koeng

22 ms·

241.
by koeng 6y ago
JCVI-Syn3A has been around for a while. Here is the genome sequence from 2018 - https://www.ncbi.nlm.nih.gov/nuccore/1241355755 Back at FreeGenes we synthesized all of the genes from this organism with codon optimizati
242.
by koeng 6y ago
Us folks in biotech have a special tool just for this :) https://blast.ncbi.nlm.nih.gov/Blast.cgi Unfortunately, the core algorithm dates back to 1990, so it can be real slow in some cases. Biotech takes a while to improve
243.
by koeng 6y ago
DNA is way more stable than RNA. Since you can easily synthesize RNA from DNA, and DNA synthesis technology is much more mature, folks normally synthesize DNA and then derive/make the RNA from it. That makes most researches default to
244.
by koeng 6y ago
Answers: a) From the mRNA you can learn the amino acid sequence of the protein very quickly. You absolutely cannot (yet) learn the function of the protein from that sequence - normally, people just do comparisons with proteins whose functio
245.
by koeng 6y ago
The thinking behind attaching a PDF with colors and not a Genbank file is why we can't have nice things in biotechnology.
246.
by koeng 6y ago
They are more complex, but the cell type doesn't matter as much. In fact, there are bacteria that cause disease using HGT ( https://en.wikipedia.org/wiki/Agrobacterium ). Modification of those bacteria is how you ge
247.
by koeng 6y ago
I also unironically use kubernetes (in particular, k3s) to run my personal blog. I run it on a colocated server I built myself, with the hope to have a couple colocated servers in the future I could network together. Right now, it has proxm
248.
by koeng 6y ago
This is kinda similar to ix.io. Cool!
249.
by koeng 6y ago
"if you have a table called messages, logs, events in your Postgres database there is a good chance it’s consuming the bulk of your storage, is your largest table, and could benefit from being moved outside of your main Postgres databa
250.
by koeng 6y ago
Can I use buildpacks with Kubernetes? When I look for it online, I find some stuff like the Cloud Native Buildpacks, but no good simple tutorials on how it actually works. I remember Dokku was a joy to use, wish I could interact with Kubern
251.
by koeng 6y ago
Josiah is an interesting guy because it turns out his opinions hold quite a bit of nuance and he’s generally a good guy (not a snake oil salesman). I think he definitely had that perspective going in - the point of the experiment is partly
252.
by koeng 6y ago
Josiah Zayner did one that looked fairly promising (believe it was either an mRNA or DNA vaccine), but unfortunately he got banned from a lot of media (like youtube) for it, so that may partially explain why you haven't seen or heard m
253.
by koeng 6y ago
terrastruct looks really awesome! Been looking for something like that for a while, I think I’ll test it out. The landing page is very well put together.
254.
by koeng 6y ago
it works but your efficiency drops by quite a bit
255.
by koeng 6y ago
The gaps are usually homopolymers and such, which should get helped by R10 pores. But true, at low coverage, things can get tougher!
256.
by koeng 6y ago
2 base pairs per byte mapping. Super simple.
257.
by koeng 6y ago
https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc7... There is a real example I ran a few months ago. How to read it is here https://en.m.wikipedia.org/wiki/Pileup_format Positions like
258.
by koeng 6y ago
At the 2014 DEFCON Biohacking village I did exactly that. I gave out like 50 tubes of plasmid, all you had to do is go sequence em to extract the private key, and boom, you get like $200 (or like 15K today...) Literally nobody did it for a
259.
by koeng 6y ago
The errors are non-random. That's why they use machine learning to figure out those errors. You could, of course, also just do traditional statistics on sequences that you want to sequence all the time. I've done that with plasmid
260.
by koeng 6y ago
Are you sure about that? My last consensus run worked with complete coverage of ~410 bp region. Here is a gist of the raw pileup without consensus - https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc7... Visua
261.
by koeng 6y ago
If you want to see what a real run looks like, here is a little gist of my last Nanopore run, raw basecall -> alignment (no consensus) https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc7...
262.
by koeng 6y ago
Yea automated sample preps are key for me. The main thing that is overlooked in synthetic biology about nanopore is it has the capability to dramatically lower cost of indexing, which turns out to be one of the main prohibiting costs for dr
263.
by koeng 6y ago
Until you also realize you need a Qubit and the library preps and oh now you need NEB next gen enzymes and wow turns out pipette technique really matters. That said, I love Nanopores, I use them in my business, and those error rates you can
264.
by koeng 6y ago
https://nebiocalculator.neb.com/#!/ssrnaamt 10 million moles of RNA of length 50 turns out to be a large amount of RNA... but then again there was like a billion years for life to develop, all around the world.
265.
by koeng 6y ago
No. Oxygen screws a lot of things up. Also, RNAses are now everywhere (organisms secrete them all the time, which is why RNAse away is a product), and since the original replicating molecules were likely RNA, pretty much the entire world is
266.
by koeng 6y ago
> hindered our understanding until very recently IMO Any specific examples of how it hindered our understanding? Like maybe some grants or something? Because as a synthetic biologist, I've never seen a heavy emphasis on genetics tak
267.
by koeng 6y ago
Small part of the picture is an exaggeration, IMO. Cellular electrical dynamics matter, but we already know that surface physics matter (see: any mammalian lab with those flat little red bottles). Those dynamics (physical, electrical, chemi
268.
by koeng 6y ago
Computationally relevant information is sometimes embedded in runtime state (for example, yeast prions), but this is very rare. For small bacteria, you can switch out the entire genome with a new genome and have them continue living just
269.
by koeng 6y ago
First approximation - 50 base pairs of RNA? (Unless I am reading the supplement wrong) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943892/ "The present study describes the directed evolution of replica
270.
by koeng 6y ago
> It would take too long to wait for desiccation between every step? Desiccation is just for the storage steps. Otherwise I just plan on passing liquids around, compensating for any evaporation. > Are you open to discussing some kind

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