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Moderna mRNA sequence released to GitHub [pdf]

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Re: Moderna mRNA sequence released to GitHub [pdf]

#251

Post by devenvdev »

drtz wrote: post #31

I'm sure it's more complex than I grasp as a layperson, but I'm utterly amazed at how simple this _appears_. I get the feeling that this is something I have a better chance of understanding than the average SaaS Terms and Conditions. I expected to have to scroll through pages upon pages of indecipherable text. Instead it's no bigger than a large paragraph of text, and I can easily fit it on my screen.

I remember a lot of features and especially bug fixes where I had to change one line of code, it took hours to figure out how exactly though. I guess this is kinda similar?

Re: Moderna mRNA sequence released to GitHub [pdf]

#252

Post by pyinstallwoes »

drtz wrote: post #31

I'm sure it's more complex than I grasp as a layperson, but I'm utterly amazed at how simple this _appears_. I get the feeling that this is something I have a better chance of understanding than the average SaaS Terms and Conditions. I expected to have to scroll through pages upon pages of indecipherable text. Instead it's no bigger than a large paragraph of text, and I can easily fit it on my screen.

See RadVac: https://radvac.org/

Make your own, open-source. Really cool.

A user on lesswrong made their own (with no prior experience): https://www.lesswrong.com/posts/niQ3heWwF6SydhS7R/making-vac...

Re: Moderna mRNA sequence released to GitHub [pdf]

#253

Post by lettergram »

sterlind wrote: post #244
lettergram wrote: post #237

Earlier quoted context omitted.

Yes, that's one of the concerns many have about this technology. Literally, anything can be injected and done at this point. Not sure where the technology is exactly at, but I suspect we're no more than 5 years from major incident related to this. Even this vaccine, we really don't know the long-term impacts or risks involved with this. For instance, this vaccine does appear more risky than the standard flu vaccine:…

How do you edit genes with an mRNA vaccine? You'd need DNA, enzymes (maybe requiring post-translational modification) to splice them in, etc. Also, you might not even be able to print full viruses with this platform. manufacturing mRNA is different from manufacturing all the random types of RNA in a virus, isn't it?

Theres really no reason you can’t have a multitude of mRNA deployed, you definitely don’t need DNA to do editing.

There are people already doing gene editing with mRNA methods:

https://m.jpost.com/health-science/israeli-scientists-use-mr...

I’m not sure about these particular platforms, but I wouldn’t be surprised if we see gene editing technology deployed live in the next 3 years.

Re: Moderna mRNA sequence released to GitHub [pdf]

#255

Post by [deleted] »

scotty79 wrote: post #229
mrfusion wrote: post #207

Earlier quoted context omitted.

Why haven’t viruses or bacteria evolved to use a lipid nano particle to evade the immune system? Seems like a big security flaw in our cells?

Maybe those lipid particles are too unstable if they are not spiked with various proteins? Moderna vaccine has to be kept in -70 C. Viruses that can survive for any extended period of time only in -70 C won't find many hosts. Also maybe the process of creating virus shell can't naturally be done without protein scaffold.

[deleted]

Re: Moderna mRNA sequence released to GitHub [pdf]

#257

Post by singularity2001 »

tangential: do biologists sometimes use some form of base 64 encoding for their triplets? so instead of AAG.TCA.GGA just g5F or something?

other than the obvious advantage of being shorter, it would also be easier to read: the boundaries would be unambiguous and each char would correspond directly to and amino acid (if applicable/coding)

Re: Moderna mRNA sequence released to GitHub [pdf]

#258

Post by ImaCake »

julienchastang wrote: post #88
koeng wrote: post #36

The thinking behind attaching a PDF with colors and not a Genbank file is why we can't have nice things in biotechnology.

Exactly. FAIR (Findable, Accessible, Interoperable and Reusable) principles are at a loss here [1]. The "Reusable" part seems to be especially problematic as the sequence is buried in a PDF file though all aspects of FAIR are compromised here. Edit: It looks like there is now a PR to address this issue [2] [1] https://www.nature.com/articles/sdata201618 [2] https://github.com/NAalytics/Assemblies-of-putative-SARS-CoV…

Things are getting better, but it still so so bad. The funny thing about that Nature article is that I recently had to parse a html table from a recent Nature article. Thankgod pd.read_html did a decent job and I then only needed another hour to hunt down all the typos and weird text issues.

Re: Moderna mRNA sequence released to GitHub [pdf]

#259

Post by ImaCake »

karolkozub wrote: post #248

It looks like a machine code snippet. I wonder if we'll develop high level languages and compilers for genetic code in the future.

I imagine we have tools in that direction, but nothing complete. Unlike math and computers, biological systems don’t really go from a uniform set of simple rules to emergent complexity - there is a whole lot of sideways complexity thrown in.

Something that might fit the computation vision of your comment are the various Ontologies for bioinformatics. The Gene Ontology is probably the most complete, although it lags many years behind the literature.

http://geneontology.org/

Re: Moderna mRNA sequence released to GitHub [pdf]

#260

Post by ImaCake »

jonplackett wrote: post #161

Rather disappointingly, neither sequence includes the string 'GATTACA'

A given combination of 7 bases has a probability of occurring of 1/16,384. Since the COVID genome is about 22k bases long I guess you have pretty good chance of it appearing in there somewhere. This assumes uniformity, which of course is not true. COVID’s genome is under crazy intense selection pressure!
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