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

[Tim Dobbs]

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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