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Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

extremetech.com

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Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#91

Post by ChuckMcM »

vph wrote: post #75
ChuckMcM wrote: post #36

I really liked their paper. Its a bit less over the top than the extremetech guys but hey, that is the difference between pop journalism and science. Clearly with some form of fountain code or LDPC codes you will be able to get the data back, but what struck me is that I always thought of DNA as relatively unstable, in the sense that cells decay/die etc, but the fact that just sitting there, DNA which isn't expressin…

do you have a link to their paper?

If you are a AAAS member: http://www.sciencemag.org/content/early/2012/08/15/science.1... (which is where I got it)

I don't know if there is a copy outside the Science Paywall, perhaps Sriram could answer that.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#92

Post by skosuri »

InclinedPlane wrote: post #80
skosuri wrote: post #78

Earlier quoted context omitted.

it's to avoid sequence features which are problematic like high GC content

Ah, interesting. In natural DNA this is achieved by using a more complex encoding scheme (3 base pairs -> one amino acid), combined with the vast majority of DNA not encoding genes directly.

well, the genetic code has presumably evolved to evolve; it's unclear that it's evolved to preserve information

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#93

Post by skosuri »

gibybo wrote: post #51
wbizzle wrote: post #44

This article is incredibly misleading. First of all there is an inconsistency. The headline says they stored 700 terrabytes (4.4 petabytes). It then later says that they actually stored 700 kilobytes (Their book) and that they did made 70 billion copies (44 petabytes?). The main thing is that storing 700 kilobytes and then making 700 billion copies is considerably less useful than storing 70 billion terabytes outrigh…

It says they stored 44 petabytes total (70 billion * 700 kilobytes), and 700 terabytes in a single gram (which is 5.5 petabits, not 4.4 petabytes).

in the paper, we say 1.5mg per petabyte at large scales. we only encode 650kB or so. this seems a little sensationalistic. we are far away from being able to do 1 petabyte of arbitrary information.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#94

Post by natrius »

sp332 wrote: post #74
refurb wrote: post #62

Earlier quoted context omitted.

Snarky reply: You've sequences every single one of those cells and confirm that the DNA all matches? Non-snarky reply: There is a huge difference between phenotype stability and genotype stability. Take 100 cells from your body and you'll find hundreds if not thousands of genetic differences between them (single mutations).

There are 3 billion base pairs in each copy of human DNA. Looks like only ~60 of them change from one generation to the next. http://www.nytimes.com/2010/03/11/health/research/11gene.htm... Just making the 4 trillion cells in my body means that each would have to be copied an average of 41-42 times. Probably some cells get replaced more often and others have a shorter path, so I'm not sure how many times DNA is dupli…

A mutation has to happen in germ cells (the cells that produce sperm and eggs) for it to pass to the next generation.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#95

Post by sp332 »

natrius wrote: post #94
sp332 wrote: post #74

Earlier quoted context omitted.

There are 3 billion base pairs in each copy of human DNA. Looks like only ~60 of them change from one generation to the next. http://www.nytimes.com/2010/03/11/health/research/11gene.htm... Just making the 4 trillion cells in my body means that each would have to be copied an average of 41-42 times. Probably some cells get replaced more often and others have a shorter path, so I'm not sure how many times DNA is dupli…

A mutation has to happen in germ cells (the cells that produce sperm and eggs) for it to pass to the next generation.

I know. If a germ cell has DNA that has been copied 41 times (the average that I calculated), and that DNA has accumulated 60 errors, that means 1 error per 2 billion base pairs copied.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#97

Post by skosuri »

skosuri wrote: post #68
conanite wrote: post #2

They're using T and G for a 1, and A and C for a 0; why not double the density and get two bits from each letter? T = 00 G = 01 A = 10 C = 11 for example.

we didn't because we wanted to avoid particular sequence features that are difficult to synthesize and sequence. we probably could have gotten away with something like 1.8 bits per base, but we were already doing fine on density, so we thought a 2x hit wouldn't be that bad.

i should clarify, because of extra sequence and the address barcode, we are technically only 0.6 bits/base

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#98

Post by natrius »

sp332 wrote: post #95
natrius wrote: post #94

Earlier quoted context omitted.

A mutation has to happen in germ cells (the cells that produce sperm and eggs) for it to pass to the next generation.

I know. If a germ cell has DNA that has been copied 41 times (the average that I calculated), and that DNA has accumulated 60 errors, that means 1 error per 2 billion base pairs copied.

Ah, I misunderstood your logic. Makes sense.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#99

Post by duaneb »

jessriedel wrote: post #47
jwr wrote: post #42

Does anybody know how to escape their horrible "mobile" version that they force onto ipad users? It can't even be zoomed :-( More and more often I find myself not reading articles because someone thought it would be a great idea to create a non-scrolling, non-obvious, paginated "iPad format" with additional misleading and unintuitive buttons looking like native ones but doing something different. Sorry for the rant.…

I'm considering buying an iPad, and I have a question: is there no browser on the iPad that allows you to choose whether you want to the mobile version or the regular version? If not, that's almost a deal breaker.

I honestly haven't run into a site (except this one) that forces mobile sites on you without allowing you to opt out - however, I also use Chrome, so my being a mobile device may not be properly detected yet.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#100

Post by brown9-2 »

skosuri wrote: post #90
vph wrote: post #75

Earlier quoted context omitted.

do you have a link to their paper?

I posted our paper on dropbox (until i get into too much trouble over it): paper http://db.tt/ZDoDJZeD supplement http://db.tt/elIqsy72

thank you!
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