| --- Log opened Wed Feb 15 00:00:11 2012 | ||
| -!- sylph_mako [~mako@118-93-21-71.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 260 seconds] | 00:15 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 00:29 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap | 02:06 | |
| -!- noahj [~noah@24.38.182.147] has quit [Ping timeout: 260 seconds] | 02:13 | |
| -!- qnm [~qnm@2001:44b8:3110:f300:208:9bff:fec0:179a] has quit [Ping timeout: 240 seconds] | 02:15 | |
| -!- qnm [~qnm@2001:44b8:3110:f300:208:9bff:fec0:179a] has joined ##hplusroadmap | 02:17 | |
| -!- ivan` [~ivan@unaffiliated/ivan/x-000001] has quit [Read error: Operation timed out] | 02:19 | |
| -!- ivan` [~ivan@unaffiliated/ivan/x-000001] has joined ##hplusroadmap | 02:20 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 245 seconds] | 02:52 | |
| foucist | hmm, i once read about a guy that used some simple 3d/evolutionary computation/genetic algorithm program to generate a table for his living room | 03:25 |
|---|---|---|
| foucist | trying to find where i read it, or what program it was hmm | 03:25 |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 245 seconds] | 03:54 | |
| -!- delinquentme [~asdfasdf@c-24-3-85-154.hsd1.pa.comcast.net] has joined ##hplusroadmap | 04:01 | |
| -!- strages_home [~strages@adsl-98-67-175-14.shv.bellsouth.net] has quit [Quit: Lost terminal] | 05:18 | |
| -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] | 05:27 | |
| -!- strages_home [~strages@adsl-98-67-175-14.shv.bellsouth.net] has joined ##hplusroadmap | 05:35 | |
| -!- delinquentme [~asdfasdf@c-24-3-85-154.hsd1.pa.comcast.net] has quit [Quit: Leaving] | 06:13 | |
| -!- eudoxia [~eudoxia@r190-135-26-252.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap | 06:55 | |
| -!- eudoxia [~eudoxia@r190-135-26-252.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] | 07:09 | |
| -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Quit: Computer has gone to sleep.] | 07:38 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap | 07:40 | |
| @kanzure | http://www.foxnews.com/us/2012/02/13/e-coli-vials-found-in-arkansas-apartment-used-for-aliment/ | 07:44 |
| chris_99 | interesting | 07:46 |
| chris_99 | is e-coli that dangerous, i don't know much about it | 07:46 |
| @kanzure | depends on the strain | 07:47 |
| @kanzure | annnd anyone in law enforcement who does not know biology is trained to escalate "petri dishes" to threat level "oh fuck oh fuck" immediately | 07:48 |
| archels | haha | 07:49 |
| archels | e-coli lives in your and my gut. | 07:50 |
| chris_99 | lol | 07:53 |
| audy | lol, vials | 07:58 |
| audy | that just makes it sound sinister | 07:58 |
| audy | "bubbling couldron of S. aureus found in home" | 07:58 |
| @kanzure | 1) buy lots of petri dishes | 07:59 |
| @kanzure | 2) buy lots of markers | 07:59 |
| @kanzure | 3) label them, "V. Venusauris" | 07:59 |
| @kanzure | and "P. Pikachuce" | 07:59 |
| audy | haha | 08:00 |
| @kanzure | 4) you know what to do | 08:00 |
| chris_99 | haha | 08:24 |
| -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has quit [Quit: Leaving.] | 08:27 | |
| -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has joined ##hplusroadmap | 08:28 | |
| -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has quit [Ping timeout: 276 seconds] | 08:35 | |
| -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has joined ##hplusroadmap | 08:38 | |
| -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has joined ##hplusroadmap | 08:39 | |
| @kanzure | http://staceyk.org/diybioworkshop/call.html | 08:58 |
| @kanzure | "During our one-day workshop, we will work directly with (DIY) biology practitioners to gain a shared understanding of the practices, materials and challenges behind hobby biology." | 08:58 |
| @kanzure | "Submissions may be sent by email to stace@cmu.edu by March 16, 2012." | 08:58 |
| @kanzure | why isn't there a game yet where you can scan in your lego creations | 09:05 |
| @kanzure | http://money.msn.com/business-news/article.aspx?feed=PR&Date=20120214&ID=14791316 | 09:09 |
| @kanzure | "Organovo Announces $6.5 Million Private Placement to Advance 3D Bioprinting for Medical Applications" | 09:09 |
| @kanzure | /win 6 | 09:11 |
| -!- augur [~augur@129.2.129.34] has joined ##hplusroadmap | 09:12 | |
| -!- archels [~foo@sascha.esrac.ele.tue.nl] has quit [Ping timeout: 245 seconds] | 09:16 | |
| -!- He||eshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has joined ##hplusroadmap | 09:17 | |
| -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has quit [Ping timeout: 252 seconds] | 09:21 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host] | 09:26 | |
| -!- archels [~foo@sascha.esrac.ele.tue.nl] has joined ##hplusroadmap | 09:26 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap | 09:29 | |
| @kanzure | wow this is some major fearmongering http://virtualbiosecuritycenter.org/organizations/diybio-org | 09:41 |
| chris_99 | guess you guys have heard of this http://openpcr.org/ | 09:50 |
| chris_99 | i want an open source synthesizer now | 09:50 |
| @kanzure | openpcr for the longest time wasn't actually open | 09:54 |
| chris_99 | interesting | 09:55 |
| chris_99 | you mean until they'd finished | 09:55 |
| chris_99 | the software? | 09:55 |
| chris_99 | etc. | 09:55 |
| @kanzure | there used to be a physically-large oligonucleotide jet printer project called posam or pogo, but the siet is down or something | 09:56 |
| @kanzure | the software, their cad files, shit like tht | 09:56 |
| @kanzure | here's posam/pogo http://www.bioinformatics.org/pogo/ | 09:56 |
| @kanzure | "The Piezoelectric Oligonucleotide Synthesizer And Microarrayer (POSAM) was developed in the Hood Laboratory to give researchers access to customizeable DNA microarrays. The result is an "open source" platform. The hardware design and protocols are being made available freely to the public and the control software is released under the GPL license." | 09:56 |
| @kanzure | it requires some strange things iirc; like an argon atmosphere | 09:56 |
| chris_99 | oh darn | 09:57 |
| chris_99 | sounds interesting though | 09:57 |
| @kanzure | hah their rotary mixer.. page 11 http://www.bioinformatics.org/pogo/POSAM_Man_Ch2_User_v1-0_040414.pdf | 09:59 |
| @kanzure | "we have found it more convenient to purchase acetonitrile in bulk, specifically 20L and 50L containers" oh boy | 10:00 |
| chris_99 | hehe | 10:01 |
| chris_99 | that looks a really interesting read | 10:02 |
| @kanzure | i've updated http://openwetware.org/wiki/DIYbio/FAQ/News#Has_DIYbio_been_in_the_news.3F | 10:05 |
| chris_99 | another site to bookmark :) | 10:05 |
| chris_99 | i just bought a book called wetware | 10:06 |
| chris_99 | Wetware: A Computer in Every Living Cell: The Computer in Every Living Cell | 10:06 |
| @kanzure | sounds like a dangerous(ly wrong) metaphor | 10:08 |
| @kanzure | this looks neat: Microevolution of Canine Influenza Virus in Shelters and Its Molecular Epidemiology in the United States (J. Virol, 84:12636) | 10:08 |
| @kanzure | http://gizmodo.com/5885295/how-to-dna+hack-yogurt-into-prozac | 10:09 |
| -!- SDr [SDr@unaffiliated/sdr] has joined ##hplusroadmap | 10:09 | |
| @kanzure | "venter envy" http://ellingtonlab.org/blog/2011/08/05/on-venter-envy/ | 10:19 |
| -!- augur [~augur@129.2.129.34] has quit [Ping timeout: 245 seconds] | 10:20 | |
| -!- delinquentme [~asdfasdf@c-67-171-66-113.hsd1.pa.comcast.net] has joined ##hplusroadmap | 10:26 | |
| -!- n_bentha [~lolicon@75.111.160.104] has joined ##hplusroadmap | 10:36 | |
| -!- augur [~augur@129.2.129.34] has joined ##hplusroadmap | 10:39 | |
| -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has quit [Quit: Leaving.] | 10:53 | |
| n_bentha | i want to make a bacteria that overproduce linaloo | 10:56 |
| n_bentha | i want to make a bacteria that overproduce linalool* | 10:56 |
| delinquentme | ^^^^ | 10:56 |
| delinquentme | you're in the right place! | 10:56 |
| n_bentha | :) | 10:56 |
| n_bentha | i want to put it into a non-pathogenic enteric bacterial strain | 10:57 |
| n_bentha | my shit would smell like flowers! | 10:57 |
| delinquentme | lol | 10:57 |
| delinquentme | sooo you need something which produces it | 10:57 |
| delinquentme | and then overexpress it? | 10:57 |
| Mokbortolan_1 | I want to re-engineer the bacteria that consume apocrine excretions so that the produced compounds are odorless | 10:58 |
| n_bentha | u don't need something that produces it, delinquetme | 10:58 |
| n_bentha | u can produce chemical compounds that have never been expressed before in organisms by combining genes from different species | 10:58 |
| delinquentme | ah ok so you get that organism to build it | 10:59 |
| n_bentha | hey now, thos apocrine secretions attract the opposite sex | 10:59 |
| n_bentha | yes | 10:59 |
| Mokbortolan_1 | not the sulfurous ones | 10:59 |
| delinquentme | ahhhh | 11:00 |
| delinquentme | ic ic | 11:00 |
| n_bentha | http://en.wikipedia.org/wiki/File:Mevalonate_pathway.png | 11:01 |
| n_bentha | + | 11:01 |
| n_bentha | http://www.plantphysiol.org/content/127/3/1256/F1.expansion.html | 11:01 |
| n_bentha | = linalool! | 11:01 |
| n_bentha | haha put it into some health food, and you're rich | 11:03 |
| n_bentha | everyone wants their shit to smell like flowers | 11:03 |
| n_bentha | put it into some yogurt ^^ | 11:03 |
| n_bentha | or maybe u'd have to bypass the stomach? | 11:03 |
| n_bentha | hmmm | 11:05 |
| n_bentha | i'd need to look up how to make a protein scaffold to increase the efficiency of my bacterial factory | 11:05 |
| Mokbortolan_1 | lilac enemas! | 11:06 |
| n_bentha | u know...scaffold all the enzymes together, so the time for the molecule to wander around and bind to the enzymes is reduced | 11:06 |
| Mokbortolan_1 | they've been out of fashion for ~150 years, maybe their time is returning? :p | 11:06 |
| n_bentha | hehe, but it's all natural (kinda-sorta) | 11:06 |
| n_bentha | would be popular w/ the anal porn industry for sure | 11:06 |
| * n_bentha shudders | 11:06 | |
| @kanzure | 'In June 2008, the aquarium announced its "Swim With Gentle Giants" program. This allows divers or snorkelers to swim with the whale sharks.' | 11:08 |
| @kanzure | http://en.wikipedia.org/wiki/Georgia_Aquarium | 11:08 |
| * n_bentha wants to do dat | 11:10 | |
| -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has joined ##hplusroadmap | 11:24 | |
| -!- He||eshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has quit [Read error: Connection reset by peer] | 11:26 | |
| -!- He||eshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has joined ##hplusroadmap | 11:27 | |
| @kanzure | hi klafka | 11:35 |
| klafka | hey kanzure | 11:38 |
| klafka | i'm working from home today co i feel sickly | 11:38 |
| @kanzure | oh you have to work in an office? | 11:40 |
| klafka | kanzure is SUUUCH a hater | 11:45 |
| klafka | it's important that we all work in the same area generally beacuse it facilitates communication | 11:45 |
| chris_99 | is there any more information on the the prozac yoghurt | 11:46 |
| @kanzure | you know what else facilitates communication and team building? working from a strip club all day | 11:46 |
| chris_99 | he doesn't say what dna he used in the video | 11:46 |
| chris_99 | there doesn't seem to be anything on parts registry | 11:50 |
| chris_99 | to do that | 11:50 |
| @kanzure | the prozac stuff? no. the parts registry will have some promoters or regulators though | 11:50 |
| chris_99 | hmm why doesnt he say what he used though | 11:50 |
| chris_99 | seems a bit odd | 11:50 |
| @kanzure | cause he's either full of it, working for a lab and believes in intellectual property, or he's working for a company that believes in intellectual pooperty | 11:51 |
| chris_99 | heh, bit crap though, as he's trying to explain DIY biotech without telling you what the hell to do heh | 11:51 |
| chris_99 | all of his work seems to be a bit like that | 11:53 |
| @kanzure | chris_99: you should post a reply to the diybio thread about this, and ask them for details | 11:58 |
| chris_99 | yeah i'll sign up to that now | 11:58 |
| chris_99 | just posted i think | 12:02 |
| @kanzure | i think jason/mac set the group to "approve first post" so it might be a few hours until one of them gets their head out of the sand to approve your email | 12:06 |
| chris_99 | its up now from what i can see | 12:07 |
| chris_99 | do you know roughly whats the number of base-pairs a synthesizer can produce | 12:10 |
| @kanzure | chris_99: can you re-ask | 12:10 |
| chris_99 | what do you mean? | 12:12 |
| @kanzure | like max length? | 12:12 |
| chris_99 | yeah | 12:12 |
| @kanzure | it depends on error rate | 12:12 |
| @kanzure | you can operate a machine for as long as you want | 12:13 |
| @kanzure | but most machines only operate at slightly above 95% accuracy | 12:13 |
| @kanzure | even 98% accuracy is a huge problem for synthesizing long strands of dna | 12:13 |
| chris_99 | ah interesting, so you'd just have to run it until you get the chain which is correct | 12:13 |
| chris_99 | would you need an electron microscope to know its correct | 12:13 |
| @kanzure | sorta kinda.. there are other strategies like.. do 1000 synthesis reactions simultaneously and hope one of them is correct | 12:13 |
| @kanzure | no but you can theoretically use such a microscope | 12:13 |
| @kanzure | you can do other types of verification | 12:14 |
| chris_99 | cool, such as? | 12:14 |
| @kanzure | like dna sequencing (tons of different methods), hybridization, spectrometry, | 12:14 |
| @kanzure | mass spec | 12:14 |
| n_bentha | gc? | 12:15 |
| @kanzure | fluorescence stuff. sequencing-by-synthesis (pyrosequencing) | 12:15 |
| chris_99 | awesome, more things to check out :) | 12:15 |
| chris_99 | back in a bit just making some homebrew beer | 12:15 |
| n_bentha | mead is betta! | 12:15 |
| chris_99 | heh, i've got a bottle of that | 12:15 |
| -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Quit: Computer has gone to sleep.] | 12:24 | |
| @kanzure | viscousplacebo? heh | 12:29 |
| @kanzure | "Firstly, this video where a guy takes yogurt and makes Prozac.http://giz..." | 12:30 |
| @kanzure | you know, he could have meant the opposite | 12:30 |
| @kanzure | the guy takes prozac, but makes yogurt | 12:30 |
| n_bentha | lol | 12:33 |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 12:38 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 244 seconds] | 12:43 | |
| -!- marainein [~marainein@114-198-72-8.dyn.iinet.net.au] has quit [Ping timeout: 252 seconds] | 12:45 | |
| -!- kvltist [~Kvltist@p5B33FAF6.dip.t-dialin.net] has quit [Ping timeout: 265 seconds] | 12:47 | |
| -!- n_bentha [~lolicon@75.111.160.104] has left ##hplusroadmap [] | 12:50 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 12:59 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has quit [Read error: Connection reset by peer] | 13:01 | |
| -!- roksprok [~Zac@74.83.205.124] has joined ##hplusroadmap | 13:14 | |
| -!- yash-phone [~yaaic@66-87-0-68.pools.spcsdns.net] has joined ##hplusroadmap | 13:17 | |
| yash-phone | so does that prozac guy explain how he gets bacteria to add the cf3 group to the prozac | 13:18 |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 13:19 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has quit [Read error: Connection reset by peer] | 13:20 | |
| yash-phone | also hey chris where in the uk you from? i grew up in chester | 13:21 |
| chris_99 | hey, yeah, i know chester :) i live in the north-west | 13:23 |
| yash-phone | no shit, i still have family up there if you know where thelwall is | 13:23 |
| chris_99 | nah | 13:24 |
| yash-phone | yeah it's a tiny village | 13:24 |
| chris_99 | heh. i just emailed that guy actually, but i got an out-of-office reply saying he's away from the net till april | 13:25 |
| yash-phone | hahaha yeah, if he can get bacteria to use fluorine he'd be way famous | 13:28 |
| yash-phone | also did you guys see that article on cathal garvey in techreview? | 13:30 |
| @kanzure | yash-phone: we decided it was a journalism mixup; see, he only *takes* prozac, not *makes* prozac | 13:31 |
| @kanzure | yes we saw the articles about cathal | 13:31 |
| @kanzure | http://bit.ly/diybionews2 | 13:31 |
| @kanzure | http://www.genomeweb.com//node/1029216 | 13:31 |
| @kanzure | http://www.technologyreview.com/business/39597/ | 13:31 |
| yash-phone | ok good; well, back to work for me bbl | 13:36 |
| -!- yash-phone [~yaaic@66-87-0-68.pools.spcsdns.net] has quit [] | 13:36 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 13:37 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has quit [Read error: Connection reset by peer] | 13:37 | |
| -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has joined ##hplusroadmap | 13:42 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 13:54 | |
| -!- eudoxia [~eudoxia@r186-52-158-63.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap | 13:58 | |
| @kanzure | klafka: sooo i have this SF-based "developer speed dating" thing | 14:10 |
| @kanzure | apparently it was sold out last year | 14:10 |
| klafka | LOL | 14:11 |
| klafka | what? | 14:11 |
| @kanzure | i purchased a ticket but i'm not actually in sf | 14:11 |
| @kanzure | it's tomorrow | 14:11 |
| klafka | so for developers to date each other? | 14:11 |
| klafka | or? | 14:11 |
| @kanzure | no it's for companies to pick up developers and people | 14:11 |
| @kanzure | do you want it :/ | 14:11 |
| klafka | that makes more sense | 14:11 |
| @kanzure | http://rubydevelopersll.eventbrite.com/ | 14:11 |
| klafka | hmmm thanks but i don't think it makes sense atm | 14:12 |
| @kanzure | know anyone else who could use it? | 14:12 |
| @kanzure | fenn: would you enjoy tolerating that | 14:12 |
| klafka | hmmmm | 14:12 |
| -!- augur [~augur@129.2.129.34] has quit [Remote host closed the connection] | 14:14 | |
| -!- strangewarp [~strangewa@c-76-25-200-47.hsd1.co.comcast.net] has quit [Read error: Connection reset by peer] | 14:20 | |
| -!- archels [~foo@sascha.esrac.ele.tue.nl] has quit [Ping timeout: 245 seconds] | 14:47 | |
| -!- archels [~foo@sascha.esrac.ele.tue.nl] has joined ##hplusroadmap | 14:58 | |
| -!- eudoxia [~eudoxia@r186-52-158-63.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] | 15:21 | |
| -!- delinquentme [~asdfasdf@c-67-171-66-113.hsd1.pa.comcast.net] has quit [Quit: Leaving] | 15:26 | |
| -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap | 15:29 | |
| -!- strages_shop [~strages@256.makerslocal.org] has joined ##hplusroadmap | 15:45 | |
| -!- strangewarp [~strangewa@c-76-25-200-47.hsd1.co.comcast.net] has joined ##hplusroadmap | 16:39 | |
| fenn | heh lots of familiar names on that ruby developer meatup | 16:41 |
| @kanzure | you want it? | 16:42 |
| fenn | no | 16:42 |
| @kanzure | jfkladjfdkal nobody's taking this | 16:43 |
| * fenn shrugs | 16:43 | |
| fenn | there's lots of events along these lines, and personally i don't know ruby/rails | 16:43 |
| @kanzure | i was thinking of going and just making up stuff, like "oh yeah i totally scaled infrastructure to send billions of messages per second" | 16:43 |
| @kanzure | or "google? yeah i worked there, whatever" | 16:43 |
| -!- jmil [~jmil@c-68-81-252-40.hsd1.pa.comcast.net] has joined ##hplusroadmap | 16:45 | |
| Mokbortolan_1 | I strategized cloud-service SAAS architecture synergies to collaboratively distribute viral crowdsourced content to billions of customers! | 16:47 |
| @kanzure | now you've got it.. you're on your way to 205k/year | 16:47 |
| fenn | is there a RoR marketspeak buzzword generator? | 16:47 |
| Mokbortolan_1 | Hehehe... Crowdsourced massively-distributed direct-contact email advertisement campaign = botnet spammer! | 16:48 |
| fenn | nikki recommends complaining about routing in rails, namedropping obi fernandez, antipatterns | 16:48 |
| @kanzure | fenn: http://ykombinator.com/ | 16:49 |
| @kanzure | man i hate it when i'm my search results http://osdir.com/ml/diybio/2010-09/msg00192.html | 16:54 |
| @kanzure | (and apologies for linking to osdir.com's spam directory) | 16:54 |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] | 16:58 | |
| @kanzure | microfluidics bootcamp http://www.princeton.edu/psoc/training/bootcamp/ | 17:02 |
| @kanzure | "Our inaugural camp is designed to familiarize researchers with microfluidic/micro-fabrication technologies. Attendees will learn to make microfluidic devices by soft lithography and perform several experiments using them. The course consists of lectures and hands-on laboratory experience." | 17:03 |
| @kanzure | August 1-5, 2011 - August 8-12, 2011 | 17:03 |
| @kanzure | aughhhh | 17:03 |
| @kanzure | http://www.princeton.edu/microfluidics/training/boot-camp/2011_Materials/bootcamp0_3_6.pdf | 17:10 |
| @kanzure | schedule http://www.princeton.edu/microfluidics/training/boot-camp/2011_Materials/schedulev3_new.pdf | 17:10 |
| roksprok | are molds for microfluidics chips usually made using laser cutters? | 17:16 |
| @kanzure | nope | 17:26 |
| @kanzure | lithography | 17:26 |
| @kanzure | but i've experimented with laser-cut acrylic, | 17:27 |
| @kanzure | and nathan has experimented with laser-cut pdms i think | 17:27 |
| roksprok | how has it worked? | 17:27 |
| @kanzure | needs more testing | 17:28 |
| @kanzure | huh, the shrinkydink stuff has been turned into a product | 17:28 |
| @kanzure | http://shrink.myshopify.com/ | 17:28 |
| @kanzure | yeah that bootcamp doc is really great | 17:43 |
| -!- ParahSailin [~parahsail@unaffiliated/parahsailin] has joined ##hplusroadmap | 17:51 | |
| @kanzure | hi ParahSailin | 17:55 |
| ParahSailin | howdy | 17:55 |
| * ParahSailin is rogue molecular biologist | 17:56 | |
| @kanzure | cool | 17:58 |
| @kanzure | ParahSailin: can you help me out with oligonucleotide synthesis chemistry | 17:58 |
| @kanzure | i threw up some notes: http://diyhpl.us/~bryan/papers2/DNA/synthesis.html | 17:59 |
| ParahSailin | i'd say go with idt | 18:00 |
| @kanzure | no thanks | 18:00 |
| @kanzure | this is for a device | 18:00 |
| ParahSailin | ah | 18:00 |
| @kanzure | my target budget is <$5k per device (final) | 18:00 |
| ParahSailin | ill check out what you are saying | 18:00 |
| @kanzure | i mean, production price | 18:00 |
| ParahSailin | that sounds awesome | 18:00 |
| @kanzure | none of this >$100k bullshit | 18:00 |
| ParahSailin | i have no qualms about breaking every single patent if it means these machines will all be cheaper | 18:01 |
| @kanzure | alright grat | 18:01 |
| @kanzure | *great | 18:01 |
| @kanzure | welcome to the club, how'd you find us | 18:01 |
| ParahSailin | a meatspace friend told me about this, im not sure what name he goes by in here | 18:02 |
| ParahSailin | i think the most significant thing about 3d printers is being able to "pirate" hardware, infringe patents | 18:02 |
| @kanzure | most stuff isn't made on 3d printers | 18:03 |
| ParahSailin | i know. im saying that the most significant use of a 3d printer would be to rip off patents | 18:03 |
| ParahSailin | in a decentralized way such that patents are impossible to enforce | 18:04 |
| jrayhawk | Personal computing has not obsoleted software patents. | 18:04 |
| ParahSailin | personally i think subtractive processes are a more reasonable way to accomplish to goal of bespoke parts | 18:04 |
| jrayhawk | Though there is an extent to which if patents started being seriously leveraged against hacker-archetypes, development would move underground. | 18:06 |
| ParahSailin | kanzure, how do you intend to reduce the price | 18:06 |
| ParahSailin | i think it might be pretty difficult to do what idt does, cheaper | 18:06 |
| @kanzure | ParahSailin: by not charging so much | 18:06 |
| @kanzure | $0.30/bp is stupid | 18:07 |
| @kanzure | george church cites $1 per 100 kbp | 18:07 |
| ParahSailin | its $0.20 now | 18:07 |
| @kanzure | $0.30/bp is the price that the synthesis services show you | 18:07 |
| @kanzure | device != service | 18:07 |
| ParahSailin | so you think their margin is ridiculously high, and their business model is propped up by patents on the machines? | 18:07 |
| @kanzure | their margin might not be so high because of sequencing costs :x but i'm not 100% sure on that | 18:08 |
| @kanzure | and it might not be patent costs but rather things like.. "if we don't charge so much, our business fails for other reasons" like "because we pay for 10 employee-years per sale we make" | 18:08 |
| @kanzure | yeah i'm p. sure the synthesis services are also doing verification/validation/sequencing and this might drive the cost up a bit | 18:09 |
| @kanzure | my plan is to do a microfluidic circuit for this, so ideally your starter reagents will last you a long, long time | 18:10 |
| ParahSailin | i know a guy who does microfluidics | 18:10 |
| @kanzure | i would like to meet him. | 18:10 |
| ParahSailin | old lab i used to work in | 18:10 |
| @kanzure | would he be into looking over my project and shit? | 18:10 |
| ParahSailin | i could see if he's interested | 18:11 |
| @kanzure | thanks. i need more mf people to tell me how dumb which parts of my plans are | 18:11 |
| @kanzure | yashgaroth (in here) also came up with a particularly strange nicking enzyme method for a giant microfluidic oligo library, which probably needs the eyes of a molecular biologist | 18:12 |
| ParahSailin | though hes pretty conservative about obeying patent laws and trying to get as much money as possible instead of deriving value from making research cheap | 18:12 |
| ParahSailin | id like to see that | 18:12 |
| @kanzure | i'm pretty sure there'd be an explosion of sales for even a $5k or $10k dna synthesizer | 18:12 |
| ParahSailin | i have worked with microfluidics a lot so i could tell you if the design will work, but my old associate would have to produce it | 18:13 |
| @kanzure | and if not, who cares.. i'd have a synthesizer :P which is good enough for me | 18:13 |
| @kanzure | oh great | 18:13 |
| @kanzure | yeah i'm gearing up to do a foundry | 18:13 |
| @kanzure | soo | 18:13 |
| @kanzure | i'm cool with doing it on my own i just don't want to reinvent the wheel | 18:13 |
| ParahSailin | foundry? | 18:13 |
| @kanzure | microfluidics foundries | 18:13 |
| @kanzure | you know.. like http://www.stanford.edu/group/foundry/ | 18:14 |
| @kanzure | http://kni.caltech.edu/foundry/ | 18:14 |
| ParahSailin | yah microfluidics takes a lot of money | 18:14 |
| ParahSailin | my old lab was at university of illinois | 18:14 |
| @kanzure | why do you say that (money) | 18:14 |
| @kanzure | the solenoid valves look expensive, but i could maybe make those | 18:14 |
| ParahSailin | the advisor there who controlled it took a lot of pride in how it was on par with stanford and caltech's | 18:15 |
| ParahSailin | well the cleanroom stuff in general | 18:15 |
| ParahSailin | of course theres the usual institutional price inflation.. | 18:15 |
| @kanzure | the stanford one looks pretty cheap if i was to just order it | 18:15 |
| @kanzure | $400 per mask, then $75/chip after that | 18:15 |
| ParahSailin | thats pretty good | 18:16 |
| @kanzure | hah - the guy published a .tex file for that guide i linked earlier, cool.. http://www.princeton.edu/microfluidics/training/boot-camp/2011_Materials/bootcamp0_3_6.tex | 18:17 |
| ParahSailin | these are pdms and glass chips? | 18:17 |
| @kanzure | yes | 18:17 |
| ParahSailin | those foul very quickly | 18:17 |
| @kanzure | yeah, and acetonitrile is pretty corrosive | 18:17 |
| ParahSailin | the deal is a professor makes them for one experiment | 18:17 |
| @kanzure | parylene might help | 18:17 |
| ParahSailin | and writes a paper out of a device | 18:18 |
| ParahSailin | parylene is extremely soft | 18:18 |
| ParahSailin | my old lab uses su8 | 18:18 |
| ParahSailin | that stands up to a lot | 18:18 |
| @kanzure | a lot of this also depends on which final design i choose; | 18:19 |
| ParahSailin | well maybe not su8, but it is some epoxy resin that is photopatternable | 18:19 |
| ParahSailin | he can do devices with multiple channel layers | 18:19 |
| ParahSailin | if thats something you would like in a design | 18:19 |
| @kanzure | i'd like to avoid pneumatic valves, but they seem the most studied | 18:19 |
| @kanzure | soo it will probably be two layer.. one for fluids, one for the pneumatics | 18:20 |
| @kanzure | i need to make up my mind if i'm doing raw phosphoramidite chemistry | 18:20 |
| @kanzure | or if i'm going to do an oligo library (6mers?) and just use overhangs/sticky ends | 18:21 |
| @kanzure | direct oligo synthesis is error-prone but studied extensively | 18:22 |
| @kanzure | an oligo library method will need a few custom/not-completely-analyzed methods.. but will probably be less error-prone and make longer strands | 18:23 |
| ParahSailin | a new technology would be great to work on, but for initial work, probably stick to the phosphoramidite | 18:23 |
| @kanzure | right | 18:24 |
| ParahSailin | anyone need biobricks? | 18:24 |
| @kanzure | yeah, can you ship me the book | 18:24 |
| ParahSailin | i've got access to the last couple years of distributions | 18:24 |
| @kanzure | they don't ship to non-institutional peeps >:| | 18:24 |
| ParahSailin | yah i'm "institutional" | 18:25 |
| @kanzure | heh | 18:25 |
| ParahSailin | if there are any specific parts you want, i can break them out of the institutional jail | 18:26 |
| @kanzure | not at the moment, but someone on diybio posted a plan of action for starting a service to distribute biobricks to amateurs | 18:28 |
| ParahSailin | yah i saw | 18:30 |
| -!- strages_shop [~strages@256.makerslocal.org] has quit [Ping timeout: 272 seconds] | 18:30 | |
| @kanzure | ParahSailin: can you ping your other foundry friend and maybe cc me? i'm Bryan Bishop <kanzure@gmail.com> | 18:32 |
| ParahSailin | ah ok i see your name in there a lot | 18:33 |
| klafka | hey | 18:34 |
| @kanzure | ParahSailin: yeah i'm a chronic spammer.. http://groups.google.com/group/diybio/about lists me as the top offender | 18:35 |
| ParahSailin | ok its sent | 18:37 |
| @kanzure | thanks | 18:37 |
| ParahSailin | austin, nice | 18:38 |
| @kanzure | ParahSailin: http://i.imgur.com/cl7Ng.jpg | 18:40 |
| @kanzure | this is the nicking enzyme method | 18:40 |
| @kanzure | the idea is to use droplet microfluidics | 18:40 |
| @kanzure | in each droplet would be a few beads with that oligo library item | 18:40 |
| @kanzure | with an overhang. | 18:40 |
| @kanzure | retrieve the library item, run the protocol and end up with some 6mers floating around | 18:40 |
| @kanzure | this way, the library does not 'deplete' over time | 18:40 |
| @kanzure | then you wash the 6mers down to your growing oligo reaction somewhere else | 18:41 |
| @kanzure | the dsDNA in the diagram would be maybe 40bp | 18:42 |
| @kanzure | you can't have a library of just 6mers since you can't PCR that | 18:42 |
| ParahSailin | try getting a thiel grant for that | 18:42 |
| ParahSailin | breakoutlabs | 18:42 |
| @kanzure | breakout labs wants like 20% of all future revenue | 18:42 |
| @kanzure | screw _that_ | 18:42 |
| -!- jmil [~jmil@c-68-81-252-40.hsd1.pa.comcast.net] has quit [Quit: jmil] | 18:42 | |
| ParahSailin | how much capital would it take you to develop the process | 18:43 |
| @kanzure | i think i have enough | 18:43 |
| @kanzure | but more is always nice :3 | 18:43 |
| ParahSailin | your gpg public key? | 18:44 |
| @kanzure | erm.. | 18:44 |
| @kanzure | let me put it up somewhere | 18:45 |
| @kanzure | what do you need it for? | 18:45 |
| ParahSailin | secure messages | 18:45 |
| @kanzure | http://diyhpl.us/~bryan/irc/kanzure.pub | 18:45 |
| ParahSailin | oh, im not sure what to do with that kind of key | 18:47 |
| ParahSailin | oh yah that home directory of pdfs you have is pretty nice | 18:47 |
| @kanzure | thanks | 18:47 |
| ParahSailin | i was browsing that for a while | 18:48 |
| @kanzure | http://diyhpl.us/~bryan/papers2/ | 18:48 |
| @kanzure | http://diyhpl.us/~bryan/papers2/longevity/ | 18:48 |
| @kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/ | 18:48 |
| ParahSailin | i was working for the sens foundation and aubrey de grey for a while | 18:48 |
| @kanzure | also try /neuro /bio /stem-cells /nanotech | 18:48 |
| @kanzure | ah cool | 18:48 |
| @kanzure | you hear they kicked out lorenzo? | 18:48 |
| ParahSailin | yah, so it sounds like you are paying a lot of attention to those guys | 18:48 |
| @kanzure | not as much as i should | 18:49 |
| @kanzure | i'm not in regular contact with them | 18:50 |
| @kanzure | ParahSailin: humanity+ is the same way | 18:51 |
| @kanzure | i'm p. sure everyone but me is just crazy and/or retarded | 18:52 |
| @kanzure | all these orgs... just pathetic | 18:52 |
| -!- yashgaroth [~f@cpe-24-94-5-223.san.res.rr.com] has joined ##hplusroadmap | 18:55 | |
| yashgaroth | whatup fuckers | 18:57 |
| @kanzure | just lots of fucking | 18:58 |
| yashgaroth | sweet | 18:58 |
| @kanzure | yashgaroth: we have a new molecular biologist person ParahSailin | 18:58 |
| yashgaroth | yeah I've been catching up on the logs | 18:58 |
| roksprok | yashgaroth: i think it was you that recommended Molecular Biology of the Cell, if so, thanks a lot. It blows the other molecular bio textbooks i've read out of the water | 18:59 |
| @kanzure | ParahSailin: regarding polymerase.. | 18:59 |
| @kanzure | ParahSailin: http://diyhpl.us/~bryan/papers2/polymerase/ | 18:59 |
| @kanzure | roksprok: :) | 18:59 |
| ParahSailin | hey | 18:59 |
| @kanzure | some of those papers might be helpful | 19:00 |
| klafka | 2oh god | 19:00 |
| @kanzure | it's definitely a hard problem | 19:00 |
| yashgaroth | finally another molecular biologist here | 19:00 |
| klafka | mol bio of the cel is a good book | 19:00 |
| klafka | also mol bio of the gene is good too | 19:00 |
| klafka | hey i'm a molecular biologist-ish | 19:00 |
| @kanzure | you're just a bioinformaticist | 19:00 |
| klafka | oh | 19:00 |
| klafka | yah true | 19:00 |
| @kanzure | :P | 19:00 |
| @kanzure | i'm totally kidding | 19:00 |
| yashgaroth | compters, bah | 19:01 |
| klafka | actually i prefer computational biologist that sold out for money | 19:01 |
| klafka | :P | 19:01 |
| yashgaroth | so parahsailin what are you working on these days? you in a lab? | 19:01 |
| ParahSailin | im working on making cheap production vectors for useful enzymes | 19:02 |
| ParahSailin | break the neb fischer etc oligopoloyt | 19:03 |
| yashgaroth | cool | 19:03 |
| ParahSailin | recently fired from my lab but my advisor is letting me have access to lab | 19:04 |
| @kanzure | uhhh | 19:04 |
| @kanzure | sounds legit to me :) alright | 19:04 |
| yashgaroth | heh, lab acces is the important thing | 19:04 |
| @kanzure | does this include literature access | 19:05 |
| ParahSailin | yah | 19:05 |
| ParahSailin | and access to the biobrick distros | 19:05 |
| ParahSailin | i want to start working with insect cells before my lab access gets revoked | 19:08 |
| ParahSailin | kanzure, you have any interest in sf21 cell line? | 19:09 |
| yashgaroth | you plan to make the restriction enzymes etc in insect cells? | 19:09 |
| ParahSailin | no | 19:10 |
| yashgaroth | oh good | 19:10 |
| ParahSailin | insect cells to produce vaccinia pol | 19:10 |
| ParahSailin | "in-fusion" | 19:10 |
| ParahSailin | "like gibson assembly, except works reliably" | 19:10 |
| ParahSailin | tbh dont have that much need for that cell line at the moment | 19:13 |
| ParahSailin | i'd like to bank it and jailbreak it for when it's needed though | 19:13 |
| yashgaroth | I'm still reading up on vaccinia pol, hadn't heard much about it before | 19:14 |
| ParahSailin | it's pretty awesome, and pretty expensive | 19:14 |
| ParahSailin | you can't just express in e coli, and probably part of that is because the pol requires cofactor proteins complexed with it | 19:15 |
| yashgaroth | including when it's polymerizing? or just for expression | 19:16 |
| -!- eudoxia [~eudoxia@r186-52-185-250.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap | 19:16 | |
| ParahSailin | probably for activity | 19:16 |
| -!- nmz787 [43f2b117@gateway/web/freenode/ip.67.242.177.23] has joined ##hplusroadmap | 19:17 | |
| ParahSailin | i dunno, takara can produce it reliably, and there hasnt been much literature on it since | 19:17 |
| ParahSailin | patent says they get a monopoly on its sale | 19:17 |
| yashgaroth | can you purify the whole complex by affinity binding? otherwise that sounds annoyingly hard | 19:17 |
| ParahSailin | yah thats how they do it | 19:17 |
| ParahSailin | i'd like to get my hands on the wr vaccinia strain | 19:18 |
| ParahSailin | might be hard at this point | 19:19 |
| nmz787 | why vaccinia? | 19:20 |
| ParahSailin | well that dna polymerase has a pretty special recombinase activity | 19:21 |
| nmz787 | oh, came in after you mentioned that | 19:21 |
| ParahSailin | clontech sells it under the name In-Fusion | 19:21 |
| @kanzure | hi nmz787 | 19:25 |
| @kanzure | ParahSailin has been kind enough to offer some microfluidics help | 19:25 |
| @kanzure | klafka: say hi to nmz787 | 19:27 |
| klafka | nmz787 | 19:27 |
| klafka | hey | 19:27 |
| nmz787 | hi klafka | 19:27 |
| nmz787 | so if we have acetone from fatty acids during fasting periods, can we huff acetone instead of cooking? | 19:28 |
| ParahSailin | acetone is the breakdown of hydroxybutyrate | 19:28 |
| nmz787 | yeah | 19:29 |
| ParahSailin | its a mistake, and not catabolized as well as the "ketones" that are intended | 19:29 |
| nmz787 | you can also get it at home depot | 19:29 |
| nmz787 | oh, mistake? the biochem video i just watched didn't say it was a mistak | 19:29 |
| nmz787 | just a branch in the path | 19:29 |
| -!- aristarchus [~aristarch@unaffiliated/aristarchus] has joined ##hplusroadmap | 19:30 | |
| yashgaroth | I'd imagine you'd need to be in ketosis to make efficient use of it, but if you're atkinsing I'd go ahead and chug a bottle of it | 19:31 |
| ParahSailin | acetone is pretty toxic though | 19:32 |
| yashgaroth | naaaaah | 19:32 |
| ParahSailin | not really a simple path to take it back to ac-coa iirc | 19:32 |
| -!- mode/##hplusroadmap [-o kanzure] by ChanServ | 19:33 | |
| ParahSailin | i was pretty keto for a while | 19:33 |
| ParahSailin | no im just struggling to keep weight on | 19:33 |
| nmz787 | hmm | 19:36 |
| nmz787 | i don't think i'd want to chug acetone | 19:36 |
| nmz787 | i guess i need to taste it first | 19:36 |
| nmz787 | hah | 19:36 |
| ParahSailin | you can get beta hydroxybutyrate pretty cheaply though | 19:36 |
| ParahSailin | ralstonia somethingsomethingia | 19:37 |
| nmz787 | i was cleaning a PCB circuit board with it the other day and got a little light headed | 19:37 |
| nmz787 | it was weird | 19:37 |
| nmz787 | i wasn't expecting it | 19:37 |
| kanzure | blah blah blah more about journal politics http://techcrunch.com/2012/02/15/the-dangerous-research-works-act/ | 19:40 |
| kanzure | more commentary: http://news.ycombinator.com/item?id=3596535 | 19:40 |
| JayDugger | Good evening, everyone. | 19:45 |
| JayDugger | "you hear they kicked out lorenzo?" Lorenzo Albanello? | 19:51 |
| ParahSailin | is he famous around here? | 19:51 |
| kanzure | famous? not quite.. we just know him | 19:52 |
| kanzure | JayDugger: yes | 19:52 |
| klafka | is he the reddit guy? | 19:53 |
| JayDugger | Thanks. In fact, I only heard his name with that reference. | 19:53 |
| klafka | i'm glad that people are finally waking up to elsevier | 19:53 |
| kanzure | no lorenzo is the sens guy | 19:53 |
| kanzure | the reddit/journal-scraping-guy is aaron swartz | 19:53 |
| klafka | man like i've been fucking RAILING against fucking elsevier for years | 19:53 |
| klafka | ah ok | 19:53 |
| JayDugger | Anyhow, welcome ParahSailin. | 19:54 |
| kanzure | we need a better name for anti-elsevier activities | 19:54 |
| ParahSailin | i dunno what lorenzo is up to these days | 19:55 |
| ParahSailin | ah i see bruce got back already, cool | 19:55 |
| kanzure | ParahSailin: hey what's the smallest pneumatic setup you've seen? | 19:56 |
| -!- uniqanomaly [~ua@dynamic-87-105-21-133.ssp.dialog.net.pl] has quit [Quit: uniqanomaly] | 19:56 | |
| ParahSailin | pneumatic for pumping fluid? | 19:56 |
| kanzure | nope | 19:57 |
| ParahSailin | i dunno | 19:57 |
| kanzure | most microfluidics i've seen use pneumatics for valves | 19:57 |
| kanzure | micropumps/micropipette pumping seems ok to me | 19:57 |
| ParahSailin | bruce has the ability to make nanopore membrane valves | 19:57 |
| kanzure | orly | 19:57 |
| kanzure | that would be useful | 19:57 |
| ParahSailin | dont quote me on that, and dont make it known i said so, i dont know if thats proprietary knowledge | 19:58 |
| kanzure | meh k | 19:58 |
| kanzure | *meh ok | 19:58 |
| ParahSailin | ill ask him about it for you | 19:59 |
| kanzure | nah not yet | 19:59 |
| ParahSailin | the devices he makes are based on electroosmotic flow | 20:00 |
| kanzure | hrm alright | 20:00 |
| ParahSailin | i believe they have a paper out on the nanopore membrane | 20:00 |
| -!- uniqanomaly [~ua@dynamic-87-105-21-133.ssp.dialog.net.pl] has joined ##hplusroadmap | 20:00 | |
| kanzure | is this for valving or just for filtering? | 20:00 |
| ParahSailin | http://mechse.illinois.edu/content/research/publications.php?faculty_id=57 is all their recent papers | 20:01 |
| ParahSailin | its for valving | 20:01 |
| kanzure | is it this one? Bae, B., J. Han, R. I. Masel, and M. A. Shannon, “A Bi-Directional Electrostatic Microvalve with Microsecond Switching Performance,” Journal of Microelectromechanical Systems, 16, 1461-1471, Dec. 2007. | 20:02 |
| kanzure | or maybe Gong, M., B. R. Flachsbart, M. A. Shannon, P. W. Bohn, and J. V. Sweedler, “Fluidic Communication Between Multiple Vertically Segregated Microfluidic Channels Connected by Nanocapillary Array Membranes,” Electrophoresis, 29, 1237-1244, 2008. | 20:02 |
| kanzure | Flachsbart, B. R., K. Wong, J. M. Iannacone, E. N. Abante, R. L. Vlach, P. A. Rauchfuss, P. W. Bohn, J. V. Sweedler, and M. A. Shannon, “Design and Fabrication of a Multilayered Polymer Microfluidic Chip with Nanofluidic Interconnects via Adhesive Contact Printing,” Lab-On-A-Chip, 6:5, 667-674, 2006. | 20:03 |
| ParahSailin | that would be the one, anything with flachsbart, is relevant | 20:06 |
| -!- eudoxia [~eudoxia@r186-52-185-250.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] | 20:24 | |
| augur | so it seems library.nu is dead :( | 20:26 |
| Mokbortolan_1 | augur: http://gen.lib.rus.ec/ | 20:28 |
| augur | \o/ | 20:29 |
| augur | spasibo, Mokbortolan_1 | 20:30 |
| -!- aristarchus [~aristarch@unaffiliated/aristarchus] has quit [Quit: Leaving] | 20:36 | |
| ParahSailin | back | 21:15 |
| Stee| | kanzure, was the thing schwartz got busted over on behalf of this channel? | 21:17 |
| kanzure | no | 21:18 |
| kanzure | Of course not, don't be silly | 21:18 |
| kanzure | he also ran the googlegroup 'getarticles' but he's since taken it down | 21:18 |
| -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has quit [Quit: leaving] | 21:21 | |
| ParahSailin | im not following the nickase dna synth scheme | 21:22 |
| kanzure | yashgaroth: ping | 21:22 |
| yashgaroth | pong | 21:23 |
| kanzure | 128ms latency fuck this | 21:23 |
| kanzure | ParahSailin: here's the problem | 21:23 |
| kanzure | imagine a microfluidic chip with an oligo library stored in individual droplets | 21:23 |
| kanzure | each droplet can have, say, a few beads with oligos attached, or just in solution | 21:23 |
| kanzure | if it's just in solution, you need to have pcr on chip to "replenish" your library | 21:24 |
| ParahSailin | ah ok | 21:24 |
| kanzure | and if you want to pcr your library items, you need the oligos to be long enough | 21:24 |
| nmz787 | sounds alright | 21:24 |
| kanzure | pcring 6mers ain't gonna happen | 21:24 |
| nmz787 | PCR would also produce dsDNA | 21:25 |
| nmz787 | not ssDNA | 21:25 |
| nmz787 | so you wouldn't exactly be producing oligos, per se | 21:25 |
| yashgaroth | ah! but | 21:25 |
| ParahSailin | so the scheme is to produce 6mers by Pamidite and then use microfluidics and enzymes to ligate them | 21:25 |
| kanzure | so my first solution to this was a long ass oligo like oligo<rs>oligo<rs>oligo<rs> (rs=restriction site) | 21:25 |
| kanzure | actually no, not through enzymatic ligation but rather sticky ends | 21:26 |
| ParahSailin | ah, so 3mer overhangs? | 21:26 |
| kanzure | erm, 6mer overhangs? | 21:26 |
| yashgaroth | 3nt overhangs | 21:26 |
| nmz787 | yeah mer overhang | 21:26 |
| kanzure | ok fine.. 3 :P | 21:27 |
| nmz787 | 3 on the growing strand | 21:27 |
| ParahSailin | id say first get Pamidite working onachip | 21:27 |
| kanzure | ParahSailin: soo the idea is to wash the final oligos down to the reaction site somewhere else | 21:27 |
| kanzure | what is pamidite | 21:28 |
| nmz787 | i think you can def extend 3 nt with polymerase | 21:28 |
| nmz787 | phosphoramidite | 21:28 |
| ParahSailin | phosphoramidite | 21:28 |
| kanzure | oh duh | 21:28 |
| nmz787 | jeez | 21:28 |
| kanzure | god | 21:28 |
| nmz787 | who are you | 21:28 |
| nmz787 | ? | 21:28 |
| kanzure | nobody of consequence | 21:28 |
| yashgaroth | ok I found it http://i.imgur.com/cl7Ng.jpg | 21:29 |
| kanzure | oh i had it heh | 21:29 |
| kanzure | the link i mean.. it was pasted above | 21:29 |
| nmz787 | where is your nicking enzyme? | 21:30 |
| kanzure | http://diyhpl.us/~bryan/papers2/DNA/nicking-library-method.jpg | 21:30 |
| nmz787 | get me a link to NEB.com | 21:30 |
| nmz787 | REs nick on both strands | 21:30 |
| yashgaroth | I think I used http://www.neb.com/nebecomm/products/productR0607.asp | 21:30 |
| nmz787 | unless we can modify the library bead to be resistant | 21:31 |
| kanzure | http://www.neb.com/nebecomm/products/productR0607.asp | 21:31 |
| kanzure | http://www.neb.com/nebecomm/products/productR0607.asp | 21:31 |
| kanzure | oh hell | 21:31 |
| nmz787 | maybe that would make them more stabile too? | 21:31 |
| nmz787 | stable* | 21:31 |
| yashgaroth | yeah no nicking enzymes only cut one strand | 21:31 |
| kanzure | not only did i paste dupe links, yashgaroth got it faster | 21:31 |
| ParahSailin | plenty of REs that cut one strand | 21:31 |
| ParahSailin | NEB sells such mutants as "nickases" | 21:31 |
| yashgaroth | and the melting temp of any 6mer below room temp, so they fall off automatically and the pcr begins again | 21:31 |
| yashgaroth | is below* | 21:31 |
| kanzure | ParahSailin: around here, we take our PCR seriously :) http://diyhpl.us/~bryan/papers2/microfluidics/pcr/PCR%20-%20Nanodroplet%20real-time%20PCR%20system%20with%20laser%20assisted%20heating.pdf | 21:32 |
| nmz787 | yash, "yeah no nicking enzymes only cut one strand" or "yeah, no, nicking enzymes only cut one strand" | 21:32 |
| nmz787 | ? | 21:32 |
| ParahSailin | ah yah thats why kanzure linked | 21:33 |
| yashgaroth | the latter, nmz | 21:33 |
| nmz787 | oh | 21:33 |
| nmz787 | hmm | 21:33 |
| nmz787 | what is their melt temp? | 21:33 |
| kanzure | "40 cycles of PCR in 370 seconds" | 21:33 |
| nmz787 | i hadn't thought about that for the synthesis chamber... | 21:33 |
| yashgaroth | 6mers? like 6-20C depending on gc content | 21:33 |
| nmz787 | oh, | 21:33 |
| nmz787 | so we chill the reaction center, and blast it with laser | 21:33 |
| nmz787 | i like it | 21:34 |
| kanzure | chilling could be as easy as cold liquid | 21:34 |
| nmz787 | no switching of the peltier/refrig | 21:34 |
| nmz787 | like with normal PCR | 21:34 |
| yashgaroth | but yeah the whole oligo synth should run at a single temp | 21:34 |
| nmz787 | eliminates need for micro/nano resistive heaters | 21:34 |
| kanzure | nmz787: how would rapid cooling work? | 21:34 |
| kanzure | 6C is obviously below room temp | 21:35 |
| nmz787 | it would always be cold | 21:35 |
| yashgaroth | well, you don't need it at 6C, as long as it's above 6 | 21:35 |
| nmz787 | thermal paste to a peltier | 21:35 |
| nmz787 | at 2 or 4 | 21:35 |
| nmz787 | C | 21:35 |
| yashgaroth | for ligating all these 6mers together, that'll be 2-4C | 21:35 |
| nmz787 | and the laser would raise it via PWM/experimental duty/time period determined | 21:36 |
| nmz787 | (experimentally determined)* | 21:36 |
| yashgaroth | wait why are there lasers now | 21:36 |
| nmz787 | lol | 21:36 |
| nmz787 | star wars | 21:36 |
| kanzure | it's tempting to go for this right off the bat since the chemistry is less intimidating.. | 21:36 |
| nmz787 | the paper kanzure last linked | 21:36 |
| yashgaroth | oh right | 21:36 |
| nmz787 | how portable do coolers get? | 21:36 |
| kanzure | just pump in cool liquid.. | 21:36 |
| nmz787 | is there a peltier sized device that is more like a heat pump? | 21:36 |
| nmz787 | so its more efficient | 21:37 |
| kanzure | you could have cooling channels :P | 21:37 |
| nmz787 | if it were say run on batterys | 21:37 |
| yashgaroth | why are we thermocycling for the 6mer synthesis? you don't need to | 21:37 |
| ParahSailin | reduce the number of uncertainties/new techniques | 21:37 |
| kanzure | ParahSailin: yeah.. i know. | 21:38 |
| nmz787 | well you want to control synthesis | 21:38 |
| ParahSailin | already a difficult problem as it is | 21:38 |
| nmz787 | you don't want repeats | 21:38 |
| kanzure | ParahSailin: buut.. oligo synthesis has lots of chemicals that are sorta uncertainties | 21:38 |
| nmz787 | you said the oligo would melt | 21:38 |
| yashgaroth | sure it will, but it'll melt at reaction temperature; as soon as the nicking enzyme cuts, it falls off | 21:38 |
| yashgaroth | and pol comes in once again | 21:38 |
| nmz787 | (i'm not talking about synthesis of new library items, i'm talking about using the library items for de novo synthesis using polymerase | 21:39 |
| kanzure | what | 21:39 |
| yashgaroth | but there's no polymerization involved when the whole desired fragment is assembled from 6mers | 21:39 |
| kanzure | are you talking about 'getting some mers out of the library' | 21:39 |
| ParahSailin | also, dont do anything that requires droplet microfluidics, or youll have to find differen foundry | 21:39 |
| nmz787 | no nicking enzyme during synth of long strands | 21:39 |
| kanzure | ParahSailin: wait, really? i'm very attracted to droplets | 21:39 |
| yashgaroth | oh, just heat inactivate | 21:39 |
| ParahSailin | well i dunno | 21:40 |
| ParahSailin | might be the way to go | 21:40 |
| kanzure | ParahSailin: droplets are probably the way to go for storing a few thousand library items | 21:40 |
| ParahSailin | bruce does not have experience with that one though | 21:40 |
| kanzure | well, i guess there's always the gated array of 'library cells' with continuous flow.. | 21:41 |
| ParahSailin | i have no idea if compatible with his current fabrication technique | 21:41 |
| nmz787 | my original idea was just to order synthetic 6mers with 3'OH removed or modified to prevent extension | 21:41 |
| kanzure | droplets are mostly just a matter of water-in-oil | 21:41 |
| kanzure | ..right? | 21:41 |
| nmz787 | then you could hybridize 3mer overhangs and extend a non 6mer strand (i.e. a DNA attached to a bead) | 21:41 |
| nmz787 | melt, return the 6mer solution to the storage library | 21:42 |
| kanzure | i was thinking the 'get your 6mers' step would be physically isolated from the growing DNA somewhere else on chip | 21:42 |
| nmz787 | and now using polymerase the DNA attached to the bead is extended | 21:42 |
| kanzure | and the only thing returned to the library would be the beads | 21:42 |
| nmz787 | wait you're saying kanzure this process: http://i.imgur.com/cl7Ng.jpg | 21:43 |
| kanzure | why would the 6mers not attach one after another after bidning to the growing strands? | 21:43 |
| nmz787 | would take place at the site where you want to synthesize a custom DNA? | 21:43 |
| kanzure | i'm saying it would /not/ take place at the same site | 21:44 |
| nmz787 | right | 21:44 |
| yashgaroth | I thought we'd be keeping the beads on the library chip permanently, and just pumping in/out the reaction mix when you need that oligo | 21:44 |
| kanzure | yashgaroth: right | 21:44 |
| klafka | argh kanzure you guys keep talking about all this oligo synth stuff | 21:44 |
| kanzure | klafka: ? | 21:44 |
| klafka | i need to set a weekend to catch up | 21:44 |
| nmz787 | lol | 21:45 |
| kanzure | yashgaroth: but i'm wondering, when you're letting the sticky ends attach and such.. why wouldn't the 6mers attach one after another and cause dupes? | 21:45 |
| nmz787 | ok so however you get your oligos doesnt matter too much to me at this point | 21:45 |
| yashgaroth | how do you mean | 21:45 |
| kanzure | yashgaroth: how is it that only one 6mer will attach to the growing strand | 21:45 |
| ParahSailin | 4**6 seems like a big number | 21:46 |
| yashgaroth | oh, I envisaged you'd just mix them all together and let the ligase sort 'em out | 21:46 |
| nmz787 | well when I did a back of the hand calculation it still seemed cheap as hell to buy 25nMol of 1024 vials of 6mer from a synth company | 21:46 |
| kanzure | yashgaroth: huh? | 21:46 |
| kanzure | yeah 1024 vials doesn't matter to me - that seems fine.. again it would be a droplet library | 21:46 |
| nmz787 | the process I want to concentrate on first is how to use the oligos as a synth library | 21:46 |
| yashgaroth | well presumably you'd make sure all the sticky ends in a given ligation would be unique | 21:46 |
| kanzure | yashgaroth: so it would cycle between using a 3' end and a 5' end? | 21:46 |
| yashgaroth | yes | 21:47 |
| kanzure | ok makes sense to me | 21:47 |
| kanzure | i thought this method was the one that did not require ligase | 21:47 |
| nmz787 | yashagaroth and kanzure... i was avoiding ligase for that reason | 21:47 |
| yashgaroth | how do you plan to reconnect the backbone? | 21:47 |
| nmz787 | using polymerase to extend the growing strand using the hybridized oligo as a template strand | 21:47 |
| nmz787 | not a primer | 21:47 |
| yashgaroth | ah | 21:47 |
| yashgaroth | but the template needs to be specifically ligated to the growing strand | 21:48 |
| nmz787 | which is again why i was thinking of recycling the oligos | 21:48 |
| mag1strate | nmz787: What are you trying to do? | 21:48 |
| nmz787 | but that would only work ensuring the oligos werent extended in a possible primer mismatch | 21:48 |
| nmz787 | otherwise if they were normal oligos I would flush for safety | 21:49 |
| nmz787 | mag1strate: grow custom DNA | 21:49 |
| nmz787 | using no harsh chemicals | 21:49 |
| mag1strate | oh cool | 21:49 |
| nmz787 | using biotools instead of synthetic chemistry | 21:49 |
| mag1strate | Wish I could help, I know no biology :( | 21:50 |
| nmz787 | after the main synth chamber reactions are worked out, THEN I think we should work out the details of oligo library production/reproduction/scalable way to do it | 21:50 |
| nmz787 | and remember even our cells have redundancy pathways, so its OK if we have to order beads and have pamidite synth the first time... or if we screw up and lose all our backup beads, etc... | 21:51 |
| kanzure | why is ligase a problem on an alternating 3'/5' availability scheme? | 21:51 |
| nmz787 | how would it help? | 21:52 |
| nmz787 | where would it be needed on chip? | 21:52 |
| kanzure | what | 21:52 |
| nmz787 | hmm | 21:52 |
| kanzure | yashgaroth: i am confused can you unbreak this | 21:52 |
| nmz787 | lemme think | 21:52 |
| yashgaroth | um you need a ligase to make the fragment not fall apart | 21:52 |
| yashgaroth | if we're not using pol to extend the fragment, that is | 21:53 |
| nmz787 | if you extended with pol, then ligated.. you wouldnt have a sticky end for the next round | 21:53 |
| yashgaroth | that's why I'm not in favor of using pol | 21:53 |
| nmz787 | and ligase can ligate blunt ends sometimes | 21:53 |
| yashgaroth | very shittily though | 21:54 |
| nmz787 | so you dont get the control i am looking for | 21:54 |
| nmz787 | yeah but 0 | 21:54 |
| nmz787 | is different than 1 % | 21:54 |
| nmz787 | or 1 in 100000 | 21:54 |
| nmz787 | 0 means no noise | 21:54 |
| nmz787 | which synthetic methods don't have | 21:54 |
| yashgaroth | hopefully only the 6mer with the matching overhang would get added | 21:54 |
| nmz787 | and all kanzures cells have all day for pennies | 21:54 |
| nmz787 | if we are making the libraries ourselves, eventually | 21:55 |
| nmz787 | we could scale up to 10mer | 21:55 |
| nmz787 | and still only have 3 mer overhangs | 21:55 |
| nmz787 | so reduce the risk of mismathc | 21:56 |
| yashgaroth | and a million wells | 21:56 |
| nmz787 | drops | 21:56 |
| nmz787 | no wells in this system | 21:56 |
| kanzure | soo what's wrong with ligase without polymerase? | 21:56 |
| nmz787 | think computer architecture | 21:56 |
| yashgaroth | I'd like to test out whether 'throwing a bunch of overlapping 6mers in with a ligase and seeing if we get a continuous fragment' works | 21:56 |
| kanzure | wait, overlapping? | 21:57 |
| yashgaroth | yes, each 6mer has 3nt that overlap the next one, and so on | 21:57 |
| -!- earcaraxe [4b5c5e98@gateway/web/freenode/ip.75.92.94.152] has joined ##hplusroadmap | 21:57 | |
| kanzure | hi earcaraxe | 21:57 |
| earcaraxe | well hello there hplusroadmap! | 21:57 |
| earcaraxe | and kanzure | 21:57 |
| nmz787 | the oligo wouldnt necessarily complex with itself | 21:57 |
| nmz787 | hello | 21:57 |
| earcaraxe | Stee just tipped me off to this channel | 21:57 |
| ParahSailin | why not ssdna ligase | 21:57 |
| -!- Stee| is now known as Steel_ | 21:58 | |
| kanzure | ParahSailin: ? | 21:58 |
| nmz787 | with ligase I still see the problem of repeats | 21:58 |
| yashgaroth | ^ | 21:58 |
| Steel_ | there we go | 21:58 |
| earcaraxe | nice nice. | 21:58 |
| earcaraxe | well, uh, introductions are in order i suppose | 21:58 |
| kanzure | nope we don't care | 21:58 |
| earcaraxe | well that was easy | 21:59 |
| kanzure | .. nah, go ahead. | 21:59 |
| earcaraxe | i just flew in from #reddit-nootropics and boy are my arms tired | 21:59 |
| nmz787 | OK, my original idea was to simulate the base-pairing electronically on some silicon/semiconductor array, a bunch of electrodes that looked complementary to the bases at digital control | 22:00 |
| nmz787 | but basically that's impossible forseeably in engineering today | 22:00 |
| earcaraxe | anyway i run smarternootropics.com, i've heard that you kanzure are formerly associated with humanity+ | 22:00 |
| nmz787 | because the pairing control for each base is Angstroms apart | 22:00 |
| kanzure | earcaraxe: i was director of r&d of humanity+ until i came to my seses | 22:00 |
| kanzure | *senses | 22:00 |
| earcaraxe | for some reason i read that as sens | 22:01 |
| kanzure | earcaraxe: i was working on a nootropics price search engine based on scraping, btw | 22:01 |
| ParahSailin | heh i was a researcher for sens | 22:01 |
| kanzure | earcaraxe: http://drugstack.com/ | 22:01 |
| nmz787 | so replace digitally controlable silicon base pairs with oligos | 22:01 |
| earcaraxe | what are you up to post-humanity+? | 22:01 |
| nmz787 | use pol to extend | 22:01 |
| nmz787 | change template | 22:01 |
| nmz787 | repeat | 22:01 |
| earcaraxe | loading up drugstack | 22:01 |
| kanzure | nmz787: doesn't that require iffy hybridization | 22:02 |
| nmz787 | i don't think its iffy | 22:02 |
| earcaraxe | drugstack was at humanity+ or on your own? | 22:02 |
| kanzure | earcaraxe: my own thing | 22:02 |
| earcaraxe | active project? | 22:02 |
| nmz787 | PCR works on 20mers | 22:02 |
| kanzure | sorta kinda | 22:02 |
| nmz787 | when there's tons of non-specific genomic DNA | 22:03 |
| kanzure | where the hell are you going to get a 20mer library | 22:03 |
| earcaraxe | well the homepage has a sleek template | 22:03 |
| nmz787 | so when its a single growing strand on a bead (or 10000), i think most of the parameters are known | 22:03 |
| kanzure | earcaraxe: yeah i get paid for things like that | 22:03 |
| earcaraxe | perhaps we can collaborate, since smart drug collaboration just makes sense | 22:03 |
| kanzure | earcaraxe: probably.. | 22:03 |
| earcaraxe | i'm a web developer but more backend | 22:04 |
| kanzure | earcaraxe: me too | 22:04 |
| kanzure | that's on a shitty heroku instance, so that's why it took a few seconds | 22:04 |
| earcaraxe | freelance now or are you with an organization post-humanity+ | 22:04 |
| kanzure | contracting. | 22:05 |
| kanzure | humanity+ was just terrible | 22:05 |
| ParahSailin | what is humanity+ | 22:05 |
| kanzure | humanity+ is the old world transhumanist association | 22:05 |
| Steel_ | what became of the world transhumanist association | 22:05 |
| Steel_ | after David Pearce left, iirc | 22:05 |
| fenn | TdT polymerase adds random nucleotides to ssDNA | 22:05 |
| kanzure | fenn: so does tth | 22:06 |
| kanzure | regarding tdt, cathal had a few thoughts: http://diyhpl.us/~bryan/papers2/polymerase/tdt.txt | 22:06 |
| fenn | earcaraxe: opinion on magnesium suppplements? | 22:07 |
| earcaraxe | fenn: i take them when i take adderall | 22:07 |
| kanzure | earcaraxe: i take adderall by the handful | 22:07 |
| kanzure | well not quite. i don't have immunity to it. | 22:07 |
| earcaraxe | fenn: seems to decrease tolerance a bit | 22:07 |
| kanzure | *tolerance | 22:07 |
| earcaraxe | but really mine's just anecdotal | 22:07 |
| kanzure | fenn: there's new stuff in http://diyhpl.us/~bryan/papers2/polymerase/ | 22:08 |
| earcaraxe | i spent some time looking for actual studies, but wasn't able to find an clinical trials | 22:08 |
| kanzure | earcaraxe: the other missing piece of drugstack.com is auto-ordering from multiple websites simultaneously | 22:09 |
| fenn | i've seen some nutritionist stuff complaining about widespread Mg deficiency | 22:09 |
| earcaraxe | kanzure: i probably shouldn't admit it, but i just came off a five day adderall/4-FA binge | 22:09 |
| fenn | no function-oriented studies though | 22:09 |
| kanzure | yashgaroth: so it sounds like we don't have a ligation method | 22:09 |
| yashgaroth | sure we do, ligase is fine just fine | 22:09 |
| earcaraxe | cleaned the house, refluxed and resoldered the RSX chip on a PS3 | 22:09 |
| kanzure | yashgaroth: i'm so confused | 22:09 |
| kanzure | 21:58 < nmz787> with ligase I still see the problem of repeats | 22:09 |
| kanzure | 21:58 < yashgaroth> ^ | 22:09 |
| yashgaroth | but there's no repeats | 22:10 |
| kanzure | nmz787: why is ligase bad? | 22:10 |
| kanzure | earcaraxe: 5 days and you just cleaned? come on man :) | 22:11 |
| yashgaroth | you've got your growing strand with a 3nt overhand, the correct 6mer comes in and gets ligated, bam new 3nt overhang, repeat | 22:11 |
| yashgaroth | hang* | 22:11 |
| kanzure | 3nt overhand is a bruce lee attack | 22:11 |
| earcaraxe | kanzure: there were two full days and nights of underground partying going on as well, i confess. | 22:12 |
| yashgaroth | I wish we had tiny bruce lees to assemble our fragments | 22:12 |
| kanzure | earcaraxe: i usually do coding binges | 22:12 |
| kanzure | and just bill for the entire time | 22:12 |
| earcaraxe | i also wrote a scraper for google alerts | 22:13 |
| earcaraxe | that uses a summarization API to write summaries | 22:13 |
| earcaraxe | and then syndicate to tumblr, facebook, and twitter | 22:13 |
| kanzure | ah that's better | 22:13 |
| kanzure | ok that's kinda useful | 22:13 |
| kanzure | for scrapers i've been pimping http://phantomjs.org/ | 22:13 |
| earcaraxe | and i was spending some time trying to decide how best to use it for SEO | 22:13 |
| kanzure | no more beautifulsoup, nokogiri, lxml, or mechanize ever again | 22:13 |
| earcaraxe | oh i just wrote my own regex | 22:14 |
| kanzure | oh god | 22:14 |
| kanzure | don't make me kick you | 22:14 |
| -!- SDr [SDr@unaffiliated/sdr] has quit [] | 22:14 | |
| klafka | LOL | 22:14 |
| klafka | please | 22:14 |
| earcaraxe | this looks much easier | 22:14 |
| klafka | don't write your own regex | 22:14 |
| earcaraxe | god i've been in here five minutes and i've already made enemies | 22:15 |
| nmz787 | yashagaroth: so you're not saying blunt end ligation? | 22:15 |
| yashgaroth | good god no | 22:15 |
| yashgaroth | it's like...I can't think of a better term than stepladdering extension at the moment | 22:16 |
| nmz787 | ok lemm think | 22:16 |
| -!- Steel [~Steel@cpe-67-246-36-165.nycap.res.rr.com] has joined ##hplusroadmap | 22:16 | |
| nmz787 | worst case is you want to extend AAA,AAA | 22:16 |
| nmz787 | you start with ATG already present | 22:16 |
| fenn | earcaraxe: kanzure is just jealous because his nootropics site is so far behind :P | 22:16 |
| nmz787 | just for kicks | 22:16 |
| kanzure | solution: don't do that, or we can have some mers that do repeats | 22:16 |
| kanzure | earcaraxe: it's true | 22:17 |
| earcaraxe | haha i'm flattered | 22:17 |
| fenn | worse is better it seems | 22:17 |
| kanzure | yeah it shouldn't be hard to have a 5nt A, a 6nt A, a 10nt A | 22:17 |
| yashgaroth | well yes, but unless you have more than 6 of the same base in a row, you're fine, though it is a problem | 22:17 |
| nmz787 | well lets think about how the ligase will work | 22:17 |
| nmz787 | it won't be ligating the same end of the oligo each time | 22:17 |
| nmz787 | so this might give us some control | 22:18 |
| kanzure | we might have to switch out ligases | 22:18 |
| kanzure | ? | 22:18 |
| nmz787 | via BAP and PNK | 22:18 |
| yashgaroth | I haven't really looked into ligase mechanics yet | 22:18 |
| kanzure | ParahSailin: any thoughts | 22:19 |
| nmz787 | well your stepladdering proposal would use that | 22:19 |
| -!- Steel_ [~Steel@cpe-67-246-36-165.nycap.res.rr.com] has quit [Ping timeout: 240 seconds] | 22:19 | |
| kanzure | fenn: keep this. http://diyhpl.us/~bryan/papers2/microfluidics/training-bootcamp.pdf | 22:19 |
| yashgaroth | hey man, kanz wanted a way to generate 6mers in droplets, that's all I've done | 22:20 |
| kanzure | fenn: http://diyhpl.us/~bryan/papers2/microfluidics/training-bootcamp.tex | 22:20 |
| ParahSailin | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC291858/?tool=pubmed | 22:22 |
| earcaraxe | just throwing this out there | 22:22 |
| earcaraxe | but none of you guys know a tattoo parlor that'll put a magnet in my finger do you? | 22:22 |
| earcaraxe | seems like the guys who did that one for the wired chick don't want to do any others | 22:22 |
| Steel | earcaraxe: there's a thread discussing that in my forum, but there's also biohack.me | 22:23 |
| earcaraxe | Steel: i'll pop over | 22:23 |
| Steel | ianmathwiz7 posted that he did his himself | 22:23 |
| nmz787 | yashagaroth: yes i understand that | 22:24 |
| nmz787 | yashagaroth: i'm talking about how to use them | 22:24 |
| ParahSailin | a lot of what i worked with was protein engineering, so i confess a lot of solutions i think of involve new enzymes | 22:24 |
| nmz787 | optoisomerization of something near the tDt active site... or somewhere on tDt that on optoisomerization disrupted the active site | 22:25 |
| nmz787 | then you could probably do short pulses to get single nt addition | 22:25 |
| earcaraxe | ok i'm gonna get some sleep | 22:25 |
| earcaraxe | ttyl | 22:25 |
| earcaraxe | you guys are on my white board so i'll pop in next time i'm on irc | 22:26 |
| ParahSailin | optoisomerization huh | 22:26 |
| earcaraxe | Steel - are you Steel on your forum? | 22:26 |
| Steel | yes | 22:26 |
| yashgaroth | oh, is this modifying tdt to respond to a wavelength with a specific nt? | 22:26 |
| earcaraxe | ok, i'll pop you a note tomorrow | 22:27 |
| yashgaroth | err, adding a specific nt | 22:27 |
| -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has joined ##hplusroadmap | 22:27 | |
| nmz787 | not a specific nt | 22:28 |
| nmz787 | just on off | 22:29 |
| nmz787 | then you could easily wash | 22:29 |
| nmz787 | with the 4 diff nt types | 22:29 |
| nmz787 | this is awesome: http://people.bu.edu/alexserg/Impression_Book.pdf | 22:29 |
| kanzure | why isn't cathal in here. hrm | 22:32 |
| kanzure | stupid timezones | 22:32 |
| yashgaroth | is he often? | 22:32 |
| kanzure | no | 22:32 |
| nmz787 | just filter out the few participants in this discussion and email it to him | 22:33 |
| kanzure | that's not how irc works :P | 22:34 |
| kanzure | but yeah.. | 22:34 |
| kanzure | or he could just, you know, come online once in a while | 22:34 |
| kanzure | nmz787: ParahSailin was talking about a non-pneumatic valve earlier, | 22:35 |
| kanzure | based on nanopores? | 22:35 |
| -!- earcaraxe [4b5c5e98@gateway/web/freenode/ip.75.92.94.152] has quit [Quit: Page closed] | 22:35 | |
| nmz787 | hmm | 22:35 |
| nmz787 | interesting | 22:35 |
| Steel | time to rewrite this simulation from scratch again, sigh | 22:35 |
| kanzure | A Bi-Directional Electrostatic Microvalve with Microsecond Switching Performance | 22:35 |
| kanzure | Fluidic Communication Between Multiple Vertically Segregated Microfluidic Channels Connected by Nanocapillary Array Membranes | 22:35 |
| kanzure | Design and Fabrication of a Multilayered Polymer Microfluidic Chip with Nanofluidic Interconnects via Adhesive Contact Printing | 22:36 |
| Steel | need those papers, kanz? | 22:36 |
| nmz787 | i think MEMS might be exploitable if we only need the dielectric valves | 22:36 |
| kanzure | Steel: would be nice | 22:36 |
| kanzure | Steel: but i haven't checked if i have access yet | 22:36 |
| Steel | first one doesn't show up for me on gscholar | 22:36 |
| Steel | second one is public | 22:36 |
| kanzure | second one is http://mechse.illinois.edu/research/shannon/publications/pdf/2008electroMG.pdf | 22:36 |
| Steel | third is public too | 22:36 |
| kanzure | http://mechse.illinois.edu/research/shannon/publications/pdf/2006LabChipBRF.pdf | 22:37 |
| Steel | anyway, gotta go rewrite my sim again | 22:37 |
| Steel | bbl | 22:37 |
| nmz787 | i have access to the first | 22:37 |
| kanzure | is it interesting :p | 22:38 |
| nmz787 | yeah | 22:39 |
| nmz787 | pretty sweet | 22:39 |
| nmz787 | seems like MEMS magnetics | 22:40 |
| nmz787 | an electrode in the PDMS layer that is flexible | 22:40 |
| kanzure | ehh how hard is it to embed electrodes o.o | 22:40 |
| Steel | hmm | 22:41 |
| Steel | what size scale are we talking here | 22:41 |
| Steel | btw | 22:41 |
| kanzure | there was a reference in some paper i was reading, where they used a physical pin array to control channels at arbitrary points | 22:41 |
| kanzure | and just press the pins down :P | 22:41 |
| kanzure | Steel: ideally microvalves | 22:42 |
| Steel | no, I mean the electrode | 22:42 |
| kanzure | ~100 micron channel width | 22:42 |
| kanzure | oh | 22:42 |
| nmz787 | kanzure: check email | 22:43 |
| Steel | anyway, my setup can print electronics fairly easily | 22:43 |
| nmz787 | you've got mail | 22:43 |
| Steel | silver, at least | 22:43 |
| nmz787 | i've heard you pattern two metals over different resistance on top of eachother, like an old home thermostat | 22:44 |
| kanzure | nmz787: cool | 22:44 |
| kanzure | thanks | 22:44 |
| nmz787 | and they deflect when current is applied | 22:44 |
| nmz787 | and that makes a nice MEMS valve | 22:44 |
| Steel | hmmm | 22:44 |
| Steel | we could do that pretty easily | 22:44 |
| Steel | 2um wide? | 22:44 |
| Steel | *once the control software is there | 22:44 |
| kanzure | haha we're ok in the software department | 22:45 |
| Steel | nah, I meant for my setup | 22:45 |
| Steel | I think the thinnest lines have been 500nm so far | 22:45 |
| Steel | granted, until you have the necessary motor stages you can't do shit with ejet printing | 22:46 |
| nmz787 | who drew the oligo making drawing? | 22:50 |
| kanzure | yashgaroth | 22:50 |
| kanzure | and his manly ms paint skills | 22:50 |
| yashgaroth | that was my company's copy of powerpoint actually | 22:50 |
| kanzure | you gave me.. an image.. of a powerpoint slide | 22:50 |
| nmz787 | yashagaroth, the stepladder seems like it will just fine with repeats and ligase | 22:50 |
| yashgaroth | did you print it out yet kanz | 22:51 |
| yashgaroth | like I say, we should test it out with a batch of 6mers from a synthesis company to get some idea of feasibility | 22:51 |
| nmz787 | yashagaroth, kanzure: phosphatase and polynucleotide kinase are required as well, but that should be fine | 22:51 |
| nmz787 | its really nice i think actually | 22:51 |
| nmz787 | i need to get to bed | 22:52 |
| nmz787 | i will draw it with my tablet PC tomorrow | 22:52 |
| nmz787 | and send it to the webs | 22:52 |
| yashgaroth | excellent | 22:52 |
| kanzure | man, why don't *i* have a tablet pc | 22:52 |
| nmz787 | you're too hacker | 22:52 |
| nmz787 | you have adderall | 22:52 |
| nmz787 | therefore no tablet pc | 22:52 |
| kanzure | ah that makes sense? | 22:53 |
| kanzure | seeya | 22:53 |
| nmz787 | lol | 22:53 |
| nmz787 | no | 22:53 |
| nmz787 | :/ | 22:53 |
| nmz787 | sleepy | 22:53 |
| nmz787 | night night | 22:53 |
| yashgaroth | you see, adderall comes in tablets, so | 22:53 |
| -!- nmz787 [43f2b117@gateway/web/freenode/ip.67.242.177.23] has quit [Quit: Page closed] | 22:53 | |
| yashgaroth | I do still have the original slide if you want that too, but since it's perfect already I saw no need :P | 22:54 |
| -!- delinquentme [~asdfasdf@c-67-171-66-113.hsd1.pa.comcast.net] has joined ##hplusroadmap | 22:57 | |
| delinquentme | kanzure, yo | 22:57 |
| kanzure | delinquentme: sup | 22:57 |
| delinquentme | I've been in ##hplusroadmap for five minutes, mentioned writing my own regex, and was summarily kicked and banned. << | 22:57 |
| delinquentme | ?? | 22:57 |
| kanzure | he was totally joking | 22:58 |
| kanzure | he's not banned, he's coming back | 22:58 |
| delinquentme | check! | 22:59 |
| delinquentme | cant sleep | 22:59 |
| delinquentme | gotta snif up on sinatra | 22:59 |
| kanzure | delinquentme: http://gnusha.org/logs/2012-02-15.log | 22:59 |
| kanzure | sinatra's nice, let me know if you need help | 22:59 |
| delinquentme | cool so Steel invited him | 23:02 |
| delinquentme | its so crazy to me how connections work | 23:03 |
| delinquentme | immmm not even sure how he got on my FB friends list | 23:03 |
| kanzure | the world is collapsing and irrelevant people are being replaced to compress the social network | 23:04 |
| kanzure | you see, when facebook started keeping track of social graphs the universe ran out of additional RAM | 23:04 |
| kanzure | too much metadata | 23:04 |
| kanzure | as a result the effects of 'small world syndrome' have been increasing exponentially | 23:04 |
| * kanzure sleeps | 23:06 | |
| strangewarp | the number of things increasing at an exponential rate seems to be increasing exponentially | 23:14 |
| kanzure | i think my formulation is wrong, you should get fenn to write it out formally for once | 23:16 |
| delinquentme | ha | 23:18 |
| -!- yashgaroth [~f@cpe-24-94-5-223.san.res.rr.com] has quit [Quit: Leaving] | 23:25 | |
| -!- sylph_mako [~mako@118-92-62-53.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 272 seconds] | 23:34 | |
| -!- Steel2_ [43f624a5@gateway/web/freenode/ip.67.246.36.165] has joined ##hplusroadmap | 23:37 | |
| Steel2_ | some simulation issues solved yay | 23:37 |
| -!- sylph_mako [~mako@118-92-92-227.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap | 23:46 | |
| --- Log closed Thu Feb 16 00:00:12 2012 | ||
Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!
