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

Tue Oct 9 21:48:29 PDT 2018

Hey Jenny.

We talked tonight, but just to put it in writing (and give some space for
anybody to object): go for it. We're only using the shelves against the
back wall.

-Tim

On Mon, Oct 8, 2018, 10:33 PM Jenny Ryan <tunabananas at gmail.com> wrote:

> 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
>
> `~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`
> "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"
> ~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`~`
>
>
> 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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