--- Log opened Thu Jul 09 00:00:05 2015
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06:55 < kanzure> .tw https://twitter.com/WanderinChild/status/618916178908438528
06:55 < yoleaux> In Polish “terminator” means “apprentice"; so in Poland, The Terminator was renamed Electronic Murderer. @GreatDismal http://t.co/4AqWWyG0T3 (@WanderinChild)
06:56 < eudoxia> anders sandberg and meredith patterson are doing an AMA about knot theory https://www.reddit.com/r/science/comments/3co2h5/science_ama_series_we_are_a_group_of_computer/
06:56 < eudoxia> .title
06:56 < yoleaux> Science AMA Series: We are a group of computer scientists who recently published a study in PeerJ which shows just how many ways there are to tie a tie. Ask us anything! : science
06:58 < kanzure> wasn't aware that they knew each other
06:58 < eudoxia> i was surprised as well
06:59 < kanzure> well maybe you should post a question about that
07:00 < kanzure> this was the approach that my graph theory advisor was using http://diyhpl.us/~bryan/papers2/DETC2009%20-%20A%20stochastic%20graph%20grammar%20algorithm%20for%20interactive%20search.pdf
07:00 < kanzure> reference 23 also counts 85 ways
07:00 < kanzure> oh nevermind
07:00 < kanzure> this is the one they referenced. i see.
07:10 < kanzure> asimov short story https://www.uni.edu/morgans/astro/course/nightfall.pdf
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07:25 < kanzure> planar mechanism kinematic simulator http://designengrlab.github.io/PMKS/ https://github.com/DesignEngrLab/PMKS
07:33 < kanzure> https://www.snellman.net/blog/archive/2015-07-09-unit-testing-a-tcp-stack/
07:34 < kanzure> mobile tcp optimization http://blog.ipspace.net/2015/03/tcp-optimization-with-juho-snellman-on.html
07:41 < CaptHindsight> kanzure: http://www.pastebin.ca/3054383  POSaM example playbook file
07:42 < CaptHindsight> if all the times are in seconds then it looks like a few minutes per layer
07:43 < CaptHindsight> layer/base
07:44 < CaptHindsight> wait times for DRY, WASH, DEPROTECT are 30 seconds
07:48 < kanzure> 0.7 seconds to deposit acetonitrile for all slides, or is that 0.7 seconds per slide?
07:49 < CaptHindsight> ##WASH WITH ACETONITRILE
07:49 < CaptHindsight> WASH 1, 0.7,
07:49 < CaptHindsight> I think that means "“WASH,” dispenses acetonitrile from nozzle 1 for 0.7 seconds" as they mentioned
07:50 < CaptHindsight> don't know for certain
07:51 < kanzure> it looks like their commands each do a lookup of their bitmap and decide whether to print or skip at each spot, dunno.
07:51 < kanzure> their visual basic source code was very poorly written
07:52 < kanzure> we should just call them or start emailing them
07:52 < CaptHindsight> they mention 3 different software apps
07:52 < CaptHindsight> 2 they even consider horrible
07:53 < CaptHindsight> on the surface it looks like they have a pretty complete spec and manual
07:53 < CaptHindsight> then when you start digging you wish they had someone as a editor
07:54 < CaptHindsight> well it's like most Linux docs
07:54 < CaptHindsight> the POSaM docs are better than most
07:59 < CaptHindsight> kanzure: http://www.pastebin.ca/3054403  here's the other file for their Arrayer application
08:11 < kanzure> http://www.systemsbiology.org/people/faculty/hood-lab/
08:13 < kanzure> chris lausted was the programmer i think
08:13 < kanzure> see http://www.bioinformatics.org/cgi-bin/viewvc.cgi/pogo/pogo-vb/ for evidence
08:14 < kanzure> see "biography" https://www.systemsbiology.org/bio/chris-lausted-phd/
08:15 < kanzure> 206-732-1276
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08:23 < CaptHindsight> they had 3 apps, PGO, Lombardi and finally Arrayer
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08:37 < eleitl> http://www.nature.com/srep/2015/150706/srep11869/full/srep11869.html
08:37 < yoleaux> 6 Jul 2015 20:00Z <kanzure> eleitl: http://www.metzdowd.com/pipermail/cryptography/2015-July/025971.html
08:39 < kanzure> .title http://www.nature.com/srep/2015/150706/srep11869/full/srep11869.html
08:39 < yoleaux> Building an organic computing device with multiple interconnected brains : Scientific Reports
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10:01 < nmz787_i> ParahSailin_: I wanted that GA2x but you never got back in touch with me
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10:02 < nmz787_i> and most likely the electrochemical portion of that microarray builder is just generating the acid
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10:41 < kanzure> agreed re: acid generation
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11:39 < justanotheruser> kanzoracle, why does the refseq project have folders in their ftp server with no actual sequences? To denote that the species exists, but doesn't have data? Or what? ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/Haloferax_elongans/
11:50 < kanzure> ncbi ftp servers are synchronized from other servers, it's possible that the data was lost or it's a replication error
11:51 < kanzure> actually what's interesting is that the following path has a file that is listed as size 0 bytes,
11:51 < kanzure> ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/Haloferax_elongans/latest_assembly_versions/
11:52 < kanzure> but if you look on some of the ncbi ftp mirrors, it is a folder
11:52 < kanzure> http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/genomes/refseq/archaea/Haloferax_elongans/latest_assembly_versions/
11:52 < kanzure> you should report that to ncbi
11:54 < kanzure> also they should be scolded for not having error checking
11:54 < kanzure> this is the sort of bug that will cause us to lose all of our genomes -_-
11:57  * justanotheruser deletes his broken mirror attempt
11:58 < kanzure> let me know if you choose not to complain to ncbi
11:58 < kanzure> /topic hplusroadmap, saving ncbi from losing genomes :-/
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12:29 < justanotheruser> kanzure: I emailed them
12:30 < justanotheruser> also, do you have an FTP mirror? I don't feel like getting rid of their html garbage
12:30 < justanotheruser> how big do you think this DB is? Maybe I should stick to viruses
12:32 < justanotheruser> or even better a single compressed copy of the entire refseq/ dir
12:33 < kanzure> "their html garbage"... what? it's an ftp server. use rsync, lftp, etc.
12:34 < justanotheruser> huh? It's http, how do I ftp in?
12:35 < kanzure> haha they don't like lftp http://www.bio-mirror.net/
12:35 < kanzure> it's ftp.ncbi.nlm.nih.gov
12:35 < kanzure> your browser is just rendering html because that's what browsers do
12:35 < justanotheruser> no
12:35 < justanotheruser> mirrors.vbi.vt.edu is http
12:35 < justanotheruser> ftp.ncbi.nlm.nih.gov is broken, remember?
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12:37 < kanzure> hm.
12:38 < justanotheruser> ftp://bio-mirror.net/biomirror/ might work
12:38 < kanzure> it's not in there
12:38 < kanzure> god damn it do i have to back this shit up myself wtf
12:39 < kanzure> jrayhawk: can you convince pdx.edu kthx
12:40 < justanotheruser> not quite sure how to navigate that ftp server though, the folder layout isn't the same and I can't find /genomes/refseq/ (/Biomirror/refseq/ isn't the same thing)
12:46 < justanotheruser> the fuck is up with these people mirroring these FTP servers with HTML files
12:46 < kanzure> they are bioinformatics people. they live in the world of cgi scripts, perl and ftp.
12:47 < justanotheruser> It seems like there would be a lot of additional effort in hosting it as html
12:47 < justanotheruser> maybe not, but they'd at least have to find a tool that serves the pages as html
12:48 < kanzure> the html files are probably an artifact of whatever mirroring technique that they are using
12:53 < justanotheruser> kanzure: good news, I found two more servers that are inconsistent or missing data! ftp://ftp.hgc.jp/pub/mirror/ncbi/genomes/genbank/ ftp://bio-mirror.net/biomirror/ncbigenomes/genbank/
12:54 < justanotheruser> perhaps they should put this data on the blockchain so they can achieve consensus
12:54  * justanotheruser rustles kanzures jimmies
12:54 < kanzure> here's the one you wanted ftp://ftp.hgc.jp/pub/mirror/ncbi/genomes/genbank/archaea/Haloferax_elongans/
12:54 < kanzure> whoops nope
12:55 < justanotheruser> yeah, the japanese one seems the most consistent
12:55 < justanotheruser> or complete I should say
12:55 < justanotheruser> yeah, I wouldn't be so whiny about it being ftp if I weren't trying to download all archaea, bacteria and viruses
12:57 < justanotheruser> kanzure: ftp://ftp.hgc.jp/pub/mirror/ncbi/genomes/genbank/archaea/Acidilobus_saccharovorans/latest_assembly_versions/
12:57 < justanotheruser> !!!!!!!!
12:57 < justanotheruser> The solution probably is downloading every copy of every server and merging them
12:58 < justanotheruser> good news is these guys have 'em http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/genomes/refseq/archaea/Acidilobus_saccharovorans/latest_assembly_versions/GCF_000144915.1_ASM14491v1/
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13:02 < kanzure> plz take notes and i will point some servers at this later
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13:20 < kanzure> justanotheruser: try http://www.ebi.ac.uk/ena
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13:20 < kanzure> http://www.ebi.ac.uk/ena/browse/sequence-download
13:20 < kanzure> ftp://ftp.ebi.ac.uk/pub/databases/embl/
13:22 < justanotheruser> is there a good way to diff directories? e.g. [/foo/bar1, /foo/bar2, ..., /foo/bar1000] only has one difference rather 1000 from [/fizz/bar1, /fizz/bar2, ..., /fizz/bar1000]
13:23 < kanzure> "A colleague found 2k of 6k FASTQ files were 'corrupted' in one way it another"
13:23 < kanzure> "i.e. paired end reads where the pairs weren't paired up on the format as they should be, etc"
13:23 < justanotheruser> did they email you back before me? unfair
13:23 < kanzure> just a friend
13:24 < justanotheruser> are you just giving me this database to check for inconsistencies? The directory structure is completely different from the other servers afaics
13:25 < kanzure> he says they should have the data, except better-kept
13:25 < kanzure> is not a mirror
13:25 < justanotheruser> ah
13:25 < justanotheruser> so they're going to fix it?
13:26 < kanzure> the friend doesn't work at ncbi
13:26 < kanzure> he's just a bioinformatics nuthead
13:27 < kanzure> he says also try ddbj
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13:33 < kanzure> "My friend Theo borm at wageningen was running a rolling archive"
13:34 < justanotheruser> well at least one copy of some of the most important data in the world exists
13:34 < justanotheruser> or at least did exist given the ambiguous "was"
13:36 < kanzure> http://www.ebi.ac.uk/ena/data/view/GCA_000336755.1
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13:41 < kanzure> http://bacteria.ensembl.org/haloferax_elongans_atcc_baa_1513/Info/Index
13:42 < kanzure> ftp://ftp.ensemblgenomes.org/pub/bacteria/release-27/fasta/bacteria_34_collection/haloferax_elongans_atcc_baa_1513/dna/
13:43 < justanotheruser> I appreciate the help, but I'm not looking for  haloferax elongans specifically, that was just one that was broken that I noticed
13:43 < justanotheruser> I am going through the VT database right now
13:46 < kanzure> weird that they classified it as bacteria
13:46 < justanotheruser> it is archaea in the ftp server
13:46 < kanzure> bacteria_34_collection
13:46 < justanotheruser> maybe they're stuck in the 70s?
13:47 < kanzure> happened to me once
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14:36 < justanotheruser> another discrepancy, ftp://ftp.hgc.jp/pub/mirror/ncbi/genomes/genbank/ doesn't have viral, ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/ does
14:38 < justanotheruser> anyways, I'm not even downloading actual content yet, still on 200MB of html pages, probably 200 more to go
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14:41 < delinquentme> john mcafee == techno jesus
14:41 < kanzure> techno jesus is just supply side jesus
14:41 < kanzure> .g site:youtube.com supply side jesus
14:41 < yoleaux> http://www.youtube.com/watch?v=Gc-LJ_3VbUA
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14:46 < nmz787_i> sous vide jesus
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14:56 < CaptHindsight> https://experiment.com/projects/sequencing-the-black-rhinoceros-genome
14:58 < kanzure> i see the names of a few hplusroadmappers there
14:58 < CaptHindsight> small world
14:59 < CaptHindsight> do you guys have conferences and meetings?
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15:00 < kanzure> just irc :-)
15:01 < CaptHindsight> kanzure: you have to stop posting new fun things to make, too many distractions  :)
15:04 < kanzure> CaptHindsight: here's a really fun thing, http://diyhpl.us/~bryan/papers2/space/Orbiting%20rainbows%20-%20optical%20manipulation%20of%20aerosols%20and%20the%20beginnings%20of%20future%20space%20construction%20-%20NASA.pdf
15:04 < kanzure> i think you could probably do this with inkjets too
15:11 < delinquentme> serious question, keeping in mind barnaby jack.
15:12 < delinquentme> At what point should you be worried about your life when infringing on markets of X size?
15:13 < kanzure> never; you get golden parachutes.
15:14 < nmz787_i> delinquentme: I think about it all the time
15:14 < nmz787_i> delinquentme: anytime you're possibly affecting enough money that would cost to put a hit out on you, and cover it up
15:14 < delinquentme> kanzure, what is a golden shower
15:15 < delinquentme> erm parachute.
15:15 < nmz787_i> s/enough/more than enough/
15:15 < nmz787_i> in reality they probably include a risk buffer of something like 10X that cost
15:24 < delinquentme> nmz787_i, you're saying that its worrysome for the hit-caller because of backlash
15:34 < nmz787_i> I'd say more for getting caught, but then yeah also backlash
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15:54 < CaptHindsight> http://www.ebay.com/itm/A3-Size-Flatbed-6-Colors-T-Shirt-Garment-Printer-With-Heating-Free-White-Ink-/121699456111  $2k (auction)
15:56 < CaptHindsight> Model: 	Modified Epson1430 Printer, they use the Epson controller with it's limitations
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19:47 < kanzure> beep
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20:47 < juri_> boop.
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--- Log closed Fri Jul 10 00:00:06 2015