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| -!- 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] | 02:49 | |
| [ Adifex|zzz] [ d3vz3r0 ] [ juul ] [ realzies ] [ uberj ] | 02:49 | |
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| [ brownies ] [ helleshin] [ paperbot ] [ strangewarp ] | 02:49 | |
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| [ cluckj ] [ juri_ ] [ phryk ] [ Twey ] | 02:49 | |
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| !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 | 02:49 | |
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| kanzure | http://dirtypcbs.com/ "10 each 5x5cm PCBs $12 • 10 each 10x10cm PCBs $24" | 09:21 |
|---|---|---|
| kanzure | "No bull, just crappy PCBs" | 09:21 |
| chris_99 | haha | 09:23 |
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| delinquentme | whats the optical resolution limit ? 250 nm ? nmz787 ? | 09:27 |
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| nmz787_i | genomics conference today! | 09:58 |
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| 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" | 12:03 |
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| 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 ? | 13:08 |
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| 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 | 13:21 |
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| FourFire | nmz787, and this infodump is desirable, why? | 13:26 |
| 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 | 13:27 |
| 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 | 13:28 |
| 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 | 13:29 |
| kanzure | how else are you going to make a personalized drug | 13:30 |
| kanzure | for example, if you want to target the mutated receptors | 13:30 |
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| 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) | 13:36 |
| nmz787_i | they were saying needing 10000 genomes to get useful info from 1 genome (i.e. yours) | 13:37 |
| nmz787_i | and also that realistically we need to do pre-cancer sequencing (of course, Leroy Hood said this years ago) | 13:38 |
| 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) | 13:39 |
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| kanzure | jrayhawk: also consider rna sequencing to figure out which strain of virus is killing you | 13:45 |
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| 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 | 14:02 |
| 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 | 14:05 |
| 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! | 14:07 |
| nsh | massive input, massive output, tiny throughput | 14:09 |
| 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 | 14:15 |
| jrayhawk | where researchers bend over backwards not to overturn theories with significant political inertia but zero epistemic grounding | 14:16 |
| kanzure | do you also think that dna barcoding is bullshit? | 14:18 |
| 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) | 14:20 |
| kanzure | "boo hoo we don't have time to do 4000 tests" well fuck you | 14:21 |
| jrayhawk | haha, yeah, I can see that being useful. | 14:22 |
| 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 | 14:24 |
| 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 | 14:25 |
| 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 | 14:26 |
| 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 | 14:27 |
| kanzure | how are they still in business now that they can't legally sell their subscription product? | 14:31 |
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| stieruridir | they can't give medical advice, iirc | 14:31 |
| stieruridir | the rest is legal | 14:31 |
| 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 | 14:32 |
| stieruridir | https://www.23andme.com/health/ | 14:33 |
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| nmz787_i | they use some company LabCorps | 14:56 |
| nmz787_i | one in L.A. and one in North Carolina | 14:56 |
| nmz787_i | hah some nerd just told the guy off | 14:57 |
| nmz787_i | since the presenter didnt mention anything about compute related things | 14:57 |
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| 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 | 15:51 |
| 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. | 15:52 |
| nmz787_i | what's it for? | 15:53 |
| 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 | 15:54 |
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| nmz787_i | people are ridiculing the use of Java | 15:56 |
| 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 ? | 16:14 |
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| 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 | 19:05 |
| 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 | 19:06 |
| 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 | 19:07 |
| 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/ | 19:08 |
| 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 | 19:09 |
| 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 | 19:10 |
| 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 | 19:11 |
| 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 | 19:12 |
| 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? | 19:13 |
| kanzure | can you be more specific. what is your question? | 19:14 |
| 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 | 19:15 |
| FourFire | nuclear power plant, 6 football fields 10 stories high | 19:16 |
| FourFire | nvm, talk to you all in the morning | 19:16 |
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| kanzure | n;iray os a;sp s[ommomg | 19:17 |
| kanzure | bluray is also spinning | 19:17 |
| dingo | ah its clear now, kanzure uses qwerty! | 19:21 |
| 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/ | 19:23 |
| 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 | 19:24 |
| nmz787 | one dude was even saying that tissue from the left vs right side of a tumor is gonna give diff reads | 19:34 |
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| 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. | 19:44 |
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| kanzure | https://twitter.com/OpenSSLFact | 20:41 |
| kanzure | "A "short" list of OpenSSL's global variables. http://pastebin.com/vQ7MPBmW " | 20:42 |
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| --- Log closed Wed Apr 09 00:00:32 2014 | ||
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