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 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@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@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@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@gmail.com> wrote:
Hi all,

You may have noticed that Keoni Gandall dropped of a brand new (ish) OpenTrons OT-2 liquid handling robot 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:


Patrik