--- Log opened Tue Feb 21 00:00:19 2012
00:16 -!- yashgaroth [~f@cpe-24-94-5-223.san.res.rr.com] has quit [Quit: Leaving]
00:31 -!- SolG [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has joined ##hplusroadmap
00:34 -!- _sol_ [Sol@c-174-57-58-11.hsd1.pa.comcast.net] has quit [Ping timeout: 265 seconds]
01:08 -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has joined ##hplusroadmap
01:27 -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has joined ##hplusroadmap
01:29 -!- He||eshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has quit [Ping timeout: 260 seconds]
01:56 -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has quit [Read error: Connection reset by peer]
01:56 -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has joined ##hplusroadmap
02:10 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has quit [Ping timeout: 240 seconds]
02:34 -!- SolG [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has quit [Read error: Connection reset by peer]
02:34 -!- _sol_ [Sol@c-174-57-58-11.hsd1.pa.comcast.net] has joined ##hplusroadmap
02:41 -!- nsh_ [~nsh@cpc21-broo7-2-0-cust83.14-2.cable.virginmedia.com] has quit [Ping timeout: 240 seconds]
02:42 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
02:48 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has joined ##hplusroadmap
02:49 -!- sylph_mako [~mako@118-93-211-24.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 252 seconds]
03:35 -!- JonnieCache [~jonnie@87.252.60.35] has quit [Quit: leaving]
03:58 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap
04:04 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: Operation timed out]
04:05 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
04:26 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
04:26 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
04:45 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
04:46 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
04:50 -!- marainein [~marainein@114-198-70-108.dyn.iinet.net.au] has joined ##hplusroadmap
05:52 -!- ParahSailin__ [~parahsail@adsl-69-151-205-240.dsl.hstntx.swbell.net] has quit [Remote host closed the connection]
06:16 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 276 seconds]
06:49 -!- ParahSailin [~parahsail@unaffiliated/parahsailin] has joined ##hplusroadmap
06:51 -!- strages_work [~qwebirc@dev.throwthemind.com] has quit [Quit: Page closed]
07:12 -!- strages_work [~qwebirc@dev.throwthemind.com] has joined ##hplusroadmap
07:30 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection]
07:54 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Quit: Computer has gone to sleep.]
08:03 -!- augur [~augur@129.2.129.33] has joined ##hplusroadmap
08:15 < kanzure> beep boop
08:22 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Ping timeout: 245 seconds]
08:24 -!- archels [~foo@sascha.esrac.ele.tue.nl] has quit [Ping timeout: 245 seconds]
08:34 -!- archels [~foo@sascha.esrac.ele.tue.nl] has joined ##hplusroadmap
08:36 -!- ThomasEgi [~thomas@pppdyn-21.stud-ko.rz-online.net] has joined ##hplusroadmap
08:36 -!- ThomasEgi [~thomas@pppdyn-21.stud-ko.rz-online.net] has quit [Changing host]
08:36 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap
08:37 -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has joined ##hplusroadmap
08:40 -!- yottabit [~heath@unaffiliated/ybit] has joined ##hplusroadmap
09:01 -!- SolG [Sol@c-174-57-58-11.hsd1.pa.comcast.net] has joined ##hplusroadmap
09:02 -!- _sol_ [Sol@c-174-57-58-11.hsd1.pa.comcast.net] has quit [Ping timeout: 245 seconds]
09:04 -!- mag1stra1e [~sac_tlm@cpe-107-10-15-158.neo.res.rr.com] has joined ##hplusroadmap
09:05 -!- mag1strate [~sac_tlm@cpe-107-10-15-158.neo.res.rr.com] has quit [Ping timeout: 245 seconds]
09:17 -!- strangewarp [~strangewa@c-76-25-200-47.hsd1.co.comcast.net] has quit [Ping timeout: 255 seconds]
09:39 < kanzure> http://mailinator.blogspot.com/2012/02/how-mailinator-compresses-email-by-90.html
09:39 < kanzure> neat. i don't know what i would do without mailinator :x
09:47 -!- strangewarp [~strangewa@c-76-25-200-47.hsd1.co.comcast.net] has joined ##hplusroadmap
10:29 < kanzure> "owell has a "suitcase lab" for biohacking on the go. As well as a mini gel electrophoresis kit by Invitrogen, you can cram in a thermocycler, dishes and pipettes. The tricky part is cold storage: "You might need a separate pouch with a cold pack in it," he advises."
10:29 < kanzure> hmmm i haven't seen this alleged suitcase lab
10:30 < Mokbortolan_> why... would you need a suitcase biohacking lab...
10:31 < uniqanomaly__> so you could do science on the shitter
10:44 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has quit [Read error: Connection reset by peer]
10:45 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
10:46 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has joined ##hplusroadmap
11:14 < audy> you could attach microcentrifuge tubes to the spokes of a bicycle and centrifuge them as you commute to wherever it is you plan on suitcase biohacking
11:15 < Mokbortolan_> you could tie vials to your socks to agitate them as you walk :p
11:15 < audy> suit lab for biohacking on the go
11:16 < audy> for biohacking super{hero,villian}s
11:18 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
11:23 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has quit [Read error: Connection reset by peer]
11:25 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has joined ##hplusroadmap
11:27 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
11:27 -!- SolG is now known as _sol_
11:33 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: Connection reset by peer]
11:33 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
11:49 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
11:51 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
11:54 -!- SDr [~SDr@unaffiliated/sdr] has joined ##hplusroadmap
12:19 -!- SDr [~SDr@unaffiliated/sdr] has quit [Ping timeout: 260 seconds]
12:28 -!- sylph_mako [~mako@118-93-211-24.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap
12:43 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: Operation timed out]
12:45 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
13:07 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
13:08 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
13:14 -!- delinquentme [~asdfasdf@c-67-171-66-113.hsd1.pa.comcast.net] has quit [Ping timeout: 240 seconds]
14:08 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
14:09 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
14:09 -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has quit [Remote host closed the connection]
14:20 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving]
14:25 -!- sylph_mako [~mako@118-93-211-24.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 255 seconds]
14:37 -!- archels [~foo@sascha.esrac.ele.tue.nl] has quit [Ping timeout: 265 seconds]
15:01 -!- archels [~foo@sascha.esrac.ele.tue.nl] has joined ##hplusroadmap
15:05 -!- delinquentme [~asdfasdf@c-67-171-66-113.hsd1.pa.comcast.net] has joined ##hplusroadmap
15:06 -!- augur [~augur@129.2.129.33] has quit [Remote host closed the connection]
15:08 -!- strages_shop [~strages@256.makerslocal.org] has joined ##hplusroadmap
15:08 -!- jmil [~jmil@SEASNet-148-05.seas.upenn.edu] has joined ##hplusroadmap
15:30 < delinquentme> ChemicalStructure inchi = ne.getFirstChemicalStructure(FormatType.INCHI);   translating this bit of java
15:30 < delinquentme> into Ruby
15:30 < delinquentme> inchi = ne.getFirstChemicalStructure(FormatType.INCHI)   << not _quite_
15:35 -!- Juul [~Juul@slim.dhcp.lbl.gov] has joined ##hplusroadmap
15:39 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap
15:46 < kanzure> Juul: how's your tex-fu
16:00 < Juul> kanzure, very basic
16:05 -!- yottabit [~heath@unaffiliated/ybit] has quit [Read error: Connection reset by peer]
16:05 -!- yottabit [~heath@unaffiliated/ybit] has joined ##hplusroadmap
16:07 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has quit [Quit: nchaimov]
16:08 < delinquentme> dude jruby
16:08 < delinquentme> is beautiful
16:10 -!- SDr [~SDr@unaffiliated/sdr] has joined ##hplusroadmap
16:16 -!- sylph_mako [~mako@118-93-211-24.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap
16:26 -!- yottabit [~heath@unaffiliated/ybit] has quit [Remote host closed the connection]
16:27 -!- yottabit [~heath@unaffiliated/ybit] has joined ##hplusroadmap
16:31 -!- Mokbortolan_ is now known as Mokstar_AFK
16:39 -!- yottabit [~heath@unaffiliated/ybit] has quit [Quit: Konversation terminated!]
16:48 < kanzure> Q01529 "Probable DNA polymerase"
16:48 < kanzure> http://www.uniprot.org/uniprot/Q01529
16:49 < kanzure> "This DNA polymerase requires a protein as a primer"
16:51 -!- SDr [~SDr@unaffiliated/sdr] has quit []
17:05 < Juul> interesting
17:10 < Juul> but this protein hasn't been studied directly
17:10 < Juul> it says "inferred from sequence homology"
17:11 < Juul> so there must be some other protein that _has_ been studied, with a similar sequence
17:11 < Juul> though i'm not finding any information about that on the uniprot page
17:11 < delinquentme> kanzure, you havnt any experience interfacing rails applications with java do you?
17:11 < Juul> delinquentme, i have a bit
17:11 < delinquentme> Juul, got my phone call from LBL .. dont recall if i mentioned .. the guy was awesome
17:11 < delinquentme> no shit!
17:12 < Juul> yeah you did :) hope you get it
17:12 < delinquentme> So I've just finished this JRuby interface and Ive got a few ideas about getting it to interface
17:12 < delinquentme> SOAP API ( w a separate server ), Tomcat servlet or jruby on rails
17:13 < delinquentme> what did your implementation look like?
17:13 < Juul> i played a bit with jruby, but decided to go with plain ruby and call rjb for java calls
17:14 < Juul> so i'm running vanilla rails with rjb for interfacing to java and rsruby for interfacing to R
17:14 < Juul> i try to stay away from the java world as much as i can
17:14 < Juul> it's all so heavy
17:14 < Juul> brb phone
17:17 < delinquentme> yeah java is a biggun
17:17 < kanzure> anything that uses soap is a waste of your time
17:18 < delinquentme> Juul, do you happen to have a code sample of that interface?
17:25 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection]
17:44 -!- eridu [~eridu@gateway/tor-sasl/eridu] has joined ##hplusroadmap
17:46 -!- eridu [~eridu@gateway/tor-sasl/eridu] has quit [Client Quit]
17:49 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has joined ##hplusroadmap
17:50 -!- eudoxia [~eudoxia@r186-52-128-209.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap
18:00 < Juul> delinquentme, yeah, let me get it for you
18:02 < Juul> delinquentme, here http://pastebin.com/2jTy86Nj
18:03 < delinquentme> danke
18:05 < Juul> tomcat/glassfish is pain if you ask me
18:12 < delinquentme> you've used em?
18:13 < Juul> yes
18:16 < Juul> it's been a few years since i used tomcat
18:16 < Juul> we're still using glassfish for some legacy code
18:18 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has quit [Quit: Adifex]
18:19 < delinquentme> its really wild that they use tools like that
18:19 < delinquentme> I guess I'd expect nothing but pure java .. like the fact ruby is mentioned at all is really wild to me
18:21 < Juul> who?
18:21 < Juul> the sad fact is that java is slow
18:22 < Juul> a lot of the time having something in 1/10th of the time is better than having something industrial grade
18:22 < Juul> not slow in execution, just slow for developing complex web apps
18:22 < Juul> Hibernate is a monster
18:23 < Juul> ActiveRecord is nicencess
18:27 < Juul> delinquentme, how's the pay at that job?
18:30 < delinquentme> no idea
18:30 < delinquentme> hoping its not 50k
18:30 < delinquentme> Juul, howd you get into rails
18:30 < delinquentme> and do you plan to stay out in SV?
18:33 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has joined ##hplusroadmap
18:41 -!- eudoxia [~eudoxia@r186-52-128-209.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving]
18:42 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Quit: ...unyaaa ~~~]
18:42 -!- nchaimov_ [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has joined ##hplusroadmap
18:45 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has joined ##hplusroadmap
18:45 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has quit [Ping timeout: 244 seconds]
18:45 -!- nchaimov_ is now known as nchaimov
18:56 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has quit [Quit: nchaimov]
18:56 -!- Juul [~Juul@slim.dhcp.lbl.gov] has quit [Ping timeout: 245 seconds]
19:03 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has joined ##hplusroadmap
19:14 < kanzure> cell mouse culture thing? http://www.ebay.com/itm/ws/eBayISAPI.dll?ViewItem&item=230735944396
19:14 < kanzure> erm
19:14 < kanzure> *mouse cell culture thing
19:14 < kanzure> "one-time-use mammalian cell culture system" is what phil goetz called it
19:15 -!- SDr [~SDr@unaffiliated/sdr] has joined ##hplusroadmap
19:23 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has quit [Quit: Adifex]
19:24 -!- aristarchus [~aristarch@unaffiliated/aristarchus] has joined ##hplusroadmap
19:39 < kanzure> this is a weird synthesizer
19:39 < kanzure> http://www.alibaba.com/product-free/109600291/OligoMaker.html
19:39 < kanzure> about $120
19:39 < kanzure> "The OligoMaker 48/6 is a fast cost-effective 48-channel oligonucleotide synthesizer. The Six base bottle positions, can be upgraded to 8 or 10 or more bottle position. The OligoMaker 48/6 can be upgraded to make 96 or 192 oligos in parallel."
19:41 < kanzure> http://www.oligomaker.com/
19:41 < kanzure> "OligoMaker ApS was founded back in 1996 as a technology R&D division of TAG Copenhagen A/S. OligoMaker ApS is located in the Symbion Science Park in Copenhagen in the center of the area known as The Medicon Valley."
19:42 < kanzure> maarrrc
19:43 < delinquentme> lerrrnin programming lernninnnn programmerang
19:43 < kanzure> "OligoMaker is a fast cost-effective oligonucleotide synthesizer
19:43 < kanzure> OligoMaker can synthesize ex. 10 oligos (20-mer) in less than 2.5 hours
19:43 < kanzure> OligoMaker can be upgraded to make 96 or 192 oligos in parallel"
19:43 < delinquentme> oh kanzure you'd know this Rjb::load(classpath = jars , jvmargs=[])
19:43 < kanzure> hm?
19:43 < delinquentme> if im after the value of classpath ... thats me looking within the Rjb class for the classpath object right
19:44 < kanzure> um, what?
19:44 < kanzure> are you asking if your rjb instance has a classpath variable?
19:45 < delinquentme> looking for 1) how to check the values within that classpath var
19:45 < delinquentme> and confirmation that im using the correct nomenclature
19:46 < bkero> http://coreyshields.com/images/bkero.png
19:46 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap
19:46 < kanzure> bkero: attach it to your ceiling and then we will talk, sir
19:46 < kanzure> delinquentme: i don't know, is it in your current namespace or not
19:47 < kanzure> oligomaker video: http://www.youtube.com/watch?v=hBbjfEj1lCc
19:48 < bkero> kanzure: impossible, I had to hold those damn cards up with yogurt containers and a proc box!
19:52 < kanzure> http://www.labbase.net/Supply/SupplyItems-1098780.html
19:52 < kanzure> "call for quote"...
19:52 < kanzure> so i bet that meant $50,000 euro not $50.000 euro
19:53 -!- strages_shop [~strages@256.makerslocal.org] has quit [Ping timeout: 252 seconds]
20:05 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has joined ##hplusroadmap
20:19 -!- SDr [~SDr@unaffiliated/sdr] has quit []
20:31 -!- yashgaroth [~f@cpe-24-94-5-223.san.res.rr.com] has joined ##hplusroadmap
20:49 < kanzure> hi yashgaroth
20:49 < yashgaroth> hey
20:55 < delinquentme> ^^^^^^^^^^^^^^^^^^^^^^^^^
20:56 < yashgaroth> ^
20:57 < kanzure> yashgaroth: i am having a brain fart
20:57 < yashgaroth> oh my
20:57 < kanzure> i'm pretty sure someone has done oligo ligation for gene assembly
20:57 < kanzure> am i making this shit up?
20:58 < yashgaroth> no, it's pretty standard for anything over 100 bp
20:58 < kanzure> yeah but i mean, from an oligo library
20:58 < kanzure> not from 100 bp-synthesized-strands
20:58 < yashgaroth> oh, then I don't think so no
20:58 < kanzure> that sounds stupid
20:58 < yashgaroth> not like the 6mer thing, but I don't keep up much on gene synthesis as long as it gets delivered
20:58 < kanzure> i've def. seen stuff like "LOL we synthesized 50 bp fragments of this GENE and REASSEMBLED IT!"
20:59 -!- aristarchus [~aristarch@unaffiliated/aristarchus] has quit [Quit: Leaving]
20:59 < yashgaroth> at a certain point, dealing with the 99% accuracy means cloning out your fragments, confirming them, and then ligating
20:59 < yashgaroth> but it's not the basic technique like we'd be doing
21:00 < kanzure> so i'm trying to be cautious against a potential argument that SU will give me:
21:00 < kanzure> "you claim oligo mail order companies will go the way of the dinosaur, but why won't they just use a ligation scheme"
21:00 < kanzure> *ligation scheme + oligo library
21:01 < yashgaroth> oh btw U.S. patent scheme is going first-to-file in 3 weeks, rather than first-to-invest like it was previously
21:01 < kanzure> *invent
21:01 < yashgaroth> yes
21:01 < yashgaroth> they totally could do it if it works, I mean they do already have the oligo synthesis infrastructure
21:02 < yashgaroth> although -invest is pretty accurate as well considering you have to demonstrate it works first, which means $
21:02 < yashgaroth> please excuse my errors as I've been out getting drunk this evening
21:04 < yashgaroth> so are we going with the oligo library assembly, or is all this speculation about modifying pol going to happen
21:04 < kanzure> oligo library
21:04 < kanzure> that google group thing is for the speculation about polymerase ;)
21:05 < yashgaroth> oh thank god, all this talk about modifying pol to selectively add nucleotides is way in the future
21:05 < kanzure> yes
21:05 < kanzure> i want to write a roadmap with that googlegroup
21:05 < kanzure> i think it would be cool to attach our names to it
21:05 < kanzure> it can basically be "Here's a bunch of shit we've thought about, and some 3d models and simulation results" or something
21:06 < yashgaroth> okay good, cuz I was worried we'd spend 10 years trying to get pol to work how we want
21:06 < kanzure> nope. but! i would very much like it to be us who comes up with that method
21:07 < yashgaroth> I think we could, no one's out commercially with something like that
21:07 < kanzure> no researchers either
21:08 < yashgaroth> I think we could test out the ligation scheme fairly easily, the 4096-droplet microfluidics is beyond my comprehension though
21:08 < kanzure> okay, new scenario
21:08 < kanzure> let's say the synthesis companies are somehow (magically) able to sell for $0.00001/bp
21:08 < yashgaroth> mm
21:08 < kanzure> so a full genome costs maybe $20
21:09 < kanzure> would an at-home synthesizer still win?
21:09 < yashgaroth> oh man that's so far beyond my...I can't even imagine what a $20 genome sequencing would do, much less a synthesis
21:10 < kanzure> yeah, synthesis
21:10 < kanzure> with the polymerase you can even imagine it costing $0.00000000001/bp (let's say it eats atmospheric nutrients, bitches)
21:10 < yashgaroth> well of course at that point the commercial synth would win, but there's no way they're getting 0.0000001/bp any time soon with pamidites
21:11 < yashgaroth> oh, with an engineered pol it's maybe possible
21:11 < kanzure> why would a commercial service win though
21:11 < yashgaroth> oh, are we assuming both are the same price or what
21:11 < kanzure> sure
21:11 < kanzure> yes same price
21:11 < kanzure> or, let's say this:
21:11 < yashgaroth> then there's always the delivery time
21:11 < kanzure> commercial is $0.0001/bp
21:11 < kanzure> at home is $5k down, but $0.000001/bp
21:12 < yashgaroth> I don't know how many biohackers we expect to have, but for any lab the 5k is nothing
21:12 < yashgaroth> academic/commercial lab, but 5k for endy's suitcase is still cheap
21:13 < yashgaroth> still, the only way to begin comparing cost per bp is to try it out
21:14 < kanzure> "thats the value I see.... put the system on 'engineer mode' and when the bell rings, I've got a freshly evolved morphine operon"
21:14 < yashgaroth> "?
21:14 < kanzure> just a quote from nate
21:15 < kanzure> so, delivery time
21:15 < yashgaroth> and for the massively-parallel panning stuff, which'll be a much bigger user
21:15 < kanzure> yeah for sure
21:15 < yashgaroth> 'oh we have a sequence, let's try 10,000 variations of it tomorrow, sequencer go!'
21:15 < kanzure> but currently the market doesn't buy that much massively-parallel dna synthesis
21:16 < kanzure> right
21:16 < kanzure> i mean, that's what i would use it for :)
21:16 < yashgaroth> the panning market's perfectly willing to adopt that for affinity maturation
21:16 < kanzure> affinity binding?
21:16 -!- nmz787 [43f2b117@gateway/web/freenode/ip.67.242.177.23] has joined ##hplusroadmap
21:16 < nmz787> hola
21:16 < nmz787> como estas
21:17 < kanzure> in this channel we speak ENGLISH
21:17 < yashgaroth> yeah, you have a clone, let's say you want to try every possible permutation of the loop
21:17 < nmz787> yo quero DIY hplus
21:17 < yashgaroth> si
21:17 < yashgaroth> see if you get better binding/expression, and repeat 'til you have a drug
21:17 < kanzure> so, delivery time & parallel reactions --
21:17 < kanzure> you can't get them to ship you 1 million test tubes
21:17 < kanzure> but you can make 1 million permutations by ligating things together differently
21:18 < yashgaroth> exactly
21:18 < kanzure> well, they probably could ship you 1 million test tubes
21:18 < kanzure> in giant boxes
21:18 < kanzure> but the costs of that would be.. tremendous
21:19 < yashgaroth> still, oligo assembly could already be better than traditional synthesis
21:19 < yashgaroth> only one way to find out
21:19 < kanzure> yeah i'm sure it is better
21:19 < kanzure> and if it is, those companies can just switch to it
21:19 < yashgaroth> not if you patent the shit outta that bitch
21:20 < yashgaroth> not that that's very DIY, but you gotta get that seed money
21:21 < yashgaroth> I'd say it's 'non-obvious' since it took me a minute to type it out, but I'm no lawyer
21:21 < kanzure> nah there's lots of patentable stuff here
21:21 < kanzure> unfortunately this means i have to kill all of yuou
21:21 < yashgaroth> I'm well armed
21:21 < nmz787> i know people that are well armed
21:22 < kanzure> hey someone just posted to diybio
21:22 < kanzure> named "brian doom"
21:22 < kanzure> doom is an awesome name
21:22 < yashgaroth> even twin eh? it happens
21:22 < kanzure> evil?
21:22 < yashgaroth> heh
21:23 < kanzure> how drunk are you
21:23 < kanzure> because you're still sorta able to think
21:23 < yashgaroth> unless you have a mustache, he's the evil one by default
21:23 < kanzure> you need to go drink mroe
21:23 < yashgaroth> I'm still coherent but im having a hard tiem tryping this stuff without am=sabjf
21:24 < kanzure> drink until my code makes sense http://diyhpl.us/~bryan/sciencedirect/sciencedirect.js
21:24 < nmz787> http://www.ncbi.nlm.nih.gov/pubmed/7590320
21:24 < yashgaroth>  does not rely on DNA ligase but instead relies on DNA polymerase to build increasingly longer DNA fragments during the assembly process HA wait lemme read it
21:25 < nmz787> i have access
21:25 < nmz787> if you dont
21:25 < yashgaroth> that's still long oligos specifically made for that gene
21:25 < kanzure> 40nt means they probably had hybridizing overlaps
21:25 < yashgaroth> I have no access to anything :(
21:25 < kanzure> yes
21:25 < kanzure> that's not an oligo libraryt
21:26 < kanzure> that's "HEY we know what we want to synthesize"
21:26 < nmz787> sortof is
21:26 < nmz787> right
21:26 < kanzure> it's 56 members of a 40mer library
21:26 < kanzure> 56 / (4^40) is.... basically 0
21:26 < yashgaroth> sideways 8
21:26 < yashgaroth> err for 4^40 that is
21:27 < kanzure> yashgaroth: you suck at unicode ∞
21:27 < yashgaroth> FUCK
21:27 < yashgaroth> ∞ copy n pasting like a pro
21:28 < nmz787> but it says .9kb
21:28 < nmz787> 56*40 =2200 ish
21:28 < nmz787> 28*40=1120
21:28 < nmz787> so even if the oligos had 20bp overlap per side, its longer than .9kb
21:28 < kanzure> yeah some parts are for overlap
21:29 < kanzure> hrm
21:29 < nmz787> and if that was the case, they wouldnt need poly
21:29 < yashgaroth> well, a 3-5 mer overlap would be enough, as long as they stick at a temperature where pol still works
21:30 < nmz787> of they say 1.1kb was synthesized
21:30 < nmz787> oh*
21:32 < yashgaroth> kanzure re: your js code, I'm far past the ballmer point sorry
21:33 < nmz787> so we need to just try this in an eppendorf
21:34 < yashgaroth> indeed, just a 200bp fragment as proof of concept
21:35 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has joined ##hplusroadmap
21:38 < yashgaroth> I can supply the ep tubes :V
21:38 < kanzure> ParahSailin: yo
21:38 < kanzure> would you be willing to do some monkey labor
21:38 < ParahSailin> monkey labor?
21:38 < ParahSailin> sounds like fun
21:38 < kanzure> you know.. lab monkeying
21:39 < ParahSailin> what you have in mind at this point?
21:39 < kanzure> nmz787: just ligase right?
21:40 < yashgaroth> if we're doing a single-strand extension, we don't need PNK etc
21:41 < nmz787> http://disinfo.s3.amazonaws.com/wp-content/uploads/2011/09/MonkeysAtTypewriters.jpg
21:42 < nmz787> we'd need it for the staircase method or whatever you called it
21:42 < yashgaroth> but if the bottom strand just guides the top one into position for the ligase, and then you wash it off
21:42 < nmz787> single stranded extension will not have polymerization control
21:43 < yashgaroth> ^and repeat
21:43 < nmz787> monkeys at typewriters today, monkeys with pipettes tomorrow
21:43 < yashgaroth> a brave new future, a monkey could do most of my job
21:44 < ParahSailin> i think the "staircase method" would probably end up making a nice smear
21:44 < yashgaroth> as long as he doesn't try to fuck my 50mL tubes I'll hire one
21:44 < yashgaroth> okay back on topic, re smear you mean a lot of incorrect strands or what
21:45 < kanzure> contaminants?
21:45 < ParahSailin> random nastiness in general
21:45 < nmz787> why do you think that?
21:45 < yashgaroth> the hope is that at least 5-10% will be correct
21:45 < ParahSailin> i dunno, thats just my intuition/molecular bio pessimism
21:45 < nmz787> with the PNK and BAP for polymerization controls...
21:46 < nmz787> 5-10%!!!!
21:46 < nmz787> i was thinking it would be >90%
21:46 < yashgaroth> pick 20 colonies til you get a good one, no problem
21:46 < yashgaroth> depends how long the strand  you're trying to make is
21:47 < kanzure> 200bp
21:47 -!- sdr__ [~SDr@c-67-174-105-171.hsd1.co.comcast.net] has joined ##hplusroadmap
21:47 < yashgaroth> considering that for straight up pamidite, 69bp is a 50% success rate
21:48 < ParahSailin> what we need is a 1000-10000bp one step synthesis
21:48 < ParahSailin> up to 200bp, pamidite is good
21:48 < yashgaroth> yeah I'm hoping we can do 1kbp, but 200 as a proof-of-concept
21:48 < ParahSailin> gotcha
21:49 < kanzure> ParahSailin: http://diyhpl.us/~bryan/papers2/DNA/enzymaticSynthesisCycle.png
21:49 < kanzure> nmz787: where's the new diagram :x
21:49 < nmz787> errr
21:49 < nmz787> umm
21:49 < nmz787> shit
21:49 < kanzure> hah
21:49 < nmz787> i got busy
21:49 < nmz787> next week is finals week
21:49 < kanzure> sounds lame
21:49 < nmz787> i'm totally lethargic
21:50 -!- Juul [~Juul@199.188.193.145] has joined ##hplusroadmap
21:50 < kanzure> Juul: http://oligomaker.com/
21:50 < nmz787> the stress of hating school has gridlocked my neural circuitry
21:50 < kanzure> Juul: do we have anyone in diybio who can go raid their facilities? they are in copenhagen
21:50 < Juul> wut
21:50 -!- sdr__ is now known as SDr
21:50 < klafka> LOL
21:50 < kanzure> on aliabbi this machine is being sold for $60 euro
21:50 -!- SDr [~SDr@c-67-174-105-171.hsd1.co.comcast.net] has quit [Changing host]
21:50 -!- SDr [~SDr@unaffiliated/sdr] has joined ##hplusroadmap
21:51 < kanzure> *alibaba
21:51 < kanzure> nmz787 suspects that it's a typo and it's supposed to be $60,000 euro
21:51 < Juul> what the hell is that machine?
21:51 < yashgaroth> I can hit them while I'm over there in vacation, get me jason statham and it'll be no problem
21:51 < kanzure> Juul: 196-channel oligo sythesizer
21:51 < Juul> that website looks like crap
21:51 < Juul> they're just reselling?
21:51 < kanzure> web design by http://www.simpelside.dk/
21:52 < kanzure> alibaba has someone reselling
21:52 < kanzure> oligomaker is the manufacturer
21:52 < kanzure> "Simpel Side leverer billige hjemmesider med CMS og høj fleksibilitet på
21:52 < kanzure> få dage. Du kan vælge mellem 4 skabeloner og altid selv redigere i
21:52 < kanzure> indholdet på din hjemmeside når som helst. "
21:52 < kanzure> something something about 4 templates
21:52 < Juul> so the manufacturer is in denmark
21:52 < kanzure> i can't read this language too well
21:53 < Juul> "Simple Page delivers cheap homepages with CMS and high flexibility in only a few days. You can choose between 4 templates and always edit the content of your website at any time"
21:53 < kanzure> lame
21:53 < Juul> yes it actually says "always at any time"
21:53 < kanzure> hehe
21:54 < kanzure> videos!
21:54 < kanzure> http://www.youtube.com/watch?v=hBbjfEj1lCc
21:54 -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has quit [Quit: leaving]
21:54 < Juul> so you want one of their machines?
21:54 < nmz787> i guess i'm heading to bed
21:54 < kanzure> Juul: possibly, depending on the price
21:54 < kanzure> i'm trying to igure out if this is actually $60 euro
21:54 < kanzure> or $60,000 euro
21:54 < nmz787> it is not $60 euro
21:54 < kanzure> will you eat your hat if it is
21:54 < nmz787> most of the parts on their parts page are =>$60
21:55 < nmz787> umm
21:55 < nmz787> ugh
21:55 < Juul> kanzure, i could ask them if they have some old broken stuff they're willing to donate to BiologiGaragen
21:55 < nmz787> what do i get if i eat my hat?
21:55 < kanzure> Juul: that would be awesome
21:55 < nmz787> its wool
21:55 < nmz787> i don't think thats healthy to eay
21:55 < Juul> kanzure, ok that's on my todo for tomorrow
21:56 < nmz787> http://news.bbc.co.uk/2/hi/health/425609.stm
21:56 < nmz787> ttyl
21:56 < nmz787> i will try to add the missing steps to the diagram tomorrow
21:56 -!- nmz787 [43f2b117@gateway/web/freenode/ip.67.242.177.23] has quit [Quit: Page closed]
21:57 < Juul> i was offered a job at upcoming Stanford BIOFAB today
21:57 < Juul> but it will only be two people until more funding is found :-/
21:57 < kanzure> would this job possibly pay you?
21:57 < kanzure> in money?
21:58 < kanzure> hmm it looks like there's a video about the team that made the POSAM dna synthesizer
21:58 < kanzure> http://youtube.com/watch?v=Nb7zxKEZzZQ
21:58 < kanzure> maybe this is a different group..
22:01 < kanzure> that was a really lame video
22:01 -!- strages_home [~strages@adsl-98-67-175-14.shv.bellsouth.net] has quit [Ping timeout: 252 seconds]
22:11 -!- SDr [~SDr@unaffiliated/sdr] has quit [Ping timeout: 260 seconds]
22:15 < Juul> yes, it would pay me in money
22:15 < Juul> but i would have to live near stanford or commute
22:16 < Juul> and it would be more time out of my life not working on my own projects
22:16 < Juul> this is sub-optimal
22:16 < kanzure> right
22:17 < Juul> also, i'm worried that it will take a while before we get funding for more people
22:17 < kanzure> hasn't biofab been around for a few years now?
22:17 < kanzure> how does it not have funding
22:18 < Juul> two years yeah
22:18 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has quit [Quit: Adifex]
22:18 < Juul> though the work is good and important, no articles have come out. also: the people involved all have other priorities
22:19 < Juul> also, academia in the u.s. is apparently hella slytherin
22:19 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has joined ##hplusroadmap
22:19 < Juul> a couple of articles are on their way out
22:19 < Juul> but it has taken crazy long, in part due to too many people being involved
22:20 < klafka> slytherin?
22:20 < kanzure> is it just me or does a lot of biofab/ginkgo/igem stuff seem to be pretentious a bit
22:21 < Juul> hm, i couldn't say. the problem at biofab has been that there are two overworked professors in charge and they're both trying to act as managers/editors, and they have to agree
22:21 < Juul> on what a good paper looks like
22:22 < Juul> klafka, harry potter reference. from wikipedia: "Slytherin house values ambition, cunning, leadership, and resourcefulness. The house mascot of Slytherin is the serpent,"
22:23 < klafka> aaah
22:23 < Juul> lots of maneuvering and strategizing. a lack of transparency in dealings and plans
22:23 < klafka> ooh yes
22:23 < klafka> fucking yes
22:23 < yashgaroth> i.e. 'fuck you I'm first author'
22:23 < klafka> oh so fucking yes
22:24 -!- Adifex [~Adifex@utdpat241140.utdallas.edu] has left ##hplusroadmap []
22:24 < klafka> man i can't sleep so i'm trying to figure out zendesk's rest api
22:24 < klafka> ugh
22:24 < kanzure> is it actually restful
22:24 < klafka> not for me
22:24 < klafka> (har har har)
22:24 < Juul> its always problematic to have many people collaborating on editing one document, especially when everyone else has other priorities and it's almost impossible to get everyone to sit down and talk at the same time
22:25 < delinquentme> anyone know where I could get more chemical formulas??
22:25 < kanzure> delinquentme: pubchem
22:25 < delinquentme> just asked in ##chemistry
22:25 < klafka> kanzure i think so
22:25 < klafka> also what would make it not restful? COMET?
22:25 < kanzure> delinquentme: pubchem > ##chemistry
22:25 < kanzure> klafka: not restful means it's not using POST, GET, PUT, etc.
22:25 < klafka> oh
22:25 < klafka> ok
22:25 < delinquentme> y no RESTful?
22:26 < kanzure> and the objects wouldnn't be resources and shit
22:26 < klafka> why would someone call a non-restful api restful then
22:26 < klafka> :(
22:26 < delinquentme> REST = Representational state transfer ... its related to POST GET DELETE etc
22:26  * klafka nods
22:26 < delinquentme> klafka, because they're not programmers
22:26 < klafka> ah
22:26 < delinquentme> and they want a brandname
22:27 < delinquentme> call it restful = street cred
22:27 < delinquentme> REST is basically HATEOS which is basically discoverability
22:27 < delinquentme> ( correct me if im wrong )
22:27 < delinquentme> Juul, Rjb is awesome   just got it working
22:28 < delinquentme> kanzure, what should i put in here
22:28 < delinquentme> just any kind of chemical and get a match
22:28 < kanzure> sure
22:29 < delinquentme> "water" << too simple
22:29 < kanzure> do an alcohol
22:30 < delinquentme> but these are pre-parsed
22:30 < delinquentme> i want the human journal descriptions
22:31 < yashgaroth> hexenal :D
22:31 < Juul> delinquentme, cool
22:32 < ParahSailin> wonder if any of the nad+ using ligases could be made electrochemically switchable
22:35 < Juul> has anyone answered the question: "why has no biological organism evolved radio communication"
22:36 < Juul> it seems like a natural progression from the electro-sensing and electro-communication found in some sea-creatures
22:36 < klafka> that's not really an answerable question
22:36 < klafka> all you can make is a convincing 'just-so story'
22:36 < Juul> well you can come up with a reasonable hypothesis
22:36 < klafka> fair enough
22:37 < Juul> i'm wondering what the difficult component is
22:37 < Juul> the oscillator?
22:37 < Juul> the antenna?
22:37 < yashgaroth> the solid metal antenna
22:37 < Juul> possibly
22:37 < Juul> would it have to be solid metal
22:37 < Juul> ?
22:38 < yashgaroth> dunno, I'm not an electronicizer
22:39 < yashgaroth> I can't think of any emission/reception of spectra that are outside of the sun's normal wavelengths, much less all the way into radio
22:40 < Juul> since it's much easier to communicate with simple electro-senses under water, but much harder / impossible to use radio, it might be that the jump between electro-sense and radio never happened, since it would have to happen in an amphibious species
22:41 < Juul> well, it's pretty great that the radio spectrum isn't flooded by animal communication
22:41 < yashgaroth> are there any examples of electro-communication underwater? I thought it was all prey detection
22:41 < Juul> that would have both sucked for us and for the animals when we started disrupting their communication globally
22:42 < Juul> yashgaroth, I believe I found some sharks that use it for communication last time i checked. let me see if i can find it again
22:43 < yashgaroth> I'd thought it was platypus detecting prey, and electric eels doing their thing, but I've never looked into it much
22:43 < delinquentme> Juul, umm ? @ the radio communication
22:43 < delinquentme> we have they're called sound waves and simply on a shorter wavelength?
22:43 < kanzure> there's some magnetoreceptor proteins
22:43 < delinquentme> and dogs hear in a greater range so you could make an argument that they do
22:43 < Juul> https://en.wikipedia.org/wiki/Electroreception#Electrocommunication
22:44 < yashgaroth> ya for compass-like stuff in birds and bacteria
22:44 < kanzure> Juul: a scifi story about us disrupting electromagnetic animal communication would be pretty neat
22:44 < delinquentme> amulae of lorezini :D
22:45 < Juul> kanzure, good idea. that's actually a good idea for how to spread the ideas you don't intend to / have time to implement
22:48 < ParahSailin> an organism could probably make an antenna out of a well-conducting melanin
22:48 < yashgaroth> oh man that radiation-eating fungus was so awesome
22:49 < yashgaroth> melanin as chloropyll aww yeah
22:49 < yashgaroth> +h*
22:50 < kanzure> sshh the radiation-eating fungus was classified
22:50 < yashgaroth> damn russkies
22:54 < Juul> delinquentme, yeah sound waves are nice for comms, but the first animal to evolve radio would be able to communicate without detection by all other species
22:54 < Juul> then everyone else would have to evolve radio to keep up
22:55 < Juul> and eventually it would be no advantage whatsoever
22:55 < Juul> and everyone would revert back to regular noisemakers as they require less energy
22:55 < ParahSailin> the reason organisms dont have stuff for radio waves is that a microwave photon of 2.4 GHz has energy of .2 cal/mol
22:55 < Juul> omg dinosaurs totally had telepathic walkie-talkie
22:55 < Juul> <-- drunk
22:56 < ParahSailin> atp = 7ish kcal/mol
22:56 < delinquentme> Juul, i dont hear bats :D
22:57 < delinquentme> $ bundle install_the_dependencies_stupid_gem_manager
22:57 < ParahSailin> i dont think there's anything else in nature that can integrate such small quanta
22:57 < kanzure> good night
22:57 < Juul> huh? what does cal/mol mean for a photon?
22:57 < Juul> kanzure, night
22:57 < delinquentme> oodles kanzure
22:58 < delinquentme> Juul, well its a source of energy right?
22:58 < delinquentme> a cal / mol is a measure of energy capacity
22:58 < ParahSailin> kcal/mol is the common biochemical unit of energy
22:58 < ParahSailin> 1.5e-24 J = .0002 kcal/mol
22:58 < foucist> ParahSailin: PariahSalin  would make more sense wouldn't it? :P
22:58  * delinquentme thinks of the orange-hot headers of a car
22:58 < delinquentme> energy = heat, sound, light
22:59  * delinquentme sinatra installed 
22:59 < Juul> per mole? why per mole?
23:00 < Juul> 1 calorie is 4.184 joules
23:00 < Juul> i'm not sure where the /mol comes in
23:00 < ParahSailin> if you multiply a scalar by 6.022e23 it becomes a mol
23:01 < Juul> oh. i've only seen that used when talking about something per number of atoms/molecules
23:01 < Juul> didn't realize it was used as a general unit
23:02 < Juul> you make a good point
23:02 < ParahSailin> the si unit of light flux involves moles
23:02 < yashgaroth> it's useful when comparing the energy of single molecule reactions
23:02 < Juul> interesting
23:02 < Juul> ok
23:02 < Juul> i have to pack up and head for bart
23:03 < ParahSailin> maybe not on the si unit
23:04 < Juul> ParahSailin, so your argument is that reception wouldn't work?
23:04 < Mokstar_AFK> hey
23:04 < ParahSailin> reception would be pretty difficult to evolve id say
23:04 < Mokstar_AFK> can microwave radiation convert l-proline into d-proline?
23:04 < ParahSailin> lots of it can
23:04 < Juul> hrm
23:04 < Juul> ok
23:05 < Juul> yep
23:05 < ParahSailin> we havent seen biological heat engines either for that matter
23:05 < Juul> what's the cal/mol of a light photon
23:05 -!- Juul [~Juul@199.188.193.145] has quit [Remote host closed the connection]
23:05 < yashgaroth> I thought the general rule was that a receptor has to be at least half the length of the wavelength it's receiving, which for radio is hella long
23:05 < ParahSailin> or biological mechanical force to atp transducers
23:07 < ParahSailin> chlorophyll a blue peak 465 nm photon is 2.666 eV
23:08 < ParahSailin> 1 eV = 23 kcal/mol
23:09 -!- He||eshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has joined ##hplusroadmap
23:10 -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has quit [Ping timeout: 244 seconds]
23:10 < ParahSailin> stuff like heat engines and radio receptors just dont scale down that well i guess
23:10 < ParahSailin> to the molecular level i mean
23:11 < delinquentme> ParahSailin, you know of the ssingle molecule sterling engine right?
23:13 < ParahSailin> hadnt heard of it, but that seems to be micron scale
23:15 < ParahSailin> also, kinda cheating to use optical tweezers as the pistons :)
23:16 < ParahSailin> big difference between Angstrom scale protein supramolecular assemblies and microparticles
23:17 < ParahSailin> a sarcomere in muscle is a 2 um supermolecular assembly
23:17 < ParahSailin> but myosin motors individually work at the angstrom level
23:17 < ParahSailin> so its evolutionarily feasible
23:19 -!- Mokstar_AFK [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has quit [Read error: Connection reset by peer]
23:20 -!- Mokbortolan_ [~Nate@c-71-59-241-82.hsd1.or.comcast.net] has joined ##hplusroadmap
23:59 -!- yashgaroth [~f@cpe-24-94-5-223.san.res.rr.com] has quit [Quit: Leaving]
--- Log closed Wed Feb 22 00:00:21 2012