--- Log opened Thu Apr 25 00:00:07 2013 00:12 -!- soylentbomb [~k@unaffiliated/soylentbomb] has joined ##hplusroadmap 00:42 -!- Suwap [~devillll@ppp-46-244-176-131.dynamic.mnet-online.de] has quit [Read error: Connection reset by peer] 00:43 -!- Suwap [~devillll@ppp-46-244-176-131.dynamic.mnet-online.de] has joined ##hplusroadmap 00:43 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap 00:43 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap 00:48 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Ping timeout: 252 seconds] 00:53 -!- Mokstar [~Moktart@c-98-246-107-5.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds] 01:13 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 01:14 -!- Charlie [~quassel@74.63.212.44] has quit [Ping timeout: 264 seconds] 01:19 <@archels> Mokstar: but see http://dspace.mit.edu/bitstream/handle/1721.1/62715/715318821.pdf 01:19 <@archels> there's still much ado about the "haemo-neural hypothesis" 01:36 -!- Charlie [~quassel@74.63.212.44] has joined ##hplusroadmap 02:05 -!- Mokstar [~Moktart@c-98-246-107-5.hsd1.or.comcast.net] has joined ##hplusroadmap 02:07 -!- wizrobe [~userdi@c-76-23-254-105.hsd1.ct.comcast.net] has left ##hplusroadmap [] 02:11 <@archels> Mokstar: see logs 02:12 < Mokstar> oh yeah 02:12 < Mokstar> I forgot kanzure obsessively logs everything 02:43 -!- Charlie [~quassel@74.63.212.44] has quit [Ping timeout: 246 seconds] 03:10 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 03:37 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 258 seconds] 03:42 -!- Charlie [~quassel@74.63.212.44] has joined ##hplusroadmap 03:48 -!- kajetan [~kmo@150.254.83.64] has joined ##hplusroadmap 03:50 -!- kajetan [~kmo@150.254.83.64] has quit [Remote host closed the connection] 03:53 -!- kajetan [~kmo@150.254.83.64] has joined ##hplusroadmap 04:07 -!- makoLime [~mako@103-9-42-48.flip.co.nz] has quit [Ping timeout: 252 seconds] 04:12 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 04:20 -!- zdap [~not@bas5-kingston08-3096457995.dsl.bell.ca] has joined ##hplusroadmap 04:20 -!- nsh_ [~nsh@obquire.infologie.co] has joined ##hplusroadmap 04:21 -!- juri__ [juri@funkykitty.net] has joined ##hplusroadmap 04:22 -!- ua_ [~ua@static.124.15.9.5.clients.your-server.de] has joined ##hplusroadmap 04:24 -!- Mokstar [~Moktart@c-98-246-107-5.hsd1.or.comcast.net] has quit [Read error: Connection reset by peer] 04:29 -!- Netsplit *.net <-> *.split quits: pad2, nsh, ua, juri_ 04:49 -!- nsh_ [~nsh@obquire.infologie.co] has quit [Read error: Connection timed out] 04:49 -!- nsh [~nsh@obquire.infologie.co] has joined ##hplusroadmap 04:54 -!- nsh [~nsh@obquire.infologie.co] has quit [Ping timeout: 252 seconds] 05:04 -!- yoleaux [~yoleaux@obquire.infologie.co] has quit [Ping timeout: 252 seconds] 05:12 -!- yoleaux [~yoleaux@obquire.infologie.co] has joined ##hplusroadmap 05:13 -!- nsh [~nsh@obquire.infologie.co] has joined ##hplusroadmap 05:21 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 05:27 -!- juri__ is now known as juri_ 05:29 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 05:32 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 260 seconds] 05:34 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 256 seconds] 06:24 -!- kajetan [~kmo@150.254.83.64] has quit [Ping timeout: 256 seconds] 06:26 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 06:34 -!- ParahSail1n [~pwang@unaffiliated/parahsailin] has quit [Ping timeout: 240 seconds] 06:50 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 258 seconds] 07:21 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has joined ##hplusroadmap 07:46 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 08:24 -!- Zarakii [~devillll@ppp-46-244-176-131.dynamic.mnet-online.de] has joined ##hplusroadmap 08:27 -!- Suwap [~devillll@ppp-46-244-176-131.dynamic.mnet-online.de] has quit [Ping timeout: 264 seconds] 08:35 -!- abumirqaan [uid2969@gateway/web/irccloud.com/x-yaqwmalwwvvldlmw] has joined ##hplusroadmap 08:44 -!- Charlie [~quassel@74.63.212.44] has quit [Ping timeout: 258 seconds] 08:52 < EnLilaSko> If a study writes "potentiates dopamine", do they refer to more dopamine relase, less dopamine break down or upregulation of receptors? 08:53 < ParahSailin> synaptic strength 08:53 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has quit [Ping timeout: 255 seconds] 08:54 -!- Charlie [~quassel@74.63.212.44] has joined ##hplusroadmap 08:54 < EnLilaSko> ParahSailin: So it could refer to everything? (From what I understand, to increase synaptic strength (LTP?) you'll either need to release more neurotransmittors or make more receptors at that place) 08:56 < ParahSailin> amplitude of change as result of presynaptic action 09:08 -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Ping timeout: 256 seconds] 09:10 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 09:20 < kanzure> "@bryan : this is not an 'interesting' approach. It's a practical one informed by decades of experience building synthetic DNA constructs and optical systems. i.e. one that might actually work. ;)" 09:20 < yoleaux> 14:26Z kanzure: if he can munge papers from scribd. e.g. http://www.scribd.com/doc/137892848/Untitled?secret_password=bz3gwxkcfe9ig2wzw4a#full 09:20 < kanzure> "The basic problem of synthesis is that serial programmatic polymer synthesis is intrinsically error-prone. Per-cycle monomer coupling efficiencies are never above 99.5% and generally more like 99% for microarrays. This means that for a 100mer the percentage of correct, full length oligo molecules is only (0.99)^100 = 0.36 -> 36% Two thirds of the stuff made at this length has deletions. If you assemble this pool your synthetic gene will ... 09:20 < kanzure> ... be riddled with frameshift errors. No good." 09:20 < kanzure> "Other companies have tried to correct this by using error-correction enzymes that chew apart mismatched DNA to eliminate the random deletions. While this is fruitful when using traditional plate oligos, the errors are so bad in microarray-sourced DNA that you end up with horrible final yields, and even if you do end up getting something correct in the end it takes so much additional screening work that the cost of post-processing erases any ... 09:20 < kanzure> ... marginal gains made by beginning at the larger microarray scale. I know several companies and academic groups that have investigated these batch pcr-strategies for making synthetic fragments from arrays, but believe that none have demonstrated sufficient speed and throughput of error-free synthetic fragments to make a convincing leap over traditional bulk-oligo assembly pipelines. (i.e. 15cents/bp for 1kb fragments from geneart w. 6 day ... 09:20 < kanzure> ... turnaround)." 09:20 < kanzure> "We're basically building a lot of custom optical / sequencing / laser gear to sample single molecules of a microarray pool and to cherry-pick out the correct ones. Instead of enzymatic tricks, we're doing physical separation upfront of the good from the bad, while simultaneously de-scrambling the ~10^5-10^6 pools into defined small assembly sets for very rapid, very high-throughput assembly of larger kilobase pieces." 09:20 < kanzure> "The key spirit of what we're doing is to minimize biological complexity and trickery throughout the process and to backload complexity onto hardware and software - the domains where we're good at engineering. I've been doing bio for over a decade, and if you don't keep it simple you're hosed!" 09:24 -!- Charlie [~quassel@74.63.212.44] has quit [Ping timeout: 256 seconds] 09:30 -!- industromatic [~chatzilla@cpe-70-113-67-117.austin.res.rr.com] has quit [Ping timeout: 240 seconds] 09:31 < ParahSailin> kanzure: who's saying this 09:32 < kanzure> anselm 09:32 < kanzure> http://anselmlevskaya.com/ 09:37 < ParahSailin> might be tricky to amplify a short oligo enzymatically 09:37 < kanzure> 20mer is doable 09:39 < kanzure> i might have seen someone pcr a 10mer? no that sounds unlikely. 09:39 < ParahSailin> you gotta have a primer... 09:40 < ParahSailin> i guess you could ligate the short oligo to a linker 09:40 < ParahSailin> and then do a bridge amplification to get clusters on your solid support, then do sequencing 09:45 < ParahSailin> and then have some reliable way to break it off the linkers? 09:46 -!- Gue______ [~textual@pool-173-53-25-16.rcmdva.fios.verizon.net] has joined ##hplusroadmap 09:47 -!- Gue______ [~textual@pool-173-53-25-16.rcmdva.fios.verizon.net] has quit [Client Quit] 09:47 -!- Charlie [~quassel@74.63.212.44] has joined ##hplusroadmap 09:51 -!- wsimons [81522db4@gateway/web/freenode/ip.129.82.45.180] has joined ##hplusroadmap 09:51 < ParahSailin> i wonder how hard optical tweezers are 09:51 < wsimons> Is Mariu present under a different username? 09:52 -!- Charlie [~quassel@74.63.212.44] has quit [Ping timeout: 276 seconds] 09:54 < ParahSailin> wow expensive 09:57 -!- industromatic [~chatzilla@cpe-70-113-67-117.austin.res.rr.com] has joined ##hplusroadmap 09:57 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap 09:58 < wsimons> Hello yorick. Seen Mariu lately? 09:58 < yorick> wsimons: april 16th 10:00 < kanzure> whois wsimons 10:00 < wsimons> Your precision is commendable. 10:00 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 10:01 < yorick> wsimons: I have seen him join on april 18th, but he didn't say anything 10:02 < wsimons> yorick: is much happening on the other network? 10:02 < yorick> wsimons: not at all 10:04 < wsimons> How about in here? 10:05 < yorick> I think there is talk most of the days 10:10 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 10:17 < ParahSailin> hm, i should try my hand at next generation synthesis 10:20 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has quit [Ping timeout: 245 seconds] 10:32 -!- Charlie [~quassel@74.63.212.44] has joined ##hplusroadmap 10:45 < wsimons> "next generation synthesis? 10:45 < ParahSailin> dna synthesis beyond amidite 10:46 < wsimons> I thought, you meant old-school procreation. 10:47 < ruphos> that's first generation 10:48 < wsimons> "Next generation" -- the generation after one's own, right? 10:48 < ruphos> fair point 10:58 -!- wsimons [81522db4@gateway/web/freenode/ip.129.82.45.180] has quit [Ping timeout: 245 seconds] 11:03 -!- Charlie [~quassel@74.63.212.44] has quit [Ping timeout: 256 seconds] 11:18 < ParahSailin> why would illumina insert size distribution have such regular "jaggies" like this http://i.imgur.com/vlmC4YU.png 11:20 < ThomasEgi> no labels on axis? 11:20 < ParahSailin> just a random curiosity-- maybe also just an artifact of the assembly of the reads and/or the bwa sampe mapping 11:21 < ParahSailin> y axis is # paired reads; x axis is nt span between reads 11:30 -!- eudoxia [~eudoxia@r190-134-17-119.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 11:30 * eudoxia does his semi-monthly check of apmc.zyvex.com 11:31 < eudoxia> well, at least they changed the favicon... i guess that means they are still working on stuff 11:35 -!- wsimons [81522db4@gateway/web/freenode/ip.129.82.45.180] has joined ##hplusroadmap 11:42 -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 256 seconds] 11:44 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 11:44 < wsimons> FooQuuxman: how much does Comcast bleed you for in IL? 11:47 < kanzure> wsimons: why are you here? 11:48 < wsimons> I am looking for someone. 11:49 -!- makoLime [~mako@103-9-42-48.flip.co.nz] has joined ##hplusroadmap 11:49 < wsimons> Are we feeling territorial already? 11:49 < kanzure> i am allowed to be curious, screw off 11:50 < kanzure> curiosity is not a sign of territorial behavior and you should feel bad for suggesting otherwise.. 11:50 < wsimons> I don't mind, in the slightest. 11:51 < wsimons> "Why are you here" conveys something greater than mere curiosity. It conveys aggression. My response was appropriate. =) 11:51 < kanzure> you're wrong. 11:51 < eudoxia> or maybe he just wanted to know why you are here 11:51 < kanzure> what! impossible. 11:52 < industromatic> Why am I here? :-) 11:52 < wsimons> Possible. 11:52 -!- ksjdhfksjdhfksd [~C@c-67-176-51-26.hsd1.co.comcast.net] has joined ##hplusroadmap 11:52 < wsimons> Because someone put you here. 11:52 -!- strangewarp [~C@c-67-176-51-26.hsd1.co.comcast.net] has quit [Read error: Connection reset by peer] 11:52 < kanzure> wrong. industromatic is here for other reasons than that. 11:53 -!- yorick [~yorick@oftn/member/yorick] has quit [Remote host closed the connection] 11:53 < wsimons> This is a transhumanist hangout, is that correct? 11:53 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap 11:53 < kanzure> no. 11:53 < wsimons> No? Uh oh. 11:53 < kanzure> this is a project channel 11:53 < kanzure> we work on projects. 11:54 < wsimons> Given that it is on freenode, that's hardly surprising. 11:54 < industromatic> Ah, I'm enjoying being here. Did some good apartment building today so far, andmore electrical wiring to come. 11:54 < wsimons> industromatic: how do you mean that? How do you "do" an apartment building? 11:54 < industromatic> Think of bio research products to build too. 11:54 < kanzure> industromatic: don't feed the troll. sorry for the inconvenience. 11:54 < kanzure> also it was wrong of him to drag you into it 11:54 -!- ua_ [~ua@static.124.15.9.5.clients.your-server.de] has quit [Ping timeout: 240 seconds] 11:54 -!- bkero [~Ben@osuosl/staff/bkero] has quit [Ping timeout: 240 seconds] 11:54 < industromatic> I was using building as a verb. I've been building. 11:55 -!- ua [~ua@static.124.15.9.5.clients.your-server.de] has joined ##hplusroadmap 11:55 < wsimons> kanzure: you seem rather preoccupied with right and wrong. Why is that? 11:55 < industromatic> I'm amused. Is he a troll. If so, sorry for feeding him. Since I'm just here on lunch break anyway. 11:55 < wsimons> industromatic: I decoded it wrong. Sorry. 11:56 < industromatic> He sounds like a troll now. 11:56 < kanzure> industromatic: what's for lunch? 11:56 < industromatic> What do you build wsimons? 11:56 < wsimons> Feeding others is the compassionate thing to do, especially if you're on your lunchbreak, industromatic. This is self-evident. 11:56 < industromatic> Really good sandwich from my own bread machine bread and a tall stack of other goodies. 11:57 < industromatic> wsimon: Oh, my. That had a lot of leading suggestive stuff in it and no answer. 11:57 < wsimons> industromatic: At present, I am attempting to rebuild an old pair of headphones, which I'd like to retrofit with some durable wiring. 11:58 < industromatic> headphones: That sounds useful. 11:58 < industromatic> We try to go beyond repair though, and innovate. 11:58 < wsimons> Sarcasm? 11:58 -!- bkero [~Ben@osuosl/staff/bkero] has joined ##hplusroadmap 11:58 < industromatic> nonsarcastic. 11:59 < industromatic> Sorry wsimons, you don't pass my turing-like test for a friendly person. No more conversation. 11:59 < wsimons> Well... I was thinking about putting in two monophonic jacks into them, but that would be more expensive. It is alluring, though. 12:00 < kanzure> ugh the glowing plant kickstarter reached $65k :( 12:00 < wsimons> From what I know of Turing, human emotions did not come easy to him. This makes your statement rather ironic. 12:00 < kanzure> wsimons: perhaps you should lurk more to get a feel for this channel 12:00 < wsimons> kanzure: what sort of "projects"? 12:01 < wsimons> Efficiency, kanzure, efficiency. 12:02 < kanzure> i believe the /topic outlines various projects very well. 12:02 < kanzure> sigh 12:02 < wsimons> Besides, any particular manner in which industromatic might interact with another, a not-me, tells me close to nothing about how he would respond to me. So, not only inefficient, but ineffective, as well! 12:03 < wsimons> Nootropics? 12:05 < brownies> glowing cats 12:05 < wsimons> Poor cats. 12:05 < rigel> World Intellectual PropertyDay is tomorrow! 12:05 < rigel> Yay(?) 12:05 < wsimons> Intellectual property: what you know more than others. 12:06 < wsimons> Thus, the wealthiest man of all is he who can keep the most secrets. 12:06 < kanzure> why are you here again? 12:06 < wsimons> I'm looking for someone. 12:07 < eudoxia> aren't we all? 12:07 < wsimons> What do you think of my defn. of intellectual property? Like/dislike? 12:07 < kanzure> can you do that quietly, or by explicitly asking your questions. 12:07 < kanzure> sigh, that question is inappropriate. get out. 12:07 < wsimons> eudoxia: not in that way :) 12:07 -!- mode/##hplusroadmap [+o kanzure] by ChanServ 12:08 < wsimons> Correction: passive-aggressive. 12:08 <@kanzure> passive aggression requires that i don't communicate with you, which i've been doing abundantly. this is ridiculous. 12:08 -!- mode/##hplusroadmap [+q wsimons!*@*] by kanzure 12:08 -!- mode/##hplusroadmap [-q wsimons!*@*] by kanzure 12:09 <@kanzure> oh darn what's the mode i want 12:09 < wsimons> The one that makes you feel most manly, of course. 12:09 < wsimons> Giving you the illusion of control. 12:09 <@kanzure> haha manly.. okay. 12:09 < ParahSailin> goddamn glowing plant shit 12:09 < wsimons> Alpha. 12:10 < ParahSailin> kanzure: send me some money so i can beat those cambrian assholes to next gen synthesis 12:10 <@kanzure> alpha was disproven years ago, you're full of shit. 12:10 < wsimons> kanzure: Just curious; how is my question "inappropriate"? 12:10 <@kanzure> you're just adding noise to the channel. that's why it's inappropriate. 12:10 <@kanzure> ParahSailin: gimme a proposal for how much money you need and where it will be going 12:11 <@kanzure> ParahSailin: also i recommend just talking to me about it before actually writing a proposal, because fuck writing proposals 12:12 < ParahSailin> have you seen wsimons before, how did you immediately know he was a troll 12:12 < eudoxia> experience, years of it 12:13 <@kanzure> oh weird it was +q that i wanted 12:13 <@kanzure> ParahSailin: writing style. notice his belief in alpha, that's a dead give-away. 12:13 < wsimons> Actually, that happened rather late in the discussion, kanzure. :) 12:14 <@kanzure> also statements like "Are we feeling territorial already?" show how he interprets other messages. 12:14 < ParahSailin> the why are you here seemed immediately like suspecting malfeasance 12:14 <@kanzure> unprovoked, off-topic comments like "I thought, you meant old-school procreation." are very telling too 12:14 < ParahSailin> after the "territorial" thing, yeah it was obvious 12:14 < wsimons> Seemed rude to me. 12:15 < ParahSailin> oh... i was looking at history starting from the 13:35 join 12:15 < ParahSailin> was missing the earlier context 12:15 < ParahSailin> yeah ok, pretty obvious now 12:15 <@kanzure> it's an art. 12:16 < wsimons> Modern art. Needs to be qualified. 12:16 <@kanzure> can you go away yet :( 12:17 < wsimons> Why won't you answer me? What was so inappropriate about my question re: intellectual property? 12:17 < wsimons> Or is unbridled openness, for the sake of openness, presumed to be universally good? 12:18 <@kanzure> pfft your assumptions are spilling out all over the place dude. it's not my job to clean up your intellectual sloppiness. 12:18 < wsimons> The good thing about faulty assumptions is that they can be corrected. 12:19 < wsimons> And, if you truly fancy yourself as an agent of global enlightenment, then, yes, it is your "job". 12:19 < wsimons> At the very least, it hurts nothing to try. 12:19 <@kanzure> wtf enlightenment 12:20 < wsimons> The purposeful, long-term improvement of the human condition? 12:20 < wsimons> Is this not the stated goal behind h+? 12:21 < wsimons> Because if it isn't, I'm really behind the times. 12:36 -!- klafka [~klafka@204-16-157-18-static.ipnetworksinc.net] has joined ##hplusroadmap 12:48 -!- AdrienG [~dextro@unaffiliated/amphetamine] has joined ##hplusroadmap 12:52 -!- AdrianG [~dextro@unaffiliated/amphetamine] has quit [Ping timeout: 272 seconds] 13:15 -!- Technicus [~Technicus@198.150.12.30] has joined ##hplusroadmap 13:17 -!- Technicus [~Technicus@198.150.12.30] has left ##hplusroadmap ["Once you know what it is you want to be true, instinct is a very useful device for enabling you to know that it is"] 13:17 <@kanzure> http://fora.tv/2013/04/25/Jack_Hitt_Talks_Bunch_of_Amateurs__At-Home_Geneticists 13:26 < nmz787> kanzure: ParahSailin i had a paper showing 6 or 8bp primers working, so short amp of a 20mer wouldn't be out of the question, but maybe ridiculous :P 13:26 -!- eudoxia [~eudoxia@r190-134-17-119.dialup.adsl.anteldata.net.uy] has quit [Quit: leaving] 13:27 < EnLilaSko> paperbot: http://www.nature.com/nrn/journal/v6/n1/abs/nrn1588.html 13:27 < paperbot> HTTP 401 unauthorized http://www.nature.com/nrn/journal/v6/n1/pdf/nrn1588.pdf 13:27 <@kanzure> oh yeah, i remember that 8 bp paper. that was crazy. 13:28 < nmz787> ParahSailin: jaggies are maybe the disparity between chunk sizesfor overlapping blocks? 13:35 -!- gnusha [~gnusha@131.252.130.248] has joined ##hplusroadmap 13:35 -!- 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 13:35 -!- Topic set by kanzure [~kanzure@131.252.130.248] [Sat Mar 23 20:40:45 2013] 13:35 [Users ##hplusroadmap] 13:35 [@archels ] [ chido ] [ HEx1 ] [ makoLime ] [ Sanky ] [ ua ] 13:35 [@kanzure ] [ chris_99 ] [ ielo ] [ monkeynipples] [ saurik ] [ Urchin ] 13:35 [ _sol_ ] [ Coornail ] [ industromatic ] [ nmz787 ] [ SDr ] [ wsimons] 13:35 [ abetusk ] [ cpopell ] [ ivan` ] [ nsh ] [ sivoais ] [ yoleaux] 13:35 [ abumirqaan ] [ DMXRoid ] [ Jaakko96 ] [ nuba ] [ smeaaagle ] [ yorick ] 13:35 [ AdrienG ] [ DonnchaC ] [ jrayhawk ] [ nully ] [ soylentbomb ] [ Zarakii] 13:35 [ AlonzoTG ] [ ElixirVitae] [ juri_ ] [ paperbot ] [ strages_home] [ zdap ] 13:35 [ AshleyWaffle] [ EnLilaSko ] [ klafka ] [ ParahSailin ] [ streety ] [ zubaz ] 13:35 [ augur_ ] [ fenn ] [ ksjdhfksjdhfksd] [ pasky ] [ superkuh ] 13:35 [ balrog ] [ gnusha ] [ Lemminkainen ] [ phryk ] [ Thomas42 ] 13:35 [ bkero ] [ heath ] [ lichen ] [ rigel ] [ ThomasEgi ] 13:35 [ brownies ] [ hehelleshin] [ lupfantomo ] [ ruphos ] [ Thorbinator ] 13:35 -!- Irssi: ##hplusroadmap: Total of 68 nicks [2 ops, 0 halfops, 0 voices, 66 normal] 13:35 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 13:35 -!- Irssi: Join to ##hplusroadmap was synced in 8 secs 13:35 < nmz787> like maybe their algorithmms don't try stiching reads at every base, maybe they skip and try every 50th base or 100th base (whatever the jaggie jump size is) 13:36 < ParahSailin> i dont think bwa does anything like that 13:37 < nmz787> or some linker they use is 10bp or whatever the peak to peak distance is along the X axis 13:38 < nmz787> welp i gotta go to the post office to see if they have my laser goggles 13:38 < nmz787> fucker's website says they left a notice on the 1st 13:38 < nmz787> but i didnt get a pink slip 13:39 < nmz787> so gonna have to drop a nerd smackdown on the post office lady 13:39 < nmz787> this is the second time recently packages with USPS have been screwed up and sat at this collection facility for weeks 13:40 <@kanzure> i let all of my mail sit at their facilities in the hope that they will just send it back and instead email me things 13:40 < nmz787> i've just been assuming that the boat from china is going slow to save on fuel 13:40 < nmz787> i didn't expect it to be sent 5 day from china 13:41 < nmz787> so i've been waiting for more than 3 weeks needlessly without being able to play with lasers 13:41 < nmz787> and i've been waiting even longer to play with this laser 14:08 -!- toiletexplosion [~qibble@pool-96-245-180-195.phlapa.fios.verizon.net] has joined ##hplusroadmap 14:10 -!- archels` [~neuralnet@sascha.esrac.ele.tue.nl] has joined ##hplusroadmap 14:10 -!- strages_1ome [~strages@98.67.161.107] has joined ##hplusroadmap 14:14 -!- Sanky_ [~SankyZNC@ip-86-49-43-65.net.upcbroadband.cz] has joined ##hplusroadmap 14:14 -!- wizrobe [~userdi@c-76-23-254-105.hsd1.ct.comcast.net] has joined ##hplusroadmap 14:15 -!- Netsplit *.net <-> *.split quits: AshleyWaffle, @archels, strages_home, Sanky 14:29 -!- toiletexplosion is now known as AshleyWaffle 14:29 < wsimons> lol 14:29 -!- AshleyWaffle [~qibble@pool-96-245-180-195.phlapa.fios.verizon.net] has quit [Changing host] 14:29 -!- AshleyWaffle [~qibble@unaffiliated/anastasiawyatt] has joined ##hplusroadmap 14:43 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has quit [Quit: - nbs-irc 2.39 - www.nbs-irc.net -] 14:54 -!- gnusha [~gnusha@131.252.130.248] has joined ##hplusroadmap 14:54 -!- 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 14:54 -!- Topic set by kanzure [~kanzure@131.252.130.248] [Sat Mar 23 20:40:45 2013] 14:54 [Users ##hplusroadmap] 14:54 [@kanzure ] [ chido ] [ ielo ] [ monkeynipples] [ saurik ] [ Urchin ] 14:54 [ _sol_ ] [ chris_99 ] [ industromatic ] [ nmz787 ] [ SDr ] [ wizrobe] 14:54 [ abetusk ] [ Coornail ] [ ivan` ] [ nsh ] [ sivoais ] [ wsimons] 14:54 [ abumirqaan ] [ cpopell ] [ Jaakko96 ] [ nuba ] [ smeaaagle ] [ yoleaux] 14:54 [ AdrienG ] [ DMXRoid ] [ jrayhawk ] [ nully ] [ soylentbomb ] [ yorick ] 14:54 [ AlonzoTG ] [ DonnchaC ] [ juri_ ] [ paperbot ] [ strages_1ome] [ Zarakii] 14:54 [ archels` ] [ ElixirVitae] [ klafka ] [ ParahSailin ] [ streety ] [ zdap ] 14:54 [ AshleyWaffle] [ fenn ] [ ksjdhfksjdhfksd] [ pasky ] [ superkuh ] [ zubaz ] 14:54 [ augur_ ] [ gnusha ] [ Lemminkainen ] [ phryk ] [ Thomas42 ] 14:54 [ balrog ] [ heath ] [ lichen ] [ rigel ] [ ThomasEgi ] 14:54 [ bkero ] [ hehelleshin] [ lupfantomo ] [ ruphos ] [ Thorbinator ] 14:54 [ brownies ] [ HEx1 ] [ makoLime ] [ Sanky_ ] [ ua ] 14:54 -!- Irssi: ##hplusroadmap: Total of 68 nicks [1 ops, 0 halfops, 0 voices, 67 normal] 14:54 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 14:54 -!- Irssi: Join to ##hplusroadmap was synced in 9 secs 14:56 -!- augur_ [~augur@208.58.5.87] has quit [Remote host closed the connection] 14:56 < ParahSailin> hm, i dont have shell access to the proton one server we just got 14:57 <@kanzure> proton one? 14:59 < ParahSailin> password changed from the default :( 15:00 < ParahSailin> i forget where proton one is one the iontorrent scale 15:01 <@kanzure> time to install a root kit on a live cd? 15:02 < ParahSailin> i think proton one is the big version 15:02 < ParahSailin> the hiseq of the family 15:11 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 15:11 < klafka> http://whatshouldwecallgradschool.tumblr.com/post/48874324965/when-my-pi-asks-about-my-data 15:15 -!- Netsplit *.net <-> *.split quits: rigel, Thorbinator 15:15 -!- Netsplit over, joins: Thorbinator, rigel 15:28 -!- soylentbomb [~k@unaffiliated/soylentbomb] has quit [Ping timeout: 258 seconds] 15:29 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has quit [Ping timeout: 240 seconds] 15:41 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 258 seconds] 15:44 -!- sivoais [~zaki@unaffiliated/sivoais] has quit [Ping timeout: 255 seconds] 15:45 -!- sivoais [~zaki@unaffiliated/sivoais] has joined ##hplusroadmap 15:46 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 15:53 -!- sivoais [~zaki@unaffiliated/sivoais] has quit [Ping timeout: 240 seconds] 15:56 -!- sivoais [~zaki@unaffiliated/sivoais] has joined ##hplusroadmap 15:57 -!- SphericalMouse [62cfd610@gateway/web/freenode/ip.98.207.214.16] has joined ##hplusroadmap 16:03 -!- sivoais [~zaki@unaffiliated/sivoais] has quit [Ping timeout: 240 seconds] 16:06 -!- sivoais [~zaki@unaffiliated/sivoais] has joined ##hplusroadmap 16:09 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 16:13 -!- augur [~augur@ip-64-134-41-137.public.wayport.net] has joined ##hplusroadmap 16:14 -!- sivoais [~zaki@unaffiliated/sivoais] has quit [Ping timeout: 252 seconds] 16:14 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 256 seconds] 16:15 -!- sivoais [~zaki@unaffiliated/sivoais] has joined ##hplusroadmap 16:17 -!- yorick [~yorick@oftn/member/yorick] has quit [Read error: Connection reset by peer] 16:19 -!- ParahSail1n [~pwang@unaffiliated/parahsailin] has joined ##hplusroadmap 16:22 <@kanzure> SphericalMouse: hi 16:24 < SphericalMouse> yo 16:34 < ParahSail1n> is cambrian a founders fund group? 16:36 <@kanzure> nah, i doubt it. they have SBIR money from DARPA. they might have thiel foundation money (i mean, the commercial offshoot). 16:36 <@kanzure> damn i don't even remember the thiel foundation commercial arm 16:37 < ParahSail1n> something from lotr 16:37 <@kanzure> it says their incubators are "singularity university, singularity university labs, alchemist accelerator" but i doubt these.. 16:40 <@kanzure> oh wait. yep. 16:41 <@kanzure> there other investors are: singularity university, andy pham, ken arnold, jeff kowalski (autodesk), tugboat ventures, felicis ventures, elaine wherry (meebo), david waxman (peoplepc, tenoneten ventures), kris gale (yammer, microsoft), una ryan, chris alden (tpg capital, six apart), steven eskenazi, frank caufield (ustream investor i think), scott nolan (founders fund, spacex employee), maurice werdegar (webmynd investor), jeremy howard (sold ... 16:41 <@kanzure> ... some stuff to opera iirc), james patterson, michael levit, founders fund, ryan junee (sold some stuff to google), joel yarmon, david beyer, nova spivack (klout investor), tim draper (DFJ- which has some other interesting singularity-related investments), aydin senkut (felicis ventures), carl bass (autodesk ceo), adam pisoni (yammer), mark jacobstein, gil elbaz (some google exit) 16:42 <@kanzure> from the looks of it, i think they raised through angel list 16:43 <@kanzure> also i screwed up and forgot to mention lukman winoto yesterday when you asked about who they were. 16:45 < nmz787> so if they fail and I have a better idea, i'll know to spam that list of investors 16:45 <@kanzure> you don't raise on angel list by spamming :P 16:46 <@kanzure> there was a good article about the amount of preparation you should aim for when you do an angel list round 16:47 <@kanzure> for instance, just like that silly tactic that omri used on kickstarter there, you have to make sure a handful of strong investors pre-commit to it, and then "the day of" you have to make sure they make that information public 16:47 <@kanzure> because you have a very short amount of time to show that there's traction even among other investors 16:47 <@kanzure> otherwise your attempts to raise a good round on angel list will probably tank (unless you have an exceptionally great deal for them, which you probably don't if you have to spam) 16:48 <@kanzure> damn where's that article. 16:48 <@kanzure> brownies: do you remember the url? 16:49 <@kanzure> this wasn't it :( http://www.josephfung.ca/blog/2011-09-29/12-rules-for-using-angel-list-like-a-boss/ 16:50 -!- klafka [~klafka@204-16-157-18-static.ipnetworksinc.net] has quit [Remote host closed the connection] 17:28 < brownies> i think it's either on venture hacks or quora 17:34 <@kanzure> quora? ok then it's lost forever.. 17:38 -!- augur [~augur@ip-64-134-41-137.public.wayport.net] has quit [Remote host closed the connection] 17:43 < ParahSail1n> paperbot: http://www.nature.com/ncomms/journal/v4/n4/full/ncomms2747.html 17:43 < paperbot> HTTP 401 unauthorized http://www.nature.com/ncomms/journal/v4/n4/pdf/ncomms2747.pdf 18:01 < nmz787> ParahSail1n: http://diyhpl.us/~nmz787/High-power%20lithium%20ion%20microbatteries%20from%20interdigitated%20three-dimensional%20bicontinuous%20nanoporous%20electrodes.pdf 18:01 < nmz787> kanzure: please figure out how to upload via jquery from a bookmarklet 18:02 <@kanzure> how about just use a filepicker.io bookmarklet 18:04 < nmz787> hmm, 18:04 < nmz787> needs looking into 18:04 < nmz787> how do they handle security 18:05 <@kanzure> it's like dropbox, except they give you a hook on the other end for where you want the file to be placed. 18:05 < nmz787> "We handle all the complicated javascript and backend APIs to give you a clean and elegant way of saving files" 18:05 < nmz787> they don't mention if they log your info, etc 18:06 <@kanzure> they might possibly store your files for you, i don't remember thatp art 18:06 <@kanzure> *that part 18:09 < nmz787> hmm, adobe reader in browser is actually flash 18:09 < nmz787> so i'm not sure i can get to the File 18:10 < nmz787> (object) 18:14 <@kanzure> i believe you can use an XHR to get the content anyway 18:14 < nmz787> one other question similar to mine 10 years ago unanswered 18:14 < nmz787> http://lists.evolt.org/archive/Week-of-Mon-20031013/080679.html 18:15 < nmz787> my search is: get embedded pdf "File object" javascript 18:15 < nmz787> yeah I could re-download the PDF, then upload it to another server and put the link in my copy-paste memory 18:16 <@kanzure> here... http://stackoverflow.com/a/7372816/687783 18:16 < nmz787> and have a bot running on upload directory write, to post the link here 18:16 < nmz787> :P 18:17 <@kanzure> except you need to have xhr.onload do something with the data, like XHR it to somewhere else that is accepting a file. 18:17 < nmz787> k 18:17 < nmz787> why base 64 encoding? 18:17 < nmz787> isn't binary base 2? 18:19 < nmz787> oh, so it can be posted as a string 18:19 < nmz787> stored 18:19 <@kanzure> by default the browser renders data in various encodings.. 18:20 -!- klafka [~klafka@c-67-174-253-229.hsd1.ca.comcast.net] has joined ##hplusroadmap 18:31 -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Remote host closed the connection] 18:37 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 18:54 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has joined ##hplusroadmap 18:59 -!- aristarchus [~aristarch@unaffiliated/aristarchus] has joined ##hplusroadmap 19:06 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 19:10 -!- wsimons [81522db4@gateway/web/freenode/ip.129.82.45.180] has quit [Quit: Page closed] 19:13 -!- ksjdhfksjdhfksd is now known as strangewarp 19:16 <@kanzure> cern is asking for donations for kicad development http://cernandsociety.web.cern.ch/technology/kicad-development 19:16 <@kanzure> they want $300k eurozenni to "Bring Kicad in line with the best proprietary tools, and outclass them" 19:26 -!- plur [~nonentity@198.48.2.4] has joined ##hplusroadmap 19:46 < klafka> whats kicad? 19:47 -!- plur [~nonentity@198.48.2.4] has quit [Read error: Connection reset by peer] 20:02 -!- plur [~nonentity@198.48.2.4] has joined ##hplusroadmap 20:16 -!- SphericalMouse [62cfd610@gateway/web/freenode/ip.98.207.214.16] has quit [Ping timeout: 245 seconds] 20:25 -!- Adifex [~Adifex@71-33-144-164.hlrn.qwest.net] has joined ##hplusroadmap 20:26 -!- Adifex [~Adifex@71-33-144-164.hlrn.qwest.net] has quit [Client Quit] 20:27 -!- Suwap [~devillll@ppp-46-244-176-131.dynamic.mnet-online.de] has joined ##hplusroadmap 20:27 -!- plur [~nonentity@198.48.2.4] has quit [Ping timeout: 245 seconds] 20:28 -!- Adifex [~Adifex@71-33-144-164.hlrn.qwest.net] has joined ##hplusroadmap 20:28 -!- Zarakii [~devillll@ppp-46-244-176-131.dynamic.mnet-online.de] has quit [Ping timeout: 264 seconds] 20:33 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Quit: Lost terminal] 21:52 -!- Adifex [~Adifex@71-33-144-164.hlrn.qwest.net] has quit [Quit: Adifex] 22:05 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Read error: Connection reset by peer] 22:05 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 22:15 -!- delinquentme [~asdfasdf@64.13.15.38] has joined ##hplusroadmap 22:15 < delinquentme> OMGhio. 22:15 < delinquentme> whereget soma dis modainil 22:27 -!- Juul [~Juul@c-67-170-193-114.hsd1.ca.comcast.net] has joined ##hplusroadmap 22:32 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 22:35 -!- delinquentme [~asdfasdf@64.13.15.38] has quit [Remote host closed the connection] 22:38 -!- aristarchus [~aristarch@unaffiliated/aristarchus] has quit [Quit: Leaving] 22:45 -!- FooQuuxman [~arik@c-98-215-254-55.hsd1.il.comcast.net] has quit [Ping timeout: 245 seconds] 22:48 -!- Juul [~Juul@c-67-170-193-114.hsd1.ca.comcast.net] has quit [Ping timeout: 252 seconds] 22:52 <@kanzure> "The cost of synthesis is a sum of the cost of the instruments (or its depreciation over time), the cost of the people running it, the fixed overhead costs of the company doing it, the cost of shipping, and lastly the cost of the reagents. Among other things. "Cost" is not a simple thing." 22:52 <@kanzure> "The cost of phosphoramidites is really low (at a minimum) given that they're produced in china. The container the phosphoramidites come in can be more expensive than the contents. CpG isn't that expensive either... I mean let's take it to a ridiculous limit-point: an oligo synthesis run costs a few hundred dollars in reagents, maybe a thousand. You're working with a ~mole of material. Divide that by avogadro's number. 1e3/6e23 = about ... 22:53 <@kanzure> ... a tenth of an attocent per monomer." 22:53 <@kanzure> "Reagents are expensive when you waste them. For traditional gene synthesis, the cost of oligos does dominate. Even the lowest-scale bulk synthesis reactions make about 1000x more material than is needed for a synthesis reaction. Microarray synthesis scales usage way down (though the amount of dna on a microarray spot is actually too low to use directly for reliable assembly, so some amount of post-processing is required) However, ... 22:53 <@kanzure> "If you had a magic daemon that coud assemble single-molecules, your reagent cost for a 100mer would be about 10 attocents. (We don't know how to make magic daemons yet, but I suspect that physics does allow for a mesoscopically-coupled polymerase that could act as a decently accurate 'molecular printer' if you coupled it to some single-molecule sequencing feedback.) Why does a bulk reagent limit the ultimate cost? If you're efficient it ... 22:53 <@kanzure> ... doesn't have to." 22:53 <@kanzure> ... microarrays jumble everything together and make the error-correction problem much more severe." 22:53 <@kanzure> "With regards to enzymes/reagents don't think that the price you pay for them is going to be the price an industrial purchaser is going to pay- most endusers of anything in biology are paying large margins. What you're paying for as an enduser isn't the stuff in the tube, it's the quality control that guarantees the stuff in the tube will do what you hope it will, as well as the convenience of that little tube shipped to you the moment you ... 22:53 <@kanzure> ... need it." 22:53 <@kanzure> "Don't get fixated on a single aspect of the cost structure. Ingots of ultrapure silicon aren't cheap, but their cost is only distantly related to the price of a cpu. If you have a relatively fixed amount of cost for people and machines and reagents, the only way you get improved cost per unit is by making a shitload more units by using more efficient processes. That's the idea." 22:53 <@kanzure> "The paper you reference used a poor sequencing strategy that made exactly the same kinds of base-calling errors as the synthesis errors is was supposed to detect. If you don't match your filter to your noise source, you're not going to get good rejection ratios." 22:53 <@kanzure> "Quick reference for error sources in DNA: 22:53 <@kanzure> chemical synthesis errors : ~1 in 100 22:53 <@kanzure> thermal depurination errors : 1 in 10^5 (or worse, depending on time spent above 60C) 22:53 <@kanzure> polymerase copy errors: 1 in 10^6 (for modern, phusion-like enzymes) 22:53 <@kanzure> in-vivo bacterial copy errors: 1 in 10^8-10^9 per replication." 22:53 <@kanzure> "Even if you magic away all the synthesis errors, you still have to worry about thermal depurination and large assembly errors. It's all about building quality control into the whole system. And that is why cheap sequencing is a big deal: it was a necessary precedent for cheap synthesis. Of course, the devil is in the details of how you leverage it." 22:55 <@kanzure> thermal depurination errors :( 22:57 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 22:58 < ParahSail1n> there's a number of challenges facing them 22:58 <@kanzure> btw have you met anselm? 22:59 < ParahSail1n> no 22:59 < ParahSail1n> im kinda out of the cool people loop 23:03 < ParahSail1n> how many of those guys do you know? 23:05 <@kanzure> i know anselm alright. we bump into each other whenever. 23:06 <@kanzure> i may have exchanged sarcastic retorts with austen once. that's about it. 23:24 -!- kajetan [122@d30-138.icpnet.pl] has joined ##hplusroadmap 23:25 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has quit [Ping timeout: 245 seconds] 23:28 -!- ielo [~ielo@cpc9-addl4-2-0-cust229.6-3.cable.virginmedia.com] has joined ##hplusroadmap 23:43 < archels`> kanzure: I'm finding that a bunch of sites are hotlinking lecture videos and books from my fileserver 23:43 < archels`> do you get this as well, and what can you do againt it? 23:44 <@kanzure> do you want to do something against it? 23:45 <@kanzure> i mean, it's not necessarily a bad thing 23:45 <@kanzure> you can check http referer headers, and if they start spoofing those and using iframes, you can use some iframe breakout javascript to do the detection for you. 23:46 <@kanzure> if the traffic volume is really high then you can just change the content to something that promotes you 23:46 < archels`> yes, they are serving an embedded video on my server with their ads next to it. fuck these guys 23:47 <@kanzure> how are they embedding the video? /?