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02:49 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA | http://gnusha.org/logs http://diyhpl.us/wiki http://groups.google.com/group/diybio | banned by the Federal Death Administration | official paperbot fan club
02:49 -!- Topic set by kanzure [~kanzure@131.252.130.248] [Sat Mar 23 20:40:45 2013]
02:49 [Users ##hplusroadmap]
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02:49 !asimov.freenode.net [freenode-info] channel trolls and no channel staff around to help? please check with freenode support: http://freenode.net/faq.shtml#gettinghelp
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09:21 < kanzure> http://dirtypcbs.com/ "10 each 5x5cm PCBs $12 • 10 each 10x10cm PCBs $24"
09:21 < kanzure> "No bull, just crappy PCBs"
09:23 < chris_99> haha
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09:27 < delinquentme> whats the optical resolution limit ? 250 nm ? nmz787 ?
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09:58 < nmz787_i> genomics conference today!
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12:03 < archels> .title http://dev.biologists.org/content/141/8/1627.full
12:03 < yoleaux> Regeneration of the aged thymus by a single transcription factor
12:03 < kanzure> http://www.silkroadequity.com/ "definitely not pirates"
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13:08 < delinquentme> ok so we've got microscopes which are made for human use which have these additional angles in the optical path.  Is there a specific term for an in-line optical path ( say something like the lens on an expensive camera ) which all of the magnification / focus optics are in-line ?
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13:21 < nmz787_i> if cancer patients got genome sequenced every 2 weeks for a year it would generate 495 exabytes of data per year313 exabytes if everyone in the U.S. got sequenced once per year
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13:26 < FourFire> nmz787, and this infodump is desirable, why?
13:27 < kanzure> ideally any time you're sick you should just get your tumors sequenced completely
13:27 < kanzure> sequence everything
13:27 < jrayhawk> we've already spent billions on sequencing for cancer and it's done approximately fuck-all good
13:27 < jrayhawk> i do not see why you want to send good money after bad
13:28 < kanzure> actually most patients that have cancer have never had their cancers sequenced
13:28 < jrayhawk> yes, because it wouldn't be useful
13:28 < jrayhawk> cancer causes mutagenesis, not vice versa
13:29 < jrayhawk> and, in fact, cancers are so mutagenic that even thousands of sequencings of a given cancer would be incomplete
13:29 < jrayhawk> and it would *still* be useless
13:30 < kanzure> how else are you going to make a personalized drug
13:30 < kanzure> for example, if you want to target the mutated receptors
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13:36 < nmz787_i> yeah basically you need those statistics to make any progress according to these folks (this is a conference, so I think its the consensus, but maybe not)
13:37 < nmz787_i> they were saying needing 10000 genomes to get useful info from 1 genome (i.e. yours)
13:38 < nmz787_i> and also that realistically we need to do pre-cancer sequencing (of course, Leroy Hood said this years ago)
13:39 < nmz787_i> and also that using cell-free DNA will give us higher hits for cancerous cells that have apoptosed or been chewed up by the immune system
13:39 < nmz787_i> (I think Hood said that too)
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13:45 < kanzure> jrayhawk: also consider rna sequencing to figure out which strain of virus is killing you
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14:02 < jrayhawk> yeah, the "statistics" claim is because their earlier claims that the somatic mutation theory would actually produce meaningful results didn't pan out
14:02 < jrayhawk> cancer sequencing is epistemically bankrupt charlatanry
14:05 < nmz787_i> 'steve schwartz is here from 23andme'
14:05 < nmz787_i> jrayhawk: I don't believe its charlatanery, I think its just too expensive today
14:07 < jrayhawk> "billions of dollars of whole-genome association studies didn't work out? well maybe if we try TEN THOUSAND TIMES AS MANY GENOMES!"
14:07 < jrayhawk> way to fill us with confidence, researchers!
14:09 < nsh> massive input, massive output, tiny throughput
14:15 < jrayhawk> nmz787_i: http://members.shaw.ca/jeanaltemeyer/drbob/TheAuthoritarians.pdf did you ever read this?
14:15 < jrayhawk> your mention of "consensus" is particularly concerning when I'm pretty sure you've seen what happened with e.g. the lipid hypothesis
14:16 < jrayhawk> where researchers bend over backwards not to overturn theories with significant political inertia but zero epistemic grounding
14:18 < kanzure> do you also think that dna barcoding is bullshit?
14:20 < jrayhawk> don't know; haven't studied claims-versus-results on that one
14:20 < kanzure> every episode of house has these kids pipetting blood samples to do virus detection which could have been done just as easily by sequencing the rna (or dna in the case of bacterial infections)
14:21 < kanzure> "boo hoo we don't have time to do 4000 tests" well fuck you
14:22 < jrayhawk> haha, yeah, I can see that being useful.
14:24 < nmz787_i> oh gosh, a new omics word
14:24 < nmz787_i> Literomics
14:24 < nmz787_i> omics of literaure
14:24 < kanzure> blame dbolser for that one
14:25 < nmz787_i> kanzure: sequencing still requires a lot of pipetting
14:25 < nmz787_i> so they could have still been doing sequencing, even though its just TV
14:25 < nmz787_i> github/amplab/snap
14:25 < nmz787_i> github/bigdatagenomics
14:26 < nmz787_i> fastlmm.codeplex.com
14:26 < nmz787_i> literome.azurewebsites.net
14:26 < kanzure> microsoft junkies
14:26 < nmz787_i> yeah it was a dude from MS
14:27 < nmz787_i> jrayhawk: no haven't read that
14:27 < nmz787_i> oO 23andme is up
14:27 < nmz787_i> Steven P Schwartz
14:27 < nmz787_i> VP biz dev and strategy
14:31 < kanzure> how are they still in business now that they can't legally sell their subscription product?
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14:31 < stieruridir> they can't give medical advice, iirc
14:31 < stieruridir> the rest is legal
14:32 < kanzure> i tohught they couldn't sell a genetic testing product?
14:32 < stieruridir> https://www.23andme.com/store/cart/ nop, still legal
14:32 < stieruridir> they just can't tell you medical risk factors anymore
14:32 < kanzure> huh. so what do they show instead?
14:32 < stieruridir> heredity shit
14:33 < stieruridir> https://www.23andme.com/health/
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14:56 < nmz787_i> they use some company LabCorps
14:56 < nmz787_i> one in L.A. and one in North Carolina
14:57 < nmz787_i> hah some nerd just told the guy off
14:57 < nmz787_i> since the presenter didnt mention anything about compute related things
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15:51 < nmz787_i> ParahSailin: you do sequencing/bioinformatics right?
15:51 < ParahSailin> yes
15:51 < nmz787_i> I haven't heard of this GATK http://www.bio-itworld.com/2014/3/20/broad-intel-announce-speed-improvements-gatk-powered-by-intel-optimizations.html
15:51 < ParahSailin> eww
15:52 < nmz787_i> basically they used IPP and AVX to get some speedup, then added parallelization too
15:52 < ParahSailin> gatk is awful
15:52 < nmz787_i> oh really?
15:52 < nmz787_i> they've been talking about it all morn
15:52 < ParahSailin> try installing it.
15:53 < nmz787_i> what's it for?
15:54 < ParahSailin> i dont even remember what i tried to getting it working for
15:54 < ParahSailin> it was java?
15:54 < nmz787_i> "when we built it we built it to test hypotheses"
15:54 < nmz787_i> they showed C++ and Java speedup comparisons
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15:56 < nmz787_i> people are ridiculing the use of Java
16:14 < ParahSailin> i was trying to use their shitty snp detection pipeline just for comparison with tools i created
16:14 < ParahSailin> couldnt even get it to run
16:14 < kanzure> wait, which one of you knows phreedom?
16:14 < kanzure> and phreedom != phantomcircuit, right?
16:14 < kanzure> and != PhantomPhreak ?
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19:05 < nmz787> another quote was that those # of exabytes (something around 475, I can't remember) would require spinning discs that covered 6 football fields 10 stories high
19:06 < nmz787> and that basically the data center to compute the bayesian kernel blah blah informatics would basically take a nuclear power station for itself
19:06 < kanzure> i don't think anyone is using spinning discs anymore
19:07 < nmz787> apparently they are
19:07 < nmz787> dude from emc talked last
19:07 < nmz787> and that was his quote
19:07 < nmz787> well not the nuke one
19:07 < jrayhawk> yeah, on a RAM price/GiB basis spinning disks are still winners
19:08 < nmz787> most of what all the ppl there were doing was software improvements using the extended instruction sets now available for SIMD MIMD operations
19:08 < nmz787> SSE IPP AVX
19:08 < jrayhawk> http://blog.backblaze.com/2014/03/19/backblaze-storage-pod-4/
19:09 < nmz787> and i asked the head of the broad institute computer bio thing (or whoever he was) about trolls (thinking of you jrayhawk :P )
19:09 < jrayhawk> http://blog.backblaze.com/2014/03/18/100-petabytes-of-cloud-data/
19:09 < nmz787> and he said all this stuff was cheap in comparison to a few new jet planes
19:09 < nmz787> like 50 mil
19:09 < nmz787> to do the sequencing alone i believe
19:10 < nmz787> something like 14000 patients to get 1% confidence for a single cancer
19:10 < nmz787> and there are like 45 cancers and 450 subtypes
19:11 < kanzure> 450 subtypes per cancer?
19:11 < nmz787> so they were def projecting these numbers
19:11 < nmz787> kanzure: yeah idk it wasn't too clear
19:12 < nmz787> he rattled off some international disease something something.... an internation disease code
19:12 < nmz787> international
19:12 < kanzure> you are terrible at transcripts
19:12 < nmz787> mm
19:12 < nmz787> i was working during it
19:12 < kanzure> http://diyhpl.us/wiki/transcripts/
19:12 < nmz787> i mean working for work stuff
19:12 < nmz787> i wasn't planning on being there actually
19:13 < nmz787> i used a door i normally don't, heading to get coffee/breakfast
19:13 < nmz787> and saw the conference sign
19:13 < FourFire> nmz787, so once it's been computed, the results are stored and can be used by anyone right?
19:14 < kanzure> can you be more specific. what is your question?
19:15 < FourFire> Spinning disks are somewhat cheaper than burning stuff onto bluray (if you ignore the costs of the burners and waiting time)
19:15 < FourFire> what nmz787 said about the types of cancer
19:16 < FourFire> nuclear power plant, 6 football fields 10 stories high
19:16 < FourFire> nvm, talk to you all in the morning
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19:17 < kanzure> n;iray os a;sp s[ommomg
19:17 < kanzure> bluray is also spinning
19:21 < dingo> ah its clear now, kanzure uses qwerty!
19:23 < jrayhawk> "13:29 < jrayhawk> and, in fact, cancers are so mutagenic that even thousands of sequencings of a given cancer would be incomplete" oh yeah, i guess this could be misinterpreted: s/given cancer/single tissue/
19:24 < kanzure> but it so happens that there are highly typical cancers
19:24 < kanzure> dingo: could've just asked =)
19:24 < kanzure> dingo: but yes
19:34 < nmz787> one dude was even saying that tissue from the left vs right side of a tumor is gonna give diff reads
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19:44 < nmz787> anyone around the bay area with a truck that could help me haul some e-waste to makerFaire on Fri May 16th and back to the recycler on Sun May 18th? We can offer free admission to the faire and pay for mileage.
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20:41 < kanzure> https://twitter.com/OpenSSLFact
20:42 < kanzure> "A "short" list of OpenSSL's global variables. http://pastebin.com/vQ7MPBmW "
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