Re: [DIYbio] Opentrons OT-2 release

Thanks for the updated link.

Reddit isn't loading on my computer right now for some reason, probably a bad cookie.

Anyway I believe this is the thread, https://www.reddit.com/r/labrats/comments/8ii734/opentrons_new_robot/

Someone half way down mentioned they were trying to turn it into a colony picker.  I'm sure Ctrl+F will let you find the user.

On Thu, Jun 21, 2018 at 10:39 PM, Koeng <koen...@gmail.com> wrote:

Yea it's been moving around a bit. As I said, under constant development still. 

https://github.com/EndyLab/bionet-synthesis/blob/master/pipeline/colony_picking.py

Got a link to the reddit post? Would love to talk to them as well. The biggest issue in our lab for colony picking is the inconsistent lighting (we have windows) so making colony picking robust is more difficult than it would be to just have a simple box. 

If you take a look in our main pipeline, we have all steps to go from getting synthesis plates in to glycerol stocking clones running on OpenTrons. I just personally ran 960 unique plasmids through this week, and am aiming for ~1500 next week. We had some issues with the colony picking code (the grid layout on our plates is determined by colony density, but variation in our competent cell mixes screwed that. Don't let competent cells settle at the bottom of the trough, kids), so I picked about 700 yesterday. It's honestly not very difficult, and only took about 2 and a half hours. 

Sort of depends on how sterile you actually need it to be. In a rather clean corner of lab, we just sort keep the plates open (on the OT1, which is completely open). The 30 plates I checked out yesterday had absolutely no contamination. Though remember, that is for bacteria. In general, for cloning, it doesn't actually seem like that big of a deal as long as you use the materials quickly and use anitbiotic. I sometimes wipe with ethanol, but most of the time I am just constantly running them. 

Koeng

On Thursday, June 21, 2018 at 5:50:47 PM UTC-7, Dakota Hamill wrote:

Hi Koeng that github is 404.  I brought back up any DIYBio OpenTrons threads because I'm scheduling a demo tomorrow.  Saw someone on reddit that was also trying to develop the OT-2 as a colony picker.  Supposedly it has a camera built in?

Interested to know if anything has progressed on the work.  OpenTrons github doesn't seem to have many open protocols shared but perhaps I'm looking in the wrong place. Wish they had an 8-span P-1000.

Anyone have any experience with sterility inside the plexiglass cabinet it has outside of a laminar flow hood?  I think based on measurements they said the OT-2 rarely fits inside biosafety cabinets.

I don't know if they have a UV light inside or if an aftermarket plus enough ethanol would do the trick.

On Tue, May 15, 2018 at 10:18 PM, Koeng <koen...@gmail.com> wrote:

I can also just provide the actual git repo of where all development is happening:

https://github.com/EndyLab/bionet-synthesis/blob/master/pipeline/testing/colony_picking/col_picking.py 

feel free to clone and pull request any changes. Or just recommend them here and we can change the code around.

@Dakota if you are careful with your calibrations, the OT1 can definitely colony pick. The OT2 is even more accurate, so I'd be willing to bet you can definitely make it colony pick.

--- Bit of wall text, sorry ---

The entire "bionet-synthesis" repo is actually the OpenFoundry, which is a codebase developed for the FreeGenes project (freegenes.org). Conary Meyer (a lab colleague of mine) and I learned python a few months ago to figure out how to clone the quantity of stuff that was coming through our pipeline. 

In theory, one should be able to deploy an OpenTrons to any lab and immediately be able to clone literally hundreds of plasmids a week with GoldenGate assembly (we've only cloned about 700 plasmids so far, but we recently got about 2500 more and are going to try to clone every single one within a week). No more thinking about DNA cloning! Just have a robot do it. So, in that way, colony picking is only a small part of a bigger idea on how to process DNA (and one that took a shocking short amount of time).

Conary is writing up a paper on the idea which should publish on bioarxiv within a couple of weeks. 

A lot of the code is quite hacked together, as these projects often are, so any help with cleaning would be appreciated. 

https://github.com/EndyLab/bionet-synthesis/tree/master/pipeline is the main location for scripts we actually use to run things. (so the basic stuff of resuspending synthetic DNA -> Building GoldenGate reactions -> Transforming -> Plating -> Picking). Picking happens to be in "testing" because so much is going on with it.

Also, for the design side, we have synbiolib (https://github.com/EndyLab/synbiolib) which has some generally useful open source synthetic bio tools that can't be found in biopython, like protein optimization or the ability to remove restriction enzymes. (A lot of the tools from the FreeGenes repo https://github.com/EndyLab/FreeGenes will be moving there, such as programs to precision recode sequences, remove restriction enzymes and repeat elements in proteins, and stuff like that). 

Any questions I'd be happy to answer. They're bleeding edge new right now, but we'd eventually like to advertise them to a lot larger crowd.

Koeng

On Tuesday, May 15, 2018 at 5:13:37 PM UTC-7, Nathan McCorkle wrote:

On Mon, May 14, 2018, 10:27 AM Koeng <koen...@gmail.com> wrote:

It is Open Source work! And it actually works now, so we can colony pick with the OT1. The problem is is that the code isn't very generalized yet. We would love to get collaboration going though!

Throw it on GitHub gist so we can take a look and maybe provide some refactoring or tips on how to do so:

https://gist.github.com

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