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Moderna mRNA sequence released to GitHub [pdf]

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Re: Moderna mRNA sequence released to GitHub [pdf]

#271

Post by weinzierl »

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.

> "Instead it's no bigger than a large paragraph of text, and I can easily fit it on my screen."

When I saw it, I thought that it could almost fit in a tweet, so I just did it:

https://twitter.com/weinzierl/status/1376807707957719041?s=2...

The sequence takes 16 tweets, 15 if you don't split at line endings and remove spaces (4175 nucleobases / 280 nucleobases/tweet ~ 14.9 tweets).

Re: Moderna mRNA sequence released to GitHub [pdf]

#273

Post by retSava »

jcims wrote: post #231
mikehollinger wrote: post #167

Earlier quoted context omitted.

Reading the primary claim is fascinating: "A composition, comprising: a messenger ribonucleic acid (mRNA) comprising an open reading frame encoding a betacoronavirus (BetaCoV) S protein or S protein subunit formulated in a lipid nanoparticle." I have a "I'm sure that means something to somebody" feeling. It's also surprising that the remaining claims seem to describe the resulting bits of the sequence, and that that…

This is a great animation of the life cycle of an HIV virus. It’s not exactly what happens with the pandemic virus but it gives you a good idea of the complexity of the process of viral reproduction (vaccine or immune response isn’t covered here): https://vimeo.com/260291607 Animation of transcription from mRNA: https://youtu.be/TfYf_rPWUdY

The "SARS-CoV-2 entry" video was really interesting too, and I recommend watching them both to see how they are different.

https://vimeo.com/510310488

Re: Moderna mRNA sequence released to GitHub [pdf]

#274

Post by baby »

csense wrote: post #263

The Human Genome Project was completed almost two decades ago, and somebody solved the protein folding problem recently. Why are we still doing genetics at the machine code level? Shouldn't we have some compilers, assemblers and linkers by now?

My thought exactly. So this thing is like a VM with a bunch of primitive opcode, why can’t someone write a higher-level language or at least some gadgets

Re: Moderna mRNA sequence released to GitHub [pdf]

#275

Post by neuronic »

WJW wrote: post #264
csense wrote: post #263

The Human Genome Project was completed almost two decades ago, and somebody solved the protein folding problem recently. Why are we still doing genetics at the machine code level? Shouldn't we have some compilers, assemblers and linkers by now?

I feel this XKCD describes the situation particularly well: https://xkcd.com/1831/

Maybe after 4 billion years of evolving our code we will get it right.

Re: Moderna mRNA sequence released to GitHub [pdf]

#277

Post by neuronic »

Duller-Finite wrote: post #220
subroutine wrote: post #160

Earlier quoted context omitted.

Meh, they probably just used lipofectamine (which has been around since the 90s) or something very similar. https://en.wikipedia.org/wiki/Lipofectamine https://www.thermofisher.com/us/en/home/brands/product-brand...

lipofectamine is used for in vitro transfection, not in vivo gene delivery. The vaccines use lipid nanoparticles rather than liposomes

I absolutely do not have a link, but I remember reading that the lipid nanoparticles are actually created by mechanical action (possibly fluid dynamics/turbulence). I thought that was pretty neat.

Re: Moderna mRNA sequence released to GitHub [pdf]

#278

Post by lifthrasiir »

weinzierl wrote: post #271
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.

> "Instead it's no bigger than a large paragraph of text, and I can easily fit it on my screen." When I saw it, I thought that it could almost fit in a tweet, so I just did it: https://twitter.com/weinzierl/status/1376807707957719041?s=2... The sequence takes 16 tweets, 15 if you don't split at line endings and remove spaces (4175 nucleobases / 280 nucleobases/tweet ~ 14.9 tweets).

Or you can use base2048 [1] to compress it down to 3 tweets (4175 nucleobases * 2 bits per nucleobase / 3080 bits per base2048 tweet = 2.7 tweets).

[1] https://github.com/qntm/base2048/

Re: Moderna mRNA sequence released to GitHub [pdf]

#279

Post by shellfishgene »

brian_herman wrote: post #105
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.

Here you go! https://github.com/brianherman/Assemblies-of-putative-SARS-C...

If there is no annotation or metadata FASTA format is usually preferred ;)

Re: Moderna mRNA sequence released to GitHub [pdf]

#280

Post by jebus989 »

singularity2001 wrote: post #257

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)

Proteins are written in standardised IUPAC amino acid codes that carry some semantic meaning, e.g. Alanine: A, Glycine: G etc. Also viral genomes often have overlapping transcription with shifted open reading frames. Biology is not as simple as you think.
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