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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

#121

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).

thank you so much for the clarifications. I read the ScienceExpress writeup and was quite puzzled by where the 700TB were hiding. "You could store a hell of a lot of FASTQ reads in 700TB of DNA... hey, wait a second..."

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

#122
post #114

Earlier quoted context omitted.

Wait, 1.5mg per petabyte at large scales? Wouldn't that mean a gram could hold (1000/1.5) 667 petabytes and presumably scalable to many grams (eventually)? I understand it's only 650kB right now, but the density is obviously still incredible.

yes. density is astounding. that's why it's in science i presume. mostly because people forget how dense dna information really is.

> i presume

you are either the most humble senior author ever or jerking all our chains. possibly both. congratulations either way.

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

#124
post #15
post #10

Earlier quoted context omitted.

Ribosomes seem to manage just fine. :) You just encode a big marker (making sure it's not a palindrome-paired version of itself!) as a header. If you see that, it's a correct order. If not, it's not.

This header idea is great because then you only need to keep one strand and can toss the other, potentially quadrupling the amount of data storage (I'm assuming you can keep single strands of DNA stable). [Left strand] A = 00 T = 01 C = 10 G = 11 [Right strand] T = 00 A = 01 G = 10 C = 11 Anyone know these guys at Harvard, b/c this might be a way to put, at most, 2800 terabytes in a gram? (I don't know how long the h…

It's possible to have single stranded DNA, but you'd have problems with error correction.

Let's say DNA breaks, or some errors appear in the code. Thanks to the double stranded structure it's "quite easy" to repair the code.

Besides that, it's not the density which is a problem right now, but the access speed. The amount of data in DNA is so immense that doubling the density won't give any practical improvements for decades to come - if ever.

Having said that, if I'm not mistaken, some viruses are encoded by single stranded DNA & ssRNA. I'm not sure, but the density might be the reason for that.

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

#126
post #86
post #83

Earlier quoted context omitted.

I'm sorry, can you clarify what that means? You wrote each piece of data 100 times? what does the 1000 refer to?

we printed the dna microarray using agilent's ink jet process (agilent is a spin off of hp; imagine an inkjet with actg instead of cmyk). each spot on the array has many hundreds of thousands of molecules. after we cleave the dna off the array, we take a portion of that, amplify and the sequence it. the portion we took off we estimate ~100 molecules for every oligo we made (55,000). we the sequence to get >55 million…

> imagine an inkjet with actg instead of cmyk

Holy shit, this exists? Wow.

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

#127
They're teaching us this in ComputerScience and I wonder if this is total crap or not. Can you please shed light into this?

"In humans, the deoxyribonucleic acid (DNA, Germ. DNS) is the carrier of genetic information, and the main constituent of the chromosomes.

DNA is a chain-like polymer of nucleotides, which differ in their nitrogen bases (Thymin/Cytosin bzw. Adenin/Guanin,) The alphabet of the code is therefore: {Thymin, Cytosin, Adenin, Guanin,} or also { T, C, A, G } Three consecutive bases form a word So there are 43 = 64 combinations per word so the word length is ld (64) bits = 6 bits A gene contains about 200 words A chromosome contains about 104 to 105 genes The number of chromosomes per cell nucleus is 46 in humans The stored data per nucleus have, a volume of 6 bit * 200 * 10^5 * 46 = 55200 bit * 10^5 * 5 * 10^9 bit * * 10^9 Byte = 1 GByte"

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

#128
post #122

Earlier quoted context omitted.

yes. density is astounding. that's why it's in science i presume. mostly because people forget how dense dna information really is.

> i presume you are either the most humble senior author ever or jerking all our chains. possibly both. congratulations either way.

this is my first senior author paper; i imagine i'll be more haughty after I start teaching a few classes.

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

#129
post #86

Earlier quoted context omitted.

we printed the dna microarray using agilent's ink jet process (agilent is a spin off of hp; imagine an inkjet with actg instead of cmyk). each spot on the array has many hundreds of thousands of molecules. after we cleave the dna off the array, we take a portion of that, amplify and the sequence it. the portion we took off we estimate ~100 molecules for every oligo we made (55,000). we the sequence to get >55 million…

> imagine an inkjet with actg instead of cmyk Holy shit, this exists? Wow.

http://www.genomics.agilent.com/GenericB.aspx?PageType=Custo...

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

#130
post #127

They're teaching us this in ComputerScience and I wonder if this is total crap or not. Can you please shed light into this? "In humans, the deoxyribonucleic acid (DNA, Germ. DNS) is the carrier of genetic information, and the main constituent of the chromosomes. DNA is a chain-like polymer of nucleotides, which differ in their nitrogen bases (Thymin/Cytosin bzw. Adenin/Guanin,) The alphabet of the code is therefore:…

You aren't far off, but there are some errors. Excuse in advance any errors below, it's been a while since I did this stuff daily.

Human genome is 23 chromosomes, 2 copies of each (46). They are not mirror copies like RAID1, but rather alleles (different versions of same gene). So you might have a different version of a gene on each half of the chromosome. This is the basis for sexual selection and why sexual organisms can evolve (esp at the population level) so much faster than asexual ones. The two alleles can be the same as well. It's called homozygous or heterozygous. This is basic Mendelian genetics. Most genes work this way, though many are more complex.

ATGC is correct, so each "bit" is base 4.

Genes encode proteins; every 3 base pairs is a codon which specifies which Amino Acid to use. While there could be 4^3=64 in practice there are only 20 amino acids used in nature to make functional proteins. Genes vary greatly in length, not sure where you got ~200 codons/gene but that's terribly wrong. Maybe close to average, but the range is large. In any case, for data storage, anything relating to codons and proteins would be irrelevant.

Also in practice not all of a chromosome encodes proteins. There is often lots of buffer region between genes, not to mention a lot of control flow sequences that help control expression of genes. Beyond that, the ends of chromosomes don't have many genes, they just contain pseudo-random information and are still being explored (junk dna, telomeres, etc).

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