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The complete sequence of a human Y chromosome

nature.com

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Re: The complete sequence of a human Y chromosome

#71

Post by iten »

dekhn wrote: post #63
jghn wrote: post #57

Earlier quoted context omitted.

Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812

Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…

Small correction: BLAT is a local alignment tool Jim Kent also wrote. I think his assembler you're referring to is GigAssembler (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311095/).

Re: The complete sequence of a human Y chromosome

#72

Post by panosfilianos »

dekhn wrote: post #54
alexchantavy wrote: post #43

Earlier quoted context omitted.

Fascinating, are there lots of people looking at genetics with this ML kind of lens?

Sure, although I'm not aware of anybody who is contemplating quite the level I believe is necessary to really nail the problem into the ground. When I worked at Google, I proposed that Google build a datacenter-sized sequencing center in Iowa or Nebraska near its data centers, buy thousands of sequencers, and run industrial-scale sequencing, push the data straight to the cloud over fat fiber, followed by machine lear…

I have spent the better part of the past year looking obsessively over genomics papers for cancer and I've grown very fond of the field.

Are there any positions at Google/ companies you wold suggest me to look into? I'm coming from algortrading/ ML research with ML MSc.

Re: The complete sequence of a human Y chromosome

#73

Post by khazhoux »

borissk wrote: post #51
ejstronge wrote: post #40

Earlier quoted context omitted.

> That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human. You'd need a cell to start the process, with the various nucleic acids distributed correctly and proteins/energy with which to create further proteins using the information encoded by the DNA. Thus the civilization would need information about cells and a set of building blocks before being able to use the DNA.

The DNA contains all the code that creates and regulates the proteins.

And how will you decode it?

Re: The complete sequence of a human Y chromosome

#74

Post by jghn »

jfoutz wrote: post #68
dekhn wrote: post #63

Earlier quoted context omitted.

Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…

I know hn isn't the place for memes, but, I'm obligated. Imagine what they could do with a beowulf cluster of pentium pros?

I feel like this is the one domain where the beowfulf cluster meme is still funny

Re: The complete sequence of a human Y chromosome

#75

Post by jhbadger »

10g1k wrote: post #5

For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…

As noted, the shotgun sequencing wasn't any worse than the traditional chromosome walking method used by the other human genome project, and neither created a truly complete sequence, which is only possible today with improvements in technology.

And it is worth noting that despite all the critiques of shotgun sequencing at the time as "cheating", chromosome walking sequencing is dead, and shotgun is what we use today. If anything replaces that it will be long read technology like that done by Oxford Nanopore sequencing, although we aren't really there yet (you still need to assemble that data and don't really get end-to-end sequences yet).

Re: The complete sequence of a human Y chromosome

#78

Post by gandalfgreybeer »

coldtea wrote: post #77

Is this like: "we have a working keyboard driver" or more like "we identified all 104 keys on a standard 104-key US QWERTY layout"?

Not answering your question, but I have to say, this is one of the best analogies I've encountered in a while.

Re: The complete sequence of a human Y chromosome

#79

Post by epistasis »

jfoutz wrote: post #68
dekhn wrote: post #63

Earlier quoted context omitted.

Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…

I know hn isn't the place for memes, but, I'm obligated. Imagine what they could do with a beowulf cluster of pentium pros?

There was a NYTimes profile at the time of Kent's efforts, and they IIRC literally got the UC Santa Cruz administration to hand over desktop computers destined to go to various people for a few months to assemble into a cluster. So it was likely a bunch of pentium pros or similar. Not a Beowulf cluster, of course, but whatever clustering software Kent had hand rolled out of C for the purpose.
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