>>
>>>>>>> Also, if you'd like to learn how to use this machine, OpenTrons is
>>>>>>> running a *FREE HANDS-ON WORKSHOP* to learn how to use the OT-2
>>>>>>> tomorrow at the Mission Bay Conference Center; Monday 2-4pm. Registration
>>>>>>> is free, but space may run out, so I would recommend you sign up asap:
>>>>>>>
>>>>>>>
>>>>>>> https://www.eventbrite.com/e/opentrons-hands-on-workshop-tickets-49398612580
>>>>>>>
>>>>>>> Patrik
>>>>>>>
>>>>>> --
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