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| 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) | 06:55 |
| 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 | 06:56 |
| kanzure | wasn't aware that they knew each other | 06:58 |
| eudoxia | i was surprised as well | 06:58 |
| kanzure | well maybe you should post a question about that | 06:59 |
| 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. | 07:00 |
| kanzure | asimov short story https://www.uni.edu/morgans/astro/course/nightfall.pdf | 07:10 |
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| kanzure | planar mechanism kinematic simulator http://designengrlab.github.io/PMKS/ https://github.com/DesignEngrLab/PMKS | 07:25 |
| kanzure | https://www.snellman.net/blog/archive/2015-07-09-unit-testing-a-tcp-stack/ | 07:33 |
| kanzure | mobile tcp optimization http://blog.ipspace.net/2015/03/tcp-optimization-with-juho-snellman-on.html | 07:34 |
| CaptHindsight | kanzure: http://www.pastebin.ca/3054383 POSaM example playbook file | 07:41 |
| CaptHindsight | if all the times are in seconds then it looks like a few minutes per layer | 07:42 |
| CaptHindsight | layer/base | 07:43 |
| CaptHindsight | wait times for DRY, WASH, DEPROTECT are 30 seconds | 07:44 |
| kanzure | 0.7 seconds to deposit acetonitrile for all slides, or is that 0.7 seconds per slide? | 07:48 |
| 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 | 07:49 |
| CaptHindsight | don't know for certain | 07:50 |
| 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 | 07:51 |
| 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 | 07:52 |
| 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 | 07:53 |
| CaptHindsight | well it's like most Linux docs | 07:54 |
| CaptHindsight | the POSaM docs are better than most | 07:54 |
| CaptHindsight | kanzure: http://www.pastebin.ca/3054403 here's the other file for their Arrayer application | 07:59 |
| kanzure | http://www.systemsbiology.org/people/faculty/hood-lab/ | 08:11 |
| 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 | 08:13 |
| kanzure | see "biography" https://www.systemsbiology.org/bio/chris-lausted-phd/ | 08:14 |
| kanzure | 206-732-1276 | 08:15 |
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| CaptHindsight | they had 3 apps, PGO, Lombardi and finally Arrayer | 08:23 |
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| 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 | 08:37 |
| 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 | 08:39 |
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| nmz787_i | ParahSailin_: I wanted that GA2x but you never got back in touch with me | 10:01 |
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| nmz787_i | and most likely the electrochemical portion of that microarray builder is just generating the acid | 10:02 |
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| kanzure | agreed re: acid generation | 10:41 |
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| 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/ | 11:39 |
| kanzure | ncbi ftp servers are synchronized from other servers, it's possible that the data was lost or it's a replication error | 11:50 |
| 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/ | 11:51 |
| 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 | 11:52 |
| 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 -_- | 11:54 |
| * justanotheruser deletes his broken mirror attempt | 11:57 | |
| kanzure | let me know if you choose not to complain to ncbi | 11:58 |
| kanzure | /topic hplusroadmap, saving ncbi from losing genomes :-/ | 11:58 |
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| justanotheruser | kanzure: I emailed them | 12:29 |
| 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 | 12:30 |
| justanotheruser | or even better a single compressed copy of the entire refseq/ dir | 12:32 |
| kanzure | "their html garbage"... what? it's an ftp server. use rsync, lftp, etc. | 12:33 |
| justanotheruser | huh? It's http, how do I ftp in? | 12:34 |
| 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? | 12:35 |
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| kanzure | hm. | 12:37 |
| 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 | 12:38 |
| kanzure | jrayhawk: can you convince pdx.edu kthx | 12:39 |
| 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) | 12:40 |
| 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. | 12:46 |
| 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 | 12:47 |
| kanzure | the html files are probably an artifact of whatever mirroring technique that they are using | 12:48 |
| 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/ | 12:53 |
| 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 | 12:54 |
| 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 | 12:55 |
| 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 | 12:57 |
| 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/ | 12:58 |
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| kanzure | plz take notes and i will point some servers at this later | 13:02 |
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| kanzure | justanotheruser: try http://www.ebi.ac.uk/ena | 13:20 |
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| kanzure | http://www.ebi.ac.uk/ena/browse/sequence-download | 13:20 |
| kanzure | ftp://ftp.ebi.ac.uk/pub/databases/embl/ | 13:20 |
| 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] | 13:22 |
| 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 | 13:23 |
| justanotheruser | are you just giving me this database to check for inconsistencies? The directory structure is completely different from the other servers afaics | 13:24 |
| 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? | 13:25 |
| kanzure | the friend doesn't work at ncbi | 13:26 |
| kanzure | he's just a bioinformatics nuthead | 13:26 |
| kanzure | he says also try ddbj | 13:27 |
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| kanzure | "My friend Theo borm at wageningen was running a rolling archive" | 13:33 |
| 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" | 13:34 |
| kanzure | http://www.ebi.ac.uk/ena/data/view/GCA_000336755.1 | 13:36 |
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| kanzure | http://bacteria.ensembl.org/haloferax_elongans_atcc_baa_1513/Info/Index | 13:41 |
| kanzure | ftp://ftp.ensemblgenomes.org/pub/bacteria/release-27/fasta/bacteria_34_collection/haloferax_elongans_atcc_baa_1513/dna/ | 13:42 |
| 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 | 13:43 |
| 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? | 13:46 |
| kanzure | happened to me once | 13:47 |
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| 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 | 14:36 |
| justanotheruser | anyways, I'm not even downloading actual content yet, still on 200MB of html pages, probably 200 more to go | 14:38 |
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| 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 | 14:41 |
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| nmz787_i | sous vide jesus | 14:46 |
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| CaptHindsight | https://experiment.com/projects/sequencing-the-black-rhinoceros-genome | 14:56 |
| kanzure | i see the names of a few hplusroadmappers there | 14:58 |
| CaptHindsight | small world | 14:58 |
| CaptHindsight | do you guys have conferences and meetings? | 14:59 |
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| kanzure | just irc :-) | 15:00 |
| CaptHindsight | kanzure: you have to stop posting new fun things to make, too many distractions :) | 15:01 |
| 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 | 15:04 |
| delinquentme | serious question, keeping in mind barnaby jack. | 15:11 |
| delinquentme | At what point should you be worried about your life when infringing on markets of X size? | 15:12 |
| kanzure | never; you get golden parachutes. | 15:13 |
| 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 | 15:14 |
| 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 | 15:15 |
| delinquentme | nmz787_i, you're saying that its worrysome for the hit-caller because of backlash | 15:24 |
| nmz787_i | I'd say more for getting caught, but then yeah also backlash | 15:34 |
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| CaptHindsight | http://www.ebay.com/itm/A3-Size-Flatbed-6-Colors-T-Shirt-Garment-Printer-With-Heating-Free-White-Ink-/121699456111 $2k (auction) | 15:54 |
| CaptHindsight | Model: Modified Epson1430 Printer, they use the Epson controller with it's limitations | 15:56 |
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| kanzure | beep | 19:47 |
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| juri_ | boop. | 20:47 |
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| --- Log closed Fri Jul 10 00:00:06 2015 | ||
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