skosuri

28 ms·

241.
by skosuri 14y ago
this is my first senior author paper; i imagine i'll be more haughty after I start teaching a few classes.
242.
by skosuri 14y ago
yes. density is astounding. that's why it's in science i presume. mostly because people forget how dense dna information really is.
243.
by skosuri 14y ago
approximately a couple of thousand dollars. while that's true (re: scalability), it's not what we did, and would be hard to scale.
244.
by skosuri 14y ago
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 im
245.
by skosuri 14y ago
yup. each fragment has an address that specifies it's location in the bitstream. we are lazy.
246.
by skosuri 14y ago
i should clarify, because of extra sequence and the address barcode, we are technically only 0.6 bits/base
247.
by skosuri 14y ago
i answered this above; basically to avoid certain problematic sequence features.
248.
by skosuri 14y ago
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.
249.
by skosuri 14y ago
well, the genetic code has presumably evolved to evolve; it's unclear that it's evolved to preserve information
250.
by skosuri 14y ago
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
251.
by skosuri 14y ago
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 a
252.
by skosuri 14y ago
i think you have the numbers wrong. at least in the supplement of our paper we say a petabyte would weigh ~1.5 milligram. It would be far too expensive to do that though; about 6-8 orders of magnitude increase in scale is necessary from cu
253.
by skosuri 14y ago
it's at the start of the first read.
254.
by skosuri 14y ago
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
255.
by skosuri 14y ago
it's to avoid sequence features which are problematic like high GC content
256.
by skosuri 14y ago
agreed, it should be comparied to other arhival media like tape drives; but it's still pretty similar; we compare in our paper a hard drive platter rather than a drive itself. even then we are approximately ~million fold more dense
257.
by skosuri 14y ago
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
258.
by skosuri 14y ago
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 tho
259.
by skosuri 14y ago
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
260.
by skosuri 14y ago
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).
261.
by skosuri 14y ago
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
262.
by skosuri 14y ago
Oh, Jason, not Jerry. This must be you then. http://jasonkelly.com/
263.
by skosuri 14y ago
Are you also the PGA driving accuracy leader? http://espn.go.com/golf/statistics/_/type/type2/sort/driveAc...
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by skosuri 14y ago
While I might agree with your general point that biology is not software, I think you might be being a little too pessimistic for the field as a whole. You don't need to predict the "outcome" as you define it. You just have to get the fun
265.
by skosuri 14y ago
I wish there was a biohacker news. While the idea is pretty trivial. Showing that it worked, getting it into plants and getting it to work well, and then getting the products through the pretty significant regulatory hurdles is not trivial
266.
by skosuri 14y ago
To my knowledge, we don't receive funding from Monsanto, nor do we do much plant research that I know of. It's a big lab.
267.
by skosuri 14y ago
Oh yes, obvious conflict and I should have disclosed this major point. I didn't even know it, but that does not excuse me. George Church was an LSRF fellow (independent non-profit fellowship), which are named after the donation company. T
268.
by skosuri 14y ago
I used that case because it's the most famous one people refer too. Runyon is another famous person. Look, I've watched Food Inc too. Again, show me the case (which I believe does not exist). You showed me a news article. Otherwise this
269.
by skosuri 14y ago
This is his claim. It doesn't make much sense. Why would he spray his entire crop with roundup? Even if it were true, he still knowingly was getting RoundUp Ready seeds to avoid paying Monsanto. That's somewhat like saying: "I found this c
270.
by skosuri 14y ago
Can you point to a case where some random pollen got into a neighbor's farm and they got sued. Please read the Schmeiser case before linking to it. It's pretty simple. Monsanto in the past would be tipped off when farmers would buy a lot

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