I can also just provide the actual git repo of where all development is happening:
On Tuesday, May 15, 2018 at 5:13:37 PM UTC-7, Nathan McCorkle wrote:
-- 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:
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