--- Log opened Mon Feb 19 00:00:03 2024
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00:33 < jrayhawk> https://biologicmodels.com/wp-content/uploads/2023/03/biologicModels_2023_custom3DPrint_Banner_4-scaled.webp
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10:22 < hprmbridge> kanzure> alabama supreme court says frozen embryos are children; can we collect tax credits from this?
10:25 < hprmbridge> kanzure> apparently dewar security is not that high yet
10:25 < hprmbridge> kanzure> even basic security like cameras and tripwire would be an industry upgrade apparently
10:25 < hprmbridge> kanzure> but also, geographically-redundantly stored cloned embryos would solve this
10:29 < hprmbridge> kanzure> groq llama 2 seems to be very fast. custom hardware behind their site methinks.
10:30 < hprmbridge> kanzure> https://chat.groq.com/
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12:03 < hprmbridge> kanzure> c-pen reading system https://youtube.com/watch?v=G3gxutd6Kto
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15:43 < L29Ah> https://manifold.markets/_next/image?url=https%3A%2F%2Ffirebasestorage.googleapis.com%2Fv0%2Fb%2Fmantic-markets.appspot.com%2Fo%2Fuser-images%252Fdefault%252FpZinyeyW4F.webp%3Falt%3Dmedia%26token%3D869061c0-1008-41d7-b6ad-ecee3705cfaa&w=640&q=75
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17:25 < hprmbridge> whobiz> Hey, anyone have recommendations for a ZNC bouncer setup? I’m wanting to have both 1.) a client on a VPS server (weechat) to be able to pipe in logged messages on reconnect, and 2.) the same on mobile as well
18:20 < fenn> frozen embryos are children, frozen adults are tissue specimens. got it
18:37 < kanzure> whobiz: no particular suggestions from me.
20:15 < fenn> a VHS cassette could store a lot of DNA spots
20:16 < fenn> single reel tapes like DLT or LTO don't waste half the space
20:19 < fenn> they're both half inch width tape substrate, VHS is 250m and ultrium/LTO is 600-1000 but i suppose that's not really a property of the form factor
20:21 < fenn> there would have to be some sort of keying mechanism so you couldn't accidentally put a DNA tape into a magnetic tape reader
20:22 < fenn> but the form factor should be the same so you can use the same tape library robots
20:23 < hprmbridge> kanzure> https://www.parkerphonics.com/post/a-brief-history-of-reading-instruction
20:25 < fenn> each LTO tape has a 4KB "memory chip" that keeps track of age, error count, last write position, etc
20:32 < hprmbridge> kanzure> https://tedium.co/2021/05/05/hooked-on-phonics-history/
20:33 < hprmbridge> kanzure> fenn this is the kind of tape system you want
20:33 < fenn> i suppose instead of a spot of DNA you could have a stripe, and subsequent reads will move down the stripe to pick up fresh DNA, until eventually it's depleted
20:33 < hprmbridge> kanzure> https://www.biosearchtech.com/products/pcr-reagents-kits-and-instruments/pcr-instruments-and-software/array-tape-ultra-high-throughput-platform/nexar
20:33 < hprmbridge> kanzure>  https://cdn.discordapp.com/attachments/1064664282450628710/1209357253241737226/image0.png?ex=65e6a0b5&is=65d42bb5&hm=090d238567d32b89e4d121bf5c87a852e6054f96d6796cb6534967415bb93a3f&
20:33 < fenn> that's a piece of lab equipment, not a computer peripheral
20:34 < fenn> i don't see why you'd want wells for a dried on droplet
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20:35 < hprmbridge> kanzure> how do you rewind or play your VHS tape without destroying the DNA spots
20:35 < fenn> the droplet shape can be regulated by printing hydrophilic/hydrophobic patterns on the tape substrate, and you'd dry it before the tape is wound onto a reel
20:35 < hprmbridge> kanzure> ok drying
20:35 < fenn> each time you read a spot it is destroyed, effectively. maybe we can get multiple uses per spot, i dunno
20:36 < fenn> i started thinking about DNA tape in the context of inkjet oligo printing
20:37 < fenn> in the scenario where you read oligos straight off the tape, it's for data storage only
20:38 < fenn> you might want to store nature-derived sequences instead, or assembled genes, or just mixtures of oligos synthesized and assembled in batches
20:38 < fenn> is there some kind of standard terminology for how many copies of the sequence are in a spot or microwell or whatever actually gets put into the sequencer?
20:39 < fenn> clearly you can't dilute to below 1 sequence, that's a hard physical limit. but i'm not sure what level of dilution we can do with existing PCR or other amplification methods before the error rate is too high
20:40 < fenn> obviously data storage can handle greater error rates because you can use error correction codes
20:44 < fenn> chatgpt says ~1000 sequence copies for reliable PCR
20:49 < fenn> amplification_error = 1 - (1 - polymerase_error_rate)^cycle_count and typical values are 1e-5 to 1e-8 errors per base per cycle, typical cycle count 20-35, so an amplification error rate of .0003 down to 2e-7
21:12 < fenn> rolling circle amplification only introduces one cycle worth of error per circle, which can make an indefinite number of copies, but practically speaking it can do 10 kbase per enzyme per circle in a few minutes
21:14 < fenn> so there's a speed vs error tradeoff you can make there at least, with the same dilution factor
21:15 < fenn> more dilution = less wear on the tape
21:17 < fenn> you can use the same tape for twice the number of reads by taking twice as long to do rolling circle amplification
21:18 < fenn> realistically, i don't expect any spot to be read more than once, because then it will be stored on a hard drive
21:25 < fenn> physically separate sequences with beads or nanowells coated in complementary standardized prefix barcodes so your sequencer can resolve them as individual blobs of light
21:26 < fenn> or another separate reading-assist tape coated in nothing but a pattern of prefix barcodes for sequence separation
21:27 < fenn> for a targeted data retrieval query you can do the PCR trick where you only amplify the data you're interested in, but if you want to read the whole tape, every sequence in every spot, that's going to be a lot more sequences, and they'll step on each other if you try to do it all at once
21:28 < fenn> but also you don't want to waste DNA spots on the tape by throwing out 99% of the rubbed off spot each time, hence the need for non-wasteful separation
21:32 < fenn> there's got to be some way to do optoelectrowetting on a tape instead of a fixed sheet of glass
21:32 < fenn> this would let you do assembly on a disposable write-scratch tape without having to transfer millions of dots around
21:34 < fenn> and with electrowetting you can move the dots around without touching them, so your final assembled dot ends up in the right place on the tape to be reel to reel contact transferred to copies. the write scratch tape would be much longer, or there would be many more write-scratch tapes per final product
21:35 < fenn> dot = microdroplet
21:40 < fenn> say we have 100 oligos combined into 1 assembly, and 100 assemblies per spot on the tape, that means we'd have 10000 write scratch tape lengths per final output tape. each write scratch tape has a repeating grid of 100 squares, and each tape has the transferred dot in a different position in that grid
21:42 < fenn> it seems horribly wasteful
21:43 < fenn> maybe chip based stuff just scales better in the end
21:44 < fenn> oh well. you can still do the sequence separation on a tape segment even when using a giant pile of crap made on a chip, all mixed together
21:47 < fenn> or i could try to actually, you know, use biology for the copying, since it's damn near perfect
21:56 < fenn> for data storage at least, synthesize long oligos on a chip, spread that oligo soup on a segment of prefix complement patterned scratch tape, wash the scratch tape, inkjet various restriction endonucleases onto the scratch tape, transfer that to a final tape, inkjet restriction endonucleases in a different pattern onto the same scratch tape, repeat
21:56 < fenn> uh, with a different grid offset for the different pattern of endonucleases
22:01 < fenn> the idea is to have all the endonuclease patterns on every grid square on the final tape. it's not perfect separation because sequences can transfer back to the scratch tape from the final tape, but should get most of the way there if you wash between transfers and the final tape binds the transferred sequences with a generic complementary post-endonuclease barcode
22:03 < fenn> it's a lot of sequence overhead
22:08 < fenn> it would be cute to engineer a two part (or n-part) restriction endonuclease, where it binds to one sequence, and cuts another sequence. then you could mix and match those endonuclease inks for inkwells^2 (or inkwells^n) multiplexing per scratch tape
22:09 < fenn> (n-part means there are multiple composable sequence recognition components)
22:14 < fenn> i ought to be able to buy a biobrick library for $10, mailed in an envelope
22:29 < fenn> the scratch tape would have a bigger droplet size so it can transfer multiple times per dot of final tape. the curved surface of the drop transfers only at the center when proper spacing is maintained
22:32 < fenn> possibly fancy droplet shaping techniques with ultrasound or electric fields to make it pointier and only transfer when you want to
22:36 < fenn> cambrian genomics used lasers to "blast" microbeads from a glass slide into a sequencer well. perhaps a solid state transfer like that could have more transfers per grid cell of the scratch tape
22:37 < fenn> a bead receiving tape would need to be coated in sticky residue but that seems easy enough
22:37 < fenn> plus no back-contamination
22:40 < fenn> the old-skool method of replicating a petri dish involves stabbing the bacterial colonies with millions of tiny needles on a sort of furry paper, then stabbing the sterile agar plate. this wouldn't work because there's not enough DNA stuck to each needle, you're wasting most of the DNA you synthesized on the scratch plate
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22:44 < fenn> cotton velveteen apparently
--- Log closed Tue Feb 20 00:00:04 2024