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

[Tim Dobbs]

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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