--- Log opened Tue Apr 16 00:00:59 2013 00:05 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] 00:11 -!- ThomasEgi [~thomas@185.5.8.81] has joined ##hplusroadmap 00:11 -!- ThomasEgi [~thomas@185.5.8.81] has quit [Changing host] 00:11 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 00:31 -!- SolG [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has joined ##hplusroadmap 00:33 -!- _Sol_ [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has quit [Ping timeout: 248 seconds] 00:44 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 00:53 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 00:55 -!- Mariu [Jimmy98@89.41.57.33] has joined ##hplusroadmap 00:56 -!- klafka [~klafka@rrcs-69-193-162-219.nyc.biz.rr.com] has quit [Remote host closed the connection] 00:57 -!- klafka [~klafka@rrcs-69-193-162-219.nyc.biz.rr.com] has joined ##hplusroadmap 01:02 -!- klafka [~klafka@rrcs-69-193-162-219.nyc.biz.rr.com] has quit [Ping timeout: 264 seconds] 01:07 -!- Coornail [~Coornail@li66-97.members.linode.com] has quit [Ping timeout: 260 seconds] 01:08 -!- Guest76021 [~Coornail@li66-97.members.linode.com] has joined ##hplusroadmap 01:10 -!- kajetan [122@d30-138.icpnet.pl] has quit [Ping timeout: 245 seconds] 01:13 -!- kajetan [122@d30-138.icpnet.pl] has joined ##hplusroadmap 02:02 -!- eugen [~eugen@beryllium.ativel.com] has joined ##hplusroadmap 02:02 -!- eugen is now known as Guest41178 02:03 -!- Guest41178 is now known as eleitl 02:04 < eleitl> paperbot: https://www.thieme-connect.com/ejournals/abstract/10.1055/s-0029-1241052?locale=de&LgSwitch=1 02:04 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/4ccedcae07582dec6309205affd7e388.txt 02:30 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has joined ##hplusroadmap 02:34 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 02:35 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 245 seconds] 02:36 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has quit [Ping timeout: 252 seconds] 02:41 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds] 02:43 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 02:54 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 02:55 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 248 seconds] 02:55 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has joined ##hplusroadmap 03:02 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 256 seconds] 03:04 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 03:12 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 245 seconds] 03:17 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 03:24 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 258 seconds] 03:26 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 03:33 < superkuh> paperbot: http://www.nature.com/nphys/journal/v9/n4/full/nphys2560.html 03:33 < paperbot> HTTP 401 unauthorized http://www.nature.com/nphys/journal/v9/n4/pdf/nphys2560.pdf 03:34 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 03:41 -!- clock [~clock@84-73-190-3.dclient.hispeed.ch] has joined ##hplusroadmap 04:00 < eleitl> what are you doing with knotted vortices? 04:14 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 256 seconds] 04:15 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has quit [Ping timeout: 246 seconds] 04:23 < chido> I need to order pipettes for my lab, has anyone a suggestion where to get them as cheap as possible? 04:25 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap 04:32 < superkuh> Absolutely nothing. I thought it was an aesthetically interesting paper. 04:38 < eleitl> Ah, thanks. 04:45 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 05:02 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 05:09 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 260 seconds] 05:33 < eleitl> Anyone looked into new alternatives to Bitcoin? 05:34 < chris_99> the litecoin thing? 05:35 < chris_99> theres also zerocoin which sounds interesting, an add-on to bitcoin 05:36 < eleitl> what do you think about PPCoin? 05:36 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 05:36 < eleitl> I'm looking for something with an improvement, or a different target. 05:36 < eleitl> I'm not sure Litecoin is that different. 05:37 < chris_99> not heard PPCoin, the bitcoin price has dropped a lot lower now :( 05:37 < eleitl> They claim their hash is ASIC-proof, but already you need a GPU to mine it 05:37 < eleitl> yeah, I'm going to buy another couple BTC 05:37 < chris_99> ASIC-proof, that sounds a bit weird 05:38 < eleitl> they try to level the playing field 05:38 < eleitl> you can ASIC-proof e.g. by way of a large lookup-table 05:38 < eleitl> or just a lot of evolving state, more than would fit on an ASIC 05:39 < chris_99> ah gotcha 05:39 < eleitl> PPCoin claims it needs way less power, once it goes off mining mode to lottery mode 05:39 < eleitl> I have no idea how true any of it is. 05:42 < chris_99> i'd be interested in knowing if any bitcoin alternatives would be adopted 05:42 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 264 seconds] 05:42 < chris_99> seen as bitcoin got in there first i guess 05:42 < eleitl> in case I find enough time for research I'll let you know the result 05:43 < chris_99> cool 05:56 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 05:58 -!- Viper168 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[~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 245 seconds] 07:48 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 07:53 -!- kajetan [122@d30-138.icpnet.pl] has quit [Ping timeout: 245 seconds] 07:54 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Read error: Connection reset by peer] 07:54 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 07:58 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 252 seconds] 08:02 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 08:04 -!- cpopell [~cpopell@pool-96-231-37-73.washdc.fios.verizon.net] has joined ##hplusroadmap 08:05 -!- eudoxia [~eudoxia@r186-52-7-106.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 08:06 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 248 seconds] 08:34 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 08:47 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has joined ##hplusroadmap 08:50 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 245 seconds] 08:56 -!- Charlie [~quassel@74.63.212.44] has joined ##hplusroadmap 08:59 -!- kajetan [~kmo@87-205-25-23.ip.netia.com.pl] has joined ##hplusroadmap 09:21 <@kanzure> "Youtube pre-Google was PHP" was it? 09:21 < eudoxia> wasn't that like back in 2005 or something 09:21 < Adifex> that's hard to imagine. 09:21 < eudoxia> seems possible 09:34 -!- eudoxia [~eudoxia@r186-52-7-106.dialup.adsl.anteldata.net.uy] has quit [Read error: Connection reset by peer] 09:34 -!- eudoxia [~eudoxia@r186-52-13-7.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 09:48 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 09:54 < brownies> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/23579320 09:54 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/92891174b826ecf71b12bcbad4ae9090.txt 09:54 < brownies> that... is not a PDF. 09:57 < brownies> .meow 09:57 < yoleaux> http://edgecats.net/cats/EYyO2.gif 09:57 < brownies> at least 1 of the robots still has it together. 10:04 < chris_99> awh poor cat 10:14 -!- ThomasEgi [~thomas@185.5.8.81] has joined ##hplusroadmap 10:14 -!- ThomasEgi [~thomas@185.5.8.81] has quit [Changing host] 10:14 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 10:31 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has joined ##hplusroadmap 10:39 <@kanzure> paperbot does not handle ncbi.nlm.nih.gov well at the moment 10:40 <@kanzure> some pubmed papers have a link to the actual publisher's site which might have the pdf 10:40 <@kanzure> also pubmedcentral.gov papers have a pdf but paperbot doesn't figure that out either i think 10:56 -!- Adifex [~Adifex@97-118-148-51.hlrn.qwest.net] has quit [Quit: Adifex] 11:24 -!- Adifex [~Adifex@97-118-148-51.hlrn.qwest.net] has joined ##hplusroadmap 11:38 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] 11:38 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 11:43 -!- augur [~augur@208.58.5.87] has quit [Ping timeout: 264 seconds] 11:45 -!- eudoxia [~eudoxia@r186-52-13-7.dialup.adsl.anteldata.net.uy] has left ##hplusroadmap ["leaving"] 11:57 < ParahSailin> paperbot: http://www.bloomberg.com/quote/CXLX:SP 11:57 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/896d267118bd63eea6e7a1a371222805.txt 12:00 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 12:15 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has joined ##hplusroadmap 12:18 <@kanzure> ParahSailin: how would you go about monitoring whether or not certain records have been removed/revoked from ncbi? 12:19 <@kanzure> it turns out that not all of the data is public domain 12:22 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 12:32 < ParahSailin> redactions from genbank? 12:33 <@kanzure> the data isn't public domain, i think it's possible for companies (perhaps those that have acquired patents from a bayh-dole compliance office) to cause information to be removed. 12:37 < ParahSailin> i've experienced gi's being culled from genbank from one month to the next, but usually its because of redundancy 12:46 -!- Mariu [Jimmy98@89.41.57.33] has joined ##hplusroadmap 12:53 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Operation timed out] 12:54 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 13:03 <@kanzure> "Celera initially announced that it would seek patent protection on "only 200–300" genes, but later amended this to seeking "intellectual property protection" on "fully-characterized important structures" amounting to 100–300 targets. The firm eventually filed preliminary ("place-holder") patent applications on 6,500 whole or partial genes. Celera also promised to publish their findings in accordance with the terms of the 1996 "Bermuda ... 13:03 <@kanzure> ... Statement", by releasing new data annually (the HGP released its new data daily), although, unlike the publicly funded project, they would not permit free redistribution or scientific use of the data." 13:03 <@kanzure> "In March 2000, President Clinton announced that the genome sequence could not be patented, and should be made freely available to all researchers. The statement sent Celera's stock plummeting and dragged down the biotechnology-heavy Nasdaq. The biotechnology sector lost about $50 billion in market capitalization in two days." 13:04 <@kanzure> haha clinton made a statement? i wonder if scotus is going to agree or not. 13:04 < Adifex> capitalization that was all fluff anyway. 13:07 <@kanzure> "But it has emerged that Celera may in fact be running behind its competitors. Human Genome Sciences, Maryland and Incyte, California, have each filed at least 6,300 full patent applications. Incyte have been granted 173." 13:09 <@kanzure> ParahSailin: do you guys just use data straight from genbank and whatever? 13:10 <@kanzure> ParahSailin: or do you audit your data's license? 13:22 <@kanzure> paperbot: http://papers.ssrn.com/sol3/Delivery.cfm?abstractid=1411328 13:22 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/6d2622ea15d9de2c9543ea88cc95cb17.txt 13:22 <@kanzure> paperbot: http://papers.ssrn.com/sol3/Delivery.cfm/SSRN_ID1411328_code857510.pdf?abstractid=1411328&mirid=5 13:22 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/d02e5c640682f111df7d975f8c5e3b3b.txt 13:23 <@kanzure> haha that's a user-agent xss hole 13:23 <@kanzure> wow even worse 13:23 <@kanzure> var sQuery = "abstract_id=1411328"; 13:23 <@kanzure> var sBrowser = "pdf-defense-force"; 13:24 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 13:26 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 13:27 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has quit [Remote host closed the connection] 13:31 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has joined ##hplusroadmap 13:34 <@kanzure> hm they seem to be filtering it pretty well 13:39 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds] 13:51 < Adifex> hey kanzure, I saw you're in #neuroscience as well - what other good rooms are there with reasonable activity? 14:01 -!- _0bitcount [~ulises11@82.159.59.4.dyn.user.ono.com] has joined ##hplusroadmap 14:03 <@kanzure> uh.. can you be more specific? what do you need? 14:03 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has quit [Ping timeout: 245 seconds] 14:04 <@kanzure> sciencedirect is using optimizely http://cdn.optimizely.com/js/180772688.js 14:05 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 264 seconds] 14:06 < Adifex> anything with good science discussion. Any favorites? 14:13 <@kanzure> woot deepdyve xss found. 14:15 <@kanzure> Adifex: no, they are all terrible at science. 14:18 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has quit [Ping timeout: 272 seconds] 14:22 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has quit [Remote host closed the connection] 14:34 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 14:35 <@kanzure> diybio-eu is crazy 14:36 <@kanzure> the london group apparently migrated their communications to use lhs-biohacking@lists.kentgeek.org a few months ago 14:36 <@kanzure> this fragmentation is really annoying 14:36 <@kanzure> https://lists.kentgeek.org/mailman/listinfo/lhs-biohacking 14:36 <@kanzure> https://lists.kentgeek.org/pipermail/lhs-biohacking/ 14:36 <@kanzure> gah since june 2011 14:37 <@kanzure> wtf.. 14:39 -!- Adifex [~Adifex@97-118-148-51.hlrn.qwest.net] has quit [Remote host closed the connection] 14:39 -!- Adifex [~Adifex@97-118-148-51.hlrn.qwest.net] has joined ##hplusroadmap 14:39 -!- _0bitcount [~ulises11@82.159.59.4.dyn.user.ono.com] has quit [Quit: Leaving] 14:53 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 14:57 < Adifex> http://trubrain.com 14:57 < Adifex> real or bunk? 14:57 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has quit [Remote host closed the connection] 14:58 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 252 seconds] 14:58 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has joined ##hplusroadmap 14:58 <@kanzure> probably just random supplements. 14:58 <@kanzure> may or may not make you feel better about yourself. 14:59 <@kanzure> some of them might be something you are missing in your system, but then again your daily intake might cover the basics already. 15:00 < Adifex> I imagine if you take Piracetam over a long period of time, your brain would simply acclimate to it, and any benefits would be wiped out. 15:01 <@kanzure> that sounds like something you would have to support with evidence dude 15:03 < ParahSailin> kanzure: ftp://ftp.ncbi.nlm.nih.gov/pub/ 15:03 -!- SolG is now known as _sol_ 15:03 < ParahSailin> havent ever paid attention to license 15:04 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 15:05 -!- Thorbinator [~Thorbinat@66-237-51-34.starstream.net] has quit [Read error: Connection reset by peer] 15:05 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has quit [Ping timeout: 260 seconds] 15:06 -!- Thorbinator [~Thorbinat@66-237-51-34.starstream.net] has joined ##hplusroadmap 15:06 <@kanzure> ParahSailin: i've been pondering that doing gene data licensing audits for biotech companies might be viable, but it's sorta scaremongery ("companies are going to sue you for using their data when you assemble genomes! of course, they don't actually have relevant evidence that you used their sequenced data, but who the hell knows until discovery.") 15:07 <@kanzure> esp. if your data is from ncbi, the likelihood of using someone else's data is increased dramatically since it's all license-unknown. 15:11 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has joined ##hplusroadmap 15:13 <@kanzure> ParahSailin: what is your company doing? just hoping? 15:13 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 15:14 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has quit [Remote host closed the connection] 15:14 -!- yorick [~yorick@oftn/member/yorick] has quit [Remote host closed the connection] 15:17 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 15:18 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 15:19 < ParahSailin> kanzure: i dont foresee an instance in which the license on ncbi data could get my employer in trouble 15:20 < ParahSailin> kanzure: main thing we're doing right now is trying to do genotyping cheaper than microarray 15:21 < ParahSailin> the rest is projects for clients, and i assume any liabilities are passed along to them 15:21 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 15:21 < ParahSailin> clients are mostly universities anyway 15:22 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 15:22 < ParahSailin> when's cory gonna gimme reads to assemble :( 15:26 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has joined ##hplusroadmap 15:26 -!- Zarakii [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 15:27 < Adifex> Which company, ParahSailin? 15:28 < ParahSailin> eurekagenomics 15:29 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Ping timeout: 272 seconds] 15:32 -!- Zarakii [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Ping timeout: 252 seconds] 15:36 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 15:47 -!- Adifex [~Adifex@97-118-148-51.hlrn.qwest.net] has quit [Quit: Adifex] 15:56 -!- yeastwest [~dad@pool-108-23-12-174.lsanca.fios.verizon.net] has quit [Ping timeout: 256 seconds] 16:01 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap 16:03 -!- klafka_ [~klafka@c-67-174-253-229.hsd1.ca.comcast.net] has joined ##hplusroadmap 16:06 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Ping timeout: 245 seconds] 16:07 -!- augur [~augur@129-2-129-34.wireless.umd.edu] has quit [Remote host closed the connection] 16:17 <@kanzure> ParahSailin: he claims his harvard collaborators haven't put them online yet. 16:23 -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has joined ##hplusroadmap 16:26 -!- radivis [~quassel@pD9F8907B.dip.t-dialin.net] has joined ##hplusroadmap 16:47 -!- augur [~augur@ip-64-134-41-137.public.wayport.net] has joined ##hplusroadmap 16:51 -!- 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[~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 18:51 -!- Zarakii [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 18:55 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Ping timeout: 264 seconds] 19:06 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 19:19 -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Quit: I am going to play computer games.] 19:23 -!- OldCoder_ [~OldCoder_@209.237.22.146] has joined ##hplusroadmap 19:23 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has joined ##hplusroadmap 19:31 <@kanzure> yashgaroth: sup 19:32 < yashgaroth> not much 19:45 -!- klafka_ [~klafka@c-67-174-253-229.hsd1.ca.comcast.net] has quit [Remote host closed the connection] 20:01 -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has quit [Ping timeout: 260 seconds] 20:39 -!- OldCoder_ [~OldCoder_@209.237.22.146] has quit [Quit: Leaving] 20:39 < Lemminkainen> hey yashgaroth how's the muscle research coming? 20:39 < yashgaroth> eh pretty good, I guess 20:40 < Lemminkainen> how're your targets coming? 20:40 < yashgaroth> targets remain unchanged 20:40 < Lemminkainen> I forget, were you doing an siRNA knockdown approach or a transfection approach? 20:41 < yashgaroth> transfection, siRNA knockdown is short-lasting and siRNA is annoyingly difficult to produce 20:41 -!- Zarakii [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 20:41 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 20:42 < Lemminkainen> were you targeting satellite cells or muscle synctycia? 20:42 < yashgaroth> both, I suppose; the protein is secreted so you shouldn't need to target satellite cells specifically 20:43 < Lemminkainen> so when will it be ready to experiment on cpopell with? 20:44 < yashgaroth> once/if it works on myself 20:44 < yashgaroth> if it doesn't have any obvious effect for me I'm gonna try fusing it to an Fc fragment, boost the half-life 20:45 < yashgaroth> which will also make it possibly immunogenic, which is why I'm not trying that from the get-go 20:45 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 20:46 < Lemminkainen> aye aye; gonna make it a liposomal transfection protocol so users of it can sensually rub it on themselves in the shower? 20:46 -!- Zarakii [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 20:47 < yashgaroth> as adjective as that would be, that would only transfect dead surface skin cells 20:47 < yashgaroth> also liposomes are expensive, toxic, and less efficient than electroporation 20:48 < Lemminkainen> waitaminute, how're you electroporating yourself? 20:49 < yashgaroth> power supply and controller, hooked up to the two syringe needles that will be located in my arm 20:49 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Ping timeout: 264 seconds] 20:50 < Lemminkainen> sufficiently kinky 20:51 < yashgaroth> probably won't be too painful, but then I don't even have any tattoos 20:53 < Lemminkainen> you including a reporter fusion to track successful transfection, right? 20:54 < yashgaroth> nah fuck no that'd be super immunogenic 20:54 < yashgaroth> maybe a serum assay for follistatin 20:55 < Lemminkainen> could do a localized assay for IGF-1 20:55 < Lemminkainen> I keep forgetting that you cant just stick GFP into people 20:55 < yashgaroth> true, but follistatin acts on several pathways for muscle growth, igf-1 being a major one admittedly 20:55 < yashgaroth> if you could stick any protein you wanted into people, we'd have cured a lot more diseases by now 20:56 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap 20:56 < ParahSail1n> why not just shoot up some aav vector 20:56 < yashgaroth> what did I just say about immunogenicity 20:56 < ParahSail1n> aav is non immunogenic 20:57 < Lemminkainen> and no guarantee that wouldn't hit his sphincter muscles 20:57 < yashgaroth> in lab animals living in controlled environments their entire lives 20:57 < yashgaroth> no protein or virus is 'non immunogenic' 20:57 < yashgaroth> especially after the first exposure to a massive dose 20:58 < yashgaroth> it's fine for people with Serious Diseases who can go into a hospital and take a heavy course of immunosuppressants 20:58 < yashgaroth> which is an assumed OK for clinical gene therapies, but not me 20:59 < Lemminkainen> seems that we'd ideally move to a multilayered nanoparticle approach for in vivo transfection, then 20:59 < ParahSail1n> eh, you should be fine, immunogenicity only reduces efficacy 20:59 < ParahSail1n> not gonna hurt you more than non-treatment 21:00 < yashgaroth> and then the immune system attacks the transduced cells 21:00 < ParahSail1n> if you're naive, the first dose should work good enough 21:00 < ParahSail1n> thats not how magic works 21:00 < ParahSail1n> immunogenicity is to capsid 21:00 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Ping timeout: 240 seconds] 21:00 < yashgaroth> yep, capsid gets enveloped and digested by the host cell, and some of that's gonna get displayed 21:01 < yashgaroth> sure if you're naive the first dose will probably go fine, but good luck figuring out dosage levels and repeat administration 21:02 < ParahSail1n> im not sure that display of capsid proteins is a frequent enough of an event to be concerned about 21:02 < yashgaroth> when you're injecting 10 billion viral particles, it might be 21:03 < yashgaroth> lemminkainen nanoparticles are fine but the advantage of viruses is their ability to transit to the nucleus and then enter it, which occurs from specific protein-protein binding; and those proteins will be immunogenic 21:03 < Lemminkainen> there's still a distinction to be made between capsid vector and its payload; may develop immune reaction against the capsid, but not its contents 21:04 < yashgaroth> sure, and immune response to the contents is more a problem for people missing the delivered gene, which admittedly is 99% of clinical gene therapy 21:05 < Lemminkainen> if the contents are genetic, there is no immune response to it 21:05 <@kanzure> heh EFF wants source code submissions to be mandatory for software patents 21:05 < yashgaroth> there is an immune response to the protein that is produced 21:05 <@kanzure> https://www.eff.org/sites/default/files/eff_comments_on_enhancement_of_quality_of_software-related_patents.pdf 21:05 < Lemminkainen> proteins like Cleaver and Artemis deal with dsRNA and weird naked cytosolic DNA 21:05 < yashgaroth> and a reaction to the capsid will destroy all the transduced cells, probably not on the first dose in a naive target, but likely on any subsequent dose 21:07 < yashgaroth> if some cells of a person with MD start producing dystrophin, eventually the immune system will notice and steamroll them 21:07 < Lemminkainen> you're overthinking it dude there are lots of viruses, e.g. cytomegalovirus, that subvert cytosolic digestion and MHC-I display of their capsids by fucking with rough ER trafficking 21:08 < yashgaroth> mhm and they either go latent without producing any protein, or use those MHC-disrupting genes while they're doing a full-scale invasion anyway 21:08 < Lemminkainen> yep they do, but why do you suppose our genomes are littered with the remains of ancient viruses? 21:08 < yashgaroth> because some of them snuck into germ cells and became latent 21:09 < yashgaroth> if it was easy to sneak foreign protein production into cells, gene therapy would have >1 clinical trial successes 21:09 < Lemminkainen> sure, some did, but also consider tumor immunology; MHC-I presentation during cancer growth becomes deranged and NK CD8+ T-cells are supposed to nip them in the bud before they get too big 21:09 < Lemminkainen> often they do, but when a tumor gets too big, IL-10 kicks in to knock down the CD8+ rager and the tumor survives 21:10 < Lemminkainen> if you're doing body-wide transfection, the immune system would have to go into sepsis death mode to deal with it and it has very specific regulatory mechanisms against it 21:10 < yashgaroth> which may not kick in until after multiple organ failure 21:11 <@kanzure> hrmm https://defendinnovation.org/ this breaks text selection. eff is now officially evil. 21:11 < Lemminkainen> true enough, but we're smarter than allowing sepsis to spiral in controlled cases if we have an inkling it may happen 21:12 < yashgaroth> and those controlled cases are why people with serious diseases will be under heavy immunosuppression when they get the gene therapy 21:12 < Lemminkainen> yashgaroth I get the impression you're laying failure of genetic engineering clinical trials at immunology's feet when I'd suggest there's a lot to do with bad targeting going on 21:12 < Lemminkainen> we still really suck at getting anything into a nucleus in vivo 21:12 < yashgaroth> nah, viruses are awesome at that shit 21:13 < yashgaroth> finding a synthetic or other non-immunogenic molecule that will bind & activate importin, that's a problem 21:15 < yashgaroth> using plasmids and other non-viral methods, you're stuck hoping really hard that a plasmid ends up in the nucleus 21:46 -!- clock [~clock@84-73-190-3.dclient.hispeed.ch] has quit [Quit: Leaving] 21:54 -!- makoLime [~mako@103-9-42-32.flip.co.nz] has joined ##hplusroadmap 21:57 -!- yoleaux [~yoleaux@obquire.infologie.co] has quit [Ping timeout: 252 seconds] 22:06 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 22:07 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 245 seconds] 22:13 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 22:14 -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 240 seconds] 22:20 -!- yoleaux [~yoleaux@obquire.infologie.co] has joined ##hplusroadmap 22:22 -!- Swordsman [~kohii@50.46.238.42] has joined ##hplusroadmap 22:23 < Swordsman> guys 22:24 < Swordsman> Did you see this? http://donottouch.org/ 22:24 < Swordsman> someone just linked it in #chemistry a little while ago, I was thinking that it seemed interesting in regards to AI research and the like 22:25 < Swordsman> I'm guessing it might be old news to you, but I got pretty excited when I saw it 22:27 -!- AdrianG [~dextro@unaffiliated/amphetamine] has joined ##hplusroadmap 22:29 -!- Zarakii [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 22:29 -!- AdrienG [~dextro@unaffiliated/amphetamine] has quit [Ping timeout: 258 seconds] 22:30 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 22:33 -!- OldCoder_ [~OldCoder_@c-67-188-115-249.hsd1.ca.comcast.net] has joined ##hplusroadmap 22:41 <@fenn> "50 years of pointing and clicking".. can you get any more depressing than that 22:42 <@kanzure> sure, how about this: englebart is proud of the mouse. 22:42 <@kanzure> engelbart 22:48 <@fenn> engelbart's mouse was mostly a selector; the commands were actually performed by the chording keyboard 23:06 -!- _sol_ [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has quit [Read error: Connection reset by peer] 23:07 -!- _Sol_ [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has joined ##hplusroadmap 23:33 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 23:33 -!- Suwap [~devillll@ppp-46-244-171-143.dynamic.mnet-online.de] has joined ##hplusroadmap 23:33 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] 23:41 <@kanzure> this is really rudimentary but it covers the basics https://www.coursera.org/course/compneuro 23:41 <@kanzure> on computational neuroscience. 23:55 -!- AdrienG [~dextro@unaffiliated/amphetamine] has joined ##hplusroadmap 23:58 -!- AdrianG [~dextro@unaffiliated/amphetamine] has quit [Ping timeout: 272 seconds] --- Log closed Wed Apr 17 00:00:00 2013