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

[Patrik D'haeseleer]

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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