koeng

9 ms·

61.
by koeng 2y ago
It is the actual electrodes. They need to be post-fabricated with gold or platinum. The typical aluminum isn't compatible with DNA synthesis chemistry.
62.
by koeng 2y ago
Analog I guess. I'm trying to make a chip for DNA synthesis, and so need physical contact with the real world, with electrodes, where electricity from the circuit will cause localized pH changes, which you can use for precise control o
63.
by koeng 2y ago
Definitely, producing open source works that would help me! Feel free to send me an email and we can talk about what makes sense to you. Also put some more above.
64.
by koeng 2y ago
Definitely! If you're willing to help, throw me an email so we can talk where it would best fit for you :) some sets of problems I have right now (on the hardware / software side): Hardware: It'd be great to have an open sour
65.
by koeng 2y ago
In this case, it is literally the Venter genome, just with removed tRNAs / codon sets. I'm collaborating with them on it (they're just doing the final transformation).
66.
by koeng 2y ago
good thing we live in real life and not a movie
67.
by koeng 2y ago
Someday hopefully soon when I raise a seed :) I think if you have the right structure, it is easier to train developers to be bioengineers than bioengineers to be developers! Bioengineering tends to be a more wicked discipline, which seriou
68.
by koeng 2y ago
yep, nothing in there prevents me from doing work. That article is mainly their legal team fluffing their own feathers for their clients, which I'd hope that one would be able to read between the lines for, considering it was published
69.
by koeng 2y ago
I'm working on synthesizing a genome at home! Here is a video with more details, as well as a picture of my home lab. I've always wanted to build life from scratch, and I finally have a chance to do it. Video on what I'm doin
70.
by koeng 2y ago
The bacteria develop resistance fairly quickly, but you can somewhat get around that with cocktails of phages (like a bunch of phages at once). > For a sick person after antibiotics therapy and after culture test results, those days&#x2F
71.
by koeng 2y ago
> So SQLite in Wasm is just doing compute, and I do all the OS level stuff in Go. No need for Wasm concurrency, cause I can load multiple instances of my Wasm which act like independent OS processes that communicate through the filesyste
72.
by koeng 2y ago
For use in Golang, I really like ncruces wasm SQLite package - https://github.com/ncruces/go-sqlite3 . Unlike cznic's go package (which is great, btw), the wasm version works well on OpenBSD and the like.
73.
by koeng 2y ago
They've tried and there are some folks who have made nanopores, but honestly they're SO many years away from Oxford it's almost incomparable. To just play with a device, I think you can buy the MR1 molecular reality device fo
74.
by koeng 2y ago
Turnaround time is about a day, so as fast as plasmidsaurus would get back to me (I'm also using nanopore, so we're gonna essentially be the same speed, with my library prep taking time but their shipments also taking time). It is
75.
by koeng 2y ago
I do a lot of plasmid sequencing in-house with nanopore, so I have some insights here! For years, the problem was mainly with the rates of mutations in nanopore sequencing, in particular, non-random mutations. The stuff you couldn't ju
76.
by koeng 2y ago
It’s really a shame that OpenBSD doesn’t have a good file system. Otherwise I’d use for my production systems (I could put it inside of proxmox, with a ZFS container outside for stability inside, but I like to run bare metal, no VMs)
77.
by koeng 2y ago
> can't you just inoculate your starting culture with a larger amount or something No, I'm doing high throughput cloning in such a way where a limiting factor is going from 1 cell to X cells (usually pickable colonies). So liqu
78.
by koeng 2y ago
Normal E.coli doubling time, which means about half the speed of Vibrio natriegens. I use NEB turbos sometimes, but they still don't bring down the liquid culture time down from overnight to within a day, mostly. I would want E.coli to
79.
by koeng 2y ago
I'm expecting that it should grow 2x the speed, sporulate if needed, have natural competence systems for large modifications / genome engineering (lambda red aint there), have some environmental resistances that are uncommon in ty
80.
by koeng 2y ago
I use E.coli on a pretty daily basis for cloning. It's alright, and there is so much work that has gone into it as a chassis organism, but overall there are definitely better organisms out there if we just took the time to figure them
81.
by koeng 2y ago
For synthesis, it’s mainly because there is a monopoly and the challenge (DNA assembly) is super boring in comparison to sexy things like DNA synthesis. For robotics, it’s because Opentrons started scaling and needed to make more $$$ rather
82.
by koeng 2y ago
Clonal DNA synthesis has increased in price over the past 6 years (even when accounting for inflation). On that metric, we’re actually regressing in our ability to modify the natural world. It’s even worse than stagnation. Or even look at l
83.
by koeng 2y ago
For me, this is very true. Most bioinformatics is done in python, but over the last ~4 years I've ported everything I do over to Go: https://github.com/koeng101/dnadesign I'm just massively more productive, a
84.
by koeng 2y ago
What is the problem with https://github.com/fergusstrange/embedded-postgres/tree/mast... ?
85.
by koeng 2y ago
I do exactly the same thing. I’m even running SQLite in wasm so I don’t have any C dependencies. Switching out for Postgres would be awesome
86.
by koeng 2y ago
Yeah but then I have to figure out the pocketbase API and keep it as a dependency. I'd rather the dependency footprint be as small as possible, accepting the minor tradeoff of having to implement auth myself.
87.
by koeng 2y ago
I have a go monolith, htmx for dynamic pages, and SQLite to back it. I really tried to find something for user login / auth / forgot password, but ended up just implementing it myself. Way easier than figuring out APIs and such to
88.
by koeng 2y ago
I'll make sure to explain it a little more! Basically, I developed a whole lot of bebop/poly, but I had some disagreements with the owner of the repo (Timothy Stiles) about direction at the later stages of development. For example
89.
by koeng 2y ago
I pretty much rebuilt my bioinformatics stack from scratch in Go, and I’m pretty proud of it! It does things that no other library, even python libraries, do for synthetic biology applications. I’m pretty sure nobody else uses it, but I use
90.
by koeng 2y ago
They added the star as an edit because of my playground link. So, neither

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