koeng

12 ms·

121.
by koeng 3y ago
I’ve been working on a synthetic DNA assembly company. Basically, I figured out how to assemble DNA for people at a fraction of what it normally costs, so they give me a sequence, and then I make it in real life for them, then ship it to th
122.
by koeng 3y ago
We’re pretty close. There’s TEM microscopy tech which basically tilts a sample to get a bunch of lines, which is then reconstructed as a 3d model. It’s stupid expensive though, and you can only really identify whole proteins. But you can do
123.
by koeng 3y ago
I'd love to try it, but pretty much all my repos are >10mb. It's not because there is that much code, but because I am doing bioinformatics and the test files (for the unit tests) inflate the repo size. It would be great if the
124.
by koeng 3y ago
Is there an API that could be used? I have a use case that I'm integrating into a larger software package, but wouldn't be using a cli/web app for that.
125.
by koeng 3y ago
I use hledger for my solo-company. It is really great, and very easy to understand what is going on. Highly recommend.
126.
by koeng 3y ago
> The big issue seems to be the size of most plastics, not that bacteria can't already eat them. Yep, that's why it is super cool things like mealworms can consume styrofoam - they have microbes in there gut that do the actual
127.
by koeng 3y ago
Back in ~2014-2015 I was looking at making this (worked in Chang Liu's orthorep lab) - the problem was that I couldn't get my hands on the PRD1 phage (which is a fascinating phage - protein primed replication, lipid membrane colip
128.
by koeng 3y ago
The most annoying part with the 200k polymerase prize is that they don't actually provide protocols for validating the polymerase works well. Me and some friends can definitely do the AI-protein design + DNA synthesis + protein synthes
129.
by koeng 3y ago
Oxford Nanopore with the new R10 cells is good enough for most synthetic biology applications (ie, plasmid sequencing and strain validation), which I'm super excited about. Combine low-capital and long-reads and you can do some really
130.
by koeng 3y ago
Yep. You can also do things like mRNA vaccines, or build industrially useful enzymes, or make crops resistant to disease. Pretty much any biotechnology that involves engineering life.
131.
by koeng 3y ago
How can we lower the price of making synthetic DNA? All the graphs on this topic are out-dated, specifically because the hype-train doesn't want to acknowledge that the price of usable synthetic DNA has gone up - not down (even when ba
132.
by koeng 3y ago
Their media is real complicated and expensive (plus difficult to prepare: can’t just throw everything in an autoclave), and they don’t grow very fast, and they don’t grow to a high concentration. Basically that means that you can easily get
133.
by koeng 3y ago
I’m well aware. I was in charge of designing and synthesizing the entire gene set, optimized for E.coli, in order for scientists to easily try to discover the function of these genes https://stanford.freegenes.org/collection
134.
by koeng 3y ago
I gave a talk at that workshop! (I’m making the 61 codon version of JCVI-Syn3a) You can get the cells as a researcher, but basically forget about it for a commercial user or hobbyist. They’re also annoying as hell to grow. I’m trying to syn
135.
by koeng 3y ago
We don’t even know what like, 20% of the genes do. Simulations are neat, but they miss a lot of underlying biology that actually makes an impact on engineering. One of my favorite papers was published 40 years ago on this topic https:&#x2F
136.
by koeng 3y ago
I love your demo for this. It's one of the best demos I've ever come across in a launch HN. Very easy to understand and use. It seems to suffer with more complex questions though. For example: Question: Why does the pUC19 plasmid
137.
by koeng 3y ago
Fair on the gatekeeping, but on the other side, keep your mind too open and your brain will fall out. > This is precisely the problem I’m pointing out. This is, ironically, also the problem I’m pointing out. Why would I trust someone who
138.
by koeng 3y ago
Eh. Most people I see who are super concerned about synthetic biology safety aren't the people actually working on it (in contrast to things like AI, or even more innocuous technology like social media). That includes me. I've wor
139.
by koeng 3y ago
Not a ginkgo project
140.
by koeng 3y ago
Hey, a project I actually know about. Used to work in Kaisha Benjamin's lab (Endy Lab at Stanford). I remember all those bioinformatics to get the glucose inducible promoter. Back then at least, the promoter wasn't controllable en
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by koeng 3y ago
Sex changes many lines at a time. But you do die if it doesn’t compile.
142.
by koeng 3y ago
I’ve worked in a lab of one of the original folks working on genetic logic gates, and honestly, no they don’t really work very well at all. I think a lot of computer scientists assume that their model of the world (binary logic) is the most
143.
by koeng 3y ago
Can you explain why the streamed WAL files are a copy and not a backup of the SQLite database?
144.
by koeng 3y ago
The broader security mindset is identifying the technologies that are most probably used in a situation where you need read and write. For example, in computer security, you wouldn't worry about a air-gapped UNIX server being infected
145.
by koeng 3y ago
From someone who has reconsistuted viruses from synthetic DNA - it’s WAY easier than working with prions, or even viroids for that matter. The fact they package themselves and release themselves, while being formed of genetic sequence, is S
146.
by koeng 3y ago
I don’t see how that has to do with obfuscating unusual reverse transcriptases, though. There are plenty of (if not more) DNA based transformation methods, and those enzymes are sufficiently widespread that it’s not unusual to find them nor
147.
by koeng 3y ago
> * A possible arms race between obfuscating and detecting unusual retrotranscriptases Why, exactly?
148.
by koeng 3y ago
> Wonder how badly it could go if the data storage container is ruptured while against someone's body? Nothing, really. Your body is good at fighting that sort of thing, because it's literally happening every second of every da
149.
by koeng 3y ago
How would you do it in Go? It is my understanding that FAISS is integrated into the SQL database itself (using embedding in the table), so writing it in Go wouldn't integrate it in the same way. > But you can try to use my build scr
150.
by koeng 3y ago
Very cool! I’ve been looking at using SQLite-vss for fast vector sorting, but it requires CGO. I imagine if I do WASM compilation directly from C, I might be able to get around using CGO. Do you have any idea able the feasibility of that us

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