Harvard cracks DNA storage, crams 700 terabytes of data into a single gram • Hacker News Board

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

#101

Post by i_cannot_hack » Fri, Aug 17, 2012, 9:07 PM UTC

shinratdr wrote: post #48

colanderman wrote: post #17

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…

HN formatting breaks the first Wikipedia link by removing the apostrophe. I ran it through a link shortener as a workaround. http://cl.ly/1r153b103k2P

One could also replace the apostrophe with %27

http://en.wikipedia.org/wiki/Coupon_collector%27s_problem

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

#102

Post by DanBC » Fri, Aug 17, 2012, 9:15 PM UTC

The paper is exciting, in the calm measured way that scientists are. I look forward to seeing huge data storage on DNA in the future.

I'm gently concerned about what'll happen to information if it's not available to the future people. Is anyone taking the most important documents of our civilisation and encoding them onto clay tablets, or some such?

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

#103

Post by subrat_rout » Fri, Aug 17, 2012, 9:40 PM UTC

The next big hurdle is to how to develop a household DNA sequence reader under $50 that will read your storage. I mean if I want to store my data onto a DNA strand, then one day I'd be in need of reading that data at my home with the help of a sequence reader.Right?

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

#104

Post by mbreese » Fri, Aug 17, 2012, 10:02 PM UTC

skosuri wrote: post #65

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…

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).

A bit of support to that: it used to be common to send plasmids (circular strand of DNA) to people on paper. You'd take a drop of the plasmid, put it onto the paper, and let it dry. When the recipient got the card in the mail, they'd cut out around your dried plasmid and put it back into water. It would be perfectly functional, if needed.

If you needed more, you could then transform E. coli with the plasmid and let them do the work for you.

I don't know if this is done very much anymore, but this helps to show just how robust DNA can be. I want to say that a few years ago, someone tried to sell our lab an archival tool for DNA that was essentially this. You dried your DNA samples onto blotting paper in a grid, then when you needed a sample, you could go back and reconstitute by punching it out of the paper.

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

#105

Post by tocomment » Fri, Aug 17, 2012, 10:03 PM UTC

skosuri wrote: post #81

tocomment wrote: post #20

To read the data out are they basically doing de novo assembly on the sequenced reads? How are they handling all of the errors in gene sequencing? How about assembly errors? Long repeats?

we don't ever assemble; we are reading 115bp (96bp data, 15bp address), and pair reads using seqprep to reduce errors; a few other things are done, but the basics is that we just take all reads at a particular barcode and call consensus by majority vote. 10 bit errors in 5.27e6

Do you don't ever make a large single molecule like you'd find inside cells? You're saying you create the fragments and then read back the same fragments?

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

#106

Post by mbreese » Fri, Aug 17, 2012, 10:12 PM UTC

Jun8 wrote: post #56

And, of course, this brings us to the question: Do we already have messages in our DNA? Here's a post (from 2007) on this: http://blog.sciencefictionbiology.com/2007/07/messages-in-ou... . Actually, if it's from the aliens who seeded life on Earth, it would probably be in a prokaryotic DNA perhaps?

Probably not... If we were seeded by aliens, then the message would have had to have been in a very primitive form, so it would necessarily be seen in all living things, including prokaryotes. Unfortunately bacterial genomes are much, much, smaller than humans, so there isn't much room to waste for hidden alien messages. Additionally, presumably, these messages wouldn't be functional, so they would be under any sort of evolutionary pressure. This means that they would likely be mutated or lost to natural selection.

That's not to say that we weren't seeded, just that if we were, any message would likely have been lost. Unless... maybe they seeded mitochondria intact, which are in all (ok, most) eukaryotes. Maybe that might work... :)

Unfortunately, chrM is pretty small too... so no hidden messages there either :(

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

#107

Post by jforman » Fri, Aug 17, 2012, 10:26 PM UTC

mbreese wrote: post #104

skosuri wrote: post #65

Earlier quoted context omitted.

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).

A bit of support to that: it used to be common to send plasmids (circular strand of DNA) to people on paper. You'd take a drop of the plasmid, put it onto the paper, and let it dry. When the recipient got the card in the mail, they'd cut out around your dried plasmid and put it back into water. It would be perfectly functional, if needed. If you needed more, you could then transform E. coli with the plasmid and let t…

Plasmids are still commonly sent in the mail dried on paper. At least they were when I dropped out of my Ph.D. program a few years ago.

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

#108

Post by skosuri » Fri, Aug 17, 2012, 10:52 PM UTC

tocomment wrote: post #105

skosuri wrote: post #81

Earlier quoted context omitted.

we don't ever assemble; we are reading 115bp (96bp data, 15bp address), and pair reads using seqprep to reduce errors; a few other things are done, but the basics is that we just take all reads at a particular barcode and call consensus by majority vote. 10 bit errors in 5.27e6

Do you don't ever make a large single molecule like you'd find inside cells? You're saying you create the fragments and then read back the same fragments?

yup. each fragment has an address that specifies it's location in the bitstream. we are lazy.

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

#109

Post by skosuri » Fri, Aug 17, 2012, 11:06 PM UTC

I'm an author of the paper. The title of this article is misleading; first, we encoded 650kB and made 70 billion copies... second, those 70 billion copies weigh 1 milligram... third, it's really only meant for archival purposes as it's immutable and not random access... fourth, it's expensive right now (at least this might be a solvable problem).

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

#110

Post by brfox » Fri, Aug 17, 2012, 11:29 PM UTC

skosuri wrote: post #109

I'm an author of the paper. The title of this article is misleading; first, we encoded 650kB and made 70 billion copies... second, those 70 billion copies weigh 1 milligram... third, it's really only meant for archival purposes as it's immutable and not random access... fourth, it's expensive right now (at least this might be a solvable problem).

Nice work, and thanks for replying to all the questions here. I didn't read the paper, maybe it is addressed in there, but how much did it cost to synthesize that much DNA? Also, it could be random access if you PCR amplified the fragments you need based on the barcodes - you could even make a FAT (file allocation TUBE) which has all the file names and their barcodes.