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

extremetech.com

61–70 of 133 posts

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

#61
post #50

Earlier quoted context omitted.

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.

Yes those browsers are available. Chrome has a "request desktop site" option and my personal favourite, iCab Mobile, has an extensive list of agent strings (custom ones can be added as well) that can be set.

Phew, thanks.

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

#62
post #30

It is incredibly stable? We better don't tell evolution.

I've got a few trillion cells in my body that say it's incredibly stable.

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).

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

#64

If you store data onto 50 DNA strands, can you always read back all the data from all 50 strands, or does one need to store multiple copies of each in case the sequencer can't "find" a particular strand? If one does need multiple copies, it would seem that this method suffers from the coupon collector's problem [1] (i.e. to collect all 50 strands requires collecting 225 random strands on average), and that the retrie…

To sequence we used about ~100x synthetic coverage on average and ~1000x sequencing coverage; so that's a whole lot of coverage. even then we did have 10 bit errors, but all the data blocks were recovered

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

#65

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…

well the dna we used never touched the inside of a cell; plain dried dna is very stable, evidenced by the ability to sequence 10's of thousands of years old samples stored in decaying flesh (albeit with some errors).

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

#66
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 thought io9 did a better job with the coverage; i put a copy of our papers for a limited time on my dropbox:

paper http://db.tt/ZDoDJZeD supplement http://db.tt/elIqsy72

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

#67
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.…

[deleted]

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

#68
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.

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

#69
post #43
post #38

Earlier quoted context omitted.

Hmm. DNA is fairly easy to duplicate though, right? Wouldn't that allow an exponential speedup?

I assumed that the microfluidic chip speed listed would include parallel processing. Even if it doesn't, you'd still need something like 5,000 experiments in parallel for it to take less than a month...

Yes, the microfluidics used today make use of this for reading large numbers of small segments of DNA in parallel. The current "gold standard" for DNA sequencing (manufactured by Illumina) uses millions of tiny fragments of DNA which are read optically as DNA sequence is extended.

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

#70
post #34

I notice that the article fails to mention how long it would take to extract all 700 terabytes of data... Assuming 5.5 petabits stored with 1 base pair representing 1 bit, we can extrapolate the time required to extract the data based off the time taken to sequence the human genome (3 billion base pairs). 5.5 petabits / 3 billion bits ~= 2 million, so theoretically it should take 2 million times longer to sequence th…

we talk about a potential petabyte storage mechanism in the supplement:

paper http://db.tt/ZDoDJZeD supplement http://db.tt/elIqsy72

tldr; we are 6-8 orders of magnitude away from doing petabytes routinely; that said costs of sequencing/synthesis have seen such drops over the last decade or so. there are many barriers though for that continuing for another decade

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