--- Log opened Thu Feb 16 00:00:12 2012
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00:42 < delinquentme> i think im hearing things?
00:42 < delinquentme> did he say .. make pigeons shit ... SOAP?
00:42 < delinquentme> http://gizmodo.com/5885295/how-to-dna+hac-$yogurt-into-prozac
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02:40 < rdb> morning all
02:40 < Steel2_> almost everyone is asleep, I'd say :P
02:40 < Steel2_> I'm up late running simulations
02:41 < rdb> ah, are most of you in the US?
02:41 < Steel2_> east coast us
02:41 < Steel2_> you?
02:41 < rdb> EU, netherlands
02:42 < Steel2_> cool
02:42 < Steel2_> gamedev?
02:42 < rdb> 3d engine developer, I'm trying to get into electrical engineering too
02:43 < Steel2_> cool, I just got an EE job
02:43 < Steel2_> what's your interest in H+?
02:44 < rdb> I've always been interested in biohacking
02:45 < rdb> I've been researching and developing cheap biometrics solutions
02:45 < rdb> sensitive ekg and eeg for low price, if you will
02:47 < rdb> it's a hobby I'm trying to transform into a profession
02:47 < Steel2_> you're perfect here
02:47 < Steel2_> mind if I send you a pm real fast?
02:47 < rdb> no problem
02:58 < chris_99> have you seen the emokit rdb?
02:58 < chris_99> Emotive Epoc
02:59 < rdb> I've seen it, but I haven't tried it yet
02:59 < chris_99> looks quite impressive for the number of sensors and the price
02:59 < rdb> the cheap version doesn't seem to allow access to raw EEG data
03:00 < chris_99> the emokit is supposed to allow you to access that
03:00 < rdb> it requires the research version of the device
03:00 < chris_99> nope
03:00 < rdb> oh
03:00 < chris_99> not with emokit
03:00 < chris_99> supposedly they reverse engineered the protocol
03:01 < chris_99> you'd have to double check that the code is there to access the EEG data though
03:01 < chris_99> http://daeken.com/emokit-hacking-the-emotiv-epoc-brain-computer-0
03:01 < rdb> ah, I see
03:01 < rdb> I've looked into OpenEEG a lot
03:02 < rdb> I'm not that satisfied with its design
03:02 < chris_99> i haven't really looked at that, what do you think is wrong with it?
03:04 < rdb> hasn't been updated in quite a while, they seem to rely on outdated components whereas nowadays you can get much better quality componetns for the same price, but I'm mostly discouraged by the fact that they have a really fancy amplifier and then throw it all into the 10-bits ADC on an atmega8.
03:05 < rdb> Also they use a tlc272 on the active electrodes, with a gain of 1, and then on the analog board side they start amplifying that
03:05 < chris_99> that sounds odd
03:05 < rdb> I mean, it fixes the issues regarding the low impedance of passive electrodes
03:06 < rdb> but it still seems very inefficient
03:06 < Steel2_> rdb, have you built an improved one yet?
03:06 < rdb> Steel2_, I got a whole bunch of samples of the ADS1x9x series from Texas Instruments, I'm actually about to order a bunch of prototype pcbs from china that I designed a while ago, to play with them
03:07 < Steel2_> awesome
03:07 < rdb> these chips look very impressive
03:07 < Steel2_> if you sign up, could you do a write up on the forum about your project as you do it?
03:07 < Steel2_> so we could follow along?
03:07 < Steel2_> *there's a blog function too
03:08 < chris_99> ADS1x9x is an ADC?
03:08 < rdb> it is, particularly aimed at biopotential measurements
03:08 < rdb> Steel2_, I'll sign up
03:09 < Steel2_> It's just really exciting to see this stuff being done
03:09 < Steel2_> I'll be playing with some more stuff once I a) have a job and b) have money :P
03:09 < rdb> chris_99, also it seemed kind of a waste that they use a medium-grade tlc272 on the electrode side but an expensive ina114 on the analog amplifier
03:09 < rdb> hehe
03:09 < Steel2_> well, I have a job, I just haven't started yet
03:09 < Steel2_> stupid thesis
03:09 < Steel2_> a) should be 'after I finish my thesis and don't hate my life'
03:10 < chris_99> what pcb fab lab are you using btw?
03:11 < rdb> I'm using seeedstudio for this batch, which is cheap for prototypes
03:12 < rdb> first time I'm ordering there, so I can't say how good they are
03:12 < chris_99> yeah thats what i plan to use at some point.  i'm going to have a go at etching my own i think first though
03:12 < chris_99> ive heard good things about them
03:13 < Steel2_> might be worthwhile to set up an h+ fab lab so that money stays in the community (at some point)
03:13 < chris_99> you need expensive equipment to make pcbs proffesionally though, like seeedstudio, it would be difficult to do it cheaper really
03:15 < Steel2_> hmm, on a mass scale yes
03:15 < Steel2_> can't you do it decently (but slowly) with <10k equipment?
03:15 < rdb> good luck making quality stuff on your own... particularly small traces
03:15 < Steel2_> yeah, it's probably the 'quality' part that gets me
03:16 < rdb> especially if you're gonna make something that you're going to hook up to your body, a failed trace or too thin through-hole plating can be fatal
03:16 < Steel2_> truth
03:16 < Steel2_> if it proved to work, though, I'd throw money at starting a business building this shit
03:16 < rdb> I actually almost finished the design for a small pick-and-place machine
03:16 < rdb> it'll help me solder pcbs on a tiny scale
03:17 < Steel2_> heh, my thesis work will eventually lead to being able to do electronics on a submicron scale
03:17 < Steel2_> like, silver road widths of <1um
03:18 < rdb> neat :-)
03:18 < rdb> a friend of mine has been looking into making his own silicon circuitry
03:18 < rdb> although doing that kind of thing in a DIY setting will probably not be very reliable or useful at first
03:19 < Steel2_> I'll probably share all my thesis work when I finish
03:19 < Steel2_> although it's really not able to be done diy
03:19 < Steel2_> needs too precise of motors
03:20 < rdb> understandable
03:20 < Steel2_> I think our setup has 2nm error bars
03:21 < rdb> that's impressive!
03:22 < Steel2_> it's expensive is what it is
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03:29 < rdb> looks like ThomasEgi already introduced the ads119x/129x chip range on the biohack.me forums
03:56 < chris_99> whats your thesis on Steel2_?
03:56 < Steel2_> electrohydrodynamic jet nanoprinting
03:57 < chris_99> sounds complex :)
03:59 < Steel2_> ehhhh
03:59 < Steel2_> lots of scanning papers
03:59 < Steel2_> not so much intuition needed
04:02 < chris_99> ah heh
04:10 < rdb> I was discussing with a friend the marketability of a 'bio-duino'- basically a board with maybe an atmega32u2 with an ADS1198 and circuitry for biopotential measurements
04:11 < rdb> it seems to me like it'd be very useful for hacking up devices to hook up to your body
04:12 < rdb> it'd be a pretty safe way to experiment with those things as it'd come with human-body model esd protection, optocouplers for the usb connection, etc
04:12 < rdb> what do you guys think?
04:13 < chris_99> sounds cool :) so you could use for EEG and other stuff you mean?
04:13 < rdb> yeah
04:13 < rdb> it'd be great for experimenting with stuff like EKG, EEG, EMG, maybe even impedance tomography
04:13 < chris_99> are electrodes cheap to obtain or can you simply make them?
04:13 < rdb> I can make them
04:14 < chris_99> essentially are they just two wires in close proximity?
04:14 < chris_99> or one wire even?
04:14 < rdb> just a conductive contact placed on the scalp
04:14 < rdb> for passive electrodes, anyway
04:14 < chris_99> so its essentially one wire connected to a plate?
04:14 < rdb> active electrodes would have an op-amp to boost the signal-to-noise ratio and increase impdance
04:15 < rdb> kind of
04:15 < chris_99> hmm interesting
04:15 < rdb> I'll be electroplating my electrodes with silver chloride
04:15 < chris_99> wheres the ground connected too on your body
04:15 < Steel2_> chris_99, what's your background?
04:15 < rdb> many suggest gold, but actually gold isn't very good for electrodes
04:15 < chris_99> i'm a computer scientist studying computer viruses
04:15 < rdb> because gold builds up a DC charge.
04:15 < Steel2_> fucking sweet :P
04:15 < Steel2_> chris_99: you usually active in here around this time?
04:15 < chris_99> :)
04:15 < Steel2_> would explain why I haven't seen you
04:16 < chris_99> yeah i'm in the UK so this is my day time
04:16 < chris_99> im also new to the channel
04:16 < rdb> silver is the best solution, except silver tarnishes, which is why I would use silver chloride.
04:16 < chris_99> that sounds really neat rdb
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04:18 < Steel2_> whoops
04:18 < chris_99> heh
04:18 < Steel2_> chris99, sent you a pm :P
04:18 < rdb> chris_99, there are various other things to consider when making electrodes of course, such as severely limiting the current in order not to get bzapped
04:18 < Steel2_> you should talk to the tdms guys
04:19 < chris_99> i'm a bit confused how you can get electrocuted, if these are passive things?
04:20 < rdb> chris_99, if you put the electrodes on even slightly different potentials, current will flow between the electrodes, right through your brain (or whatever you hooked it up to)
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04:21 < chris_99> oh scary!, how do you stop that
04:22 < rdb> high-value resistors
04:22 < chris_99> ah, would a mega-ohm be enough?
04:22 < rdb> probably, maybe even too much.  depends on your circuit and the input impedance of your amplifier
04:23 < rdb> OpenEEG uses a rather inventive method of hooking up a bunch of transistors and using them as diodes above a certain threshold or something like that
04:23 < chris_99> interesting, i'm going to have to read the open eeg docs
04:24 < chris_99> so essentially         electrode --- resistor --- high gain op-amp --- adc ---- pc
04:24 < rdb> yeah, the OpenEEG site and mailing lists have a lot of helpful information on the subject
04:24 < rdb> depending on what you measure, you also want to do filtering
04:24 < chris_99> ah
04:24 < rdb> for EEG, everything above 30 Hz is noise
04:25 < rdb> so just lowpass that out
04:25 < chris_99> gotcha
04:25 < chris_99> they're easy enough to make with a capacitor
04:25 < chris_99> and resistor
04:25 < chris_99> (+ompamp)
04:25 < rdb> a first-order one is easy, you'll probably want something with a stronger falloff
04:25 < rdb> and, you want to get rid of the 50 or 60 Hz EM noise from the mains supply
04:25 < chris_99> could even do it DSP
04:25 < rdb> not entirely
04:26 < rdb> you get sampling artifacts if you don't do it analog
04:26 < chris_99> what do you mean, if you do an FFT couldnt' you easily remove any freq above a certain threshold
04:27 < rdb> you don't want to have frequencies around your sampling rate when you sample with your ADC
04:27 < rdb> or you'll get artifacts in the result
04:28 < chris_99> the sample rate of the ADC could easily be say 10MHz though, to avoid that
04:28 < chris_99> surely
04:28 < rdb> try getting a 10 MHz ADC with that kind of accuracy ;-) certainly overkill though
04:28 < chris_99> 10MHz arent hard to get hold of i thought, i was looking for a 1GHz one i think it was at one point
04:28 < chris_99> for van eck stuff
04:29 < rdb> the ADS119x has a sampling rate of 8 kSPS, which should be enough
04:29 < rdb> they are 16-bits
04:29 < rdb> the ADS129x  has 32 kSPS, at 24 bits, which is probably overkill for both of us
04:30 < chris_99> cool, are you planning on using a microcontroller too
04:31 < rdb> I'll probably hook it up to an atmega*u2, which is basically an atmega with the ADC removed but it has a USB controller.
04:32 < chris_99> nice, i've only got experience with PIC chips atm
04:33 < rdb> I have no experience with PIC, the sound of 'basic' scares me off ;-)
04:33 < chris_99> huh, im using either C or ASM
04:33 < chris_99> are you thinking of the picaxe
04:34 < rdb> ah
04:34 < rdb> didn't know.
04:34 < rdb> I grew up with an arduino, so I just never bothered to try it I guess
04:37  * rdb goes to grab some lunch.
04:38 < rdb> By the way, when I get these fabbed, I'll have a few spare (very simple) ads1192 breakouts, if anyone is interested
04:41 < chris_99> ooh yeah i'm interested
04:50 < rdb> back
04:50 < rdb> where do you live?
04:55 < rdb> so I have an idea of where to ship them
04:55 < chris_99> in the UK
04:55 < rdb> ah, I live in the Netherlands
04:58 < Steel2_> jesus christ
04:58 < Steel2_> I can finally go to bed
04:59 < rdb> have a pleasant rest :-)
04:59 < Steel2_> thanks :P
04:59 < Steel2_> I look forward to talking with you in the future
05:00 < rdb> same here :-)
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07:38 < kanzure> wait, what the fuck? stee| is sending pms to everyone to join his forum?
07:38 < kanzure> don't do that..
07:38 < ParahSailin> yah he sent to me
07:39 < kanzure> rdb: homecmos is doing alright with small traces on a small budget
07:39 < rdb> kanzure, nice :-)
07:39 < ParahSailin> home cmos sounds pretty wild
07:39 < rdb> hey there, by the way
07:39  * rdb shakes hands
07:40 < ParahSailin> you know, some things just benefit from economies of scale
07:40 < ParahSailin> we shouldnt expect every technology to be productive to miniaturize for decentralization
07:40 < ParahSailin> biology? awesome for decentralization
07:41 < ParahSailin> steam turbines? not so much
07:41 < kanzure> you only say that because you don't have your own machine shop
07:41 < ParahSailin> probably
07:41 < kanzure> :)
07:41 < kanzure> yeah i'm not too cool with stee| sending that to everyone
07:43 < ParahSailin> my assessment is that what intel does, it's a pretty competitive market that is not based on force to guarantee revenues
07:43 < kanzure> ah, well, scaling up immediately to what intel does is a little impractical
07:43 < kanzure> but you have to remember their first product had 2200 transistors
07:43 < kanzure> which is on the order of.. something that you could etch at home
07:44 < ParahSailin> but whats the benefit of doing it at home? saving money or just fun?
07:45 < ParahSailin> thats my beef with the reprap people
07:45 < ParahSailin> make the machine as cheap as possible -- i dont care so much if it can "replicate itself"
07:45 < ParahSailin> i dont want to have a unique 3d printer -- i want one that's the same as everyone else's so that i can print unique items that i want
07:45 < kanzure> reprap doesn't replicate itself - that's my beef with reprap
07:47 < ParahSailin> make a 3d printer out of injection molded pieces to reduce the price as much as possible
07:47 < kanzure> but it won't be able to replicate
07:47 < rdb> it's meant for rapid prototyping, and that's the only thing it's good at
07:47 < kanzure> none of those reprap derivatives do
07:47 < ParahSailin> printed pieces are just so wasteful if you want to print a thousand of them
07:47 < kanzure> rdb: right..
07:47 < rdb> I have one of them actually
07:47 < rdb> they can plot PCB traces too, but that's pretty much it
07:47 < rdb> oh, and milling
07:47 < kanzure> there's lots of other extruders of course
07:48 < rdb> but the structure isn't sturdy enough for serious milling
07:48 < kanzure> but it doesn't completely replicate and they should stop claiming it
07:48 < kanzure> rdb: fenn in here was working on a stewart platform for desktop milling with low-mass
07:48 < rdb> yeah, that's just silly
07:48 < rdb> oh, cool
07:48 < kanzure> it should be on http://fennetic.net/
07:48 < rdb> I don't see the machine turning into a metal foundry and a lathe and all that, so...
07:49 < ParahSailin> but to bring it back to cmos, if anyone could do it cheaper than the big foundries, then they would be the big foundry
07:51 < kanzure> well obv. nobody is doing 22nm features at home
07:52 < mag1strate> That would be really expensive wouldn't it?
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07:56 < ParahSailin> i would like to see an explanation of how doing whatever sized features they do has some benefit over buying a commercial product
07:57 < mag1strate> well you would have control over the quality
07:57 < mag1strate> unless the quality of what you buy is really good
07:58 < ParahSailin> can one make a custom asic for cheaper than an fpga would be?
07:59 < kanzure> i don't think cost is the point
08:00 < kanzure> commercial large-scale production will always have cheaper per-unit costs
08:01 < ParahSailin> the point is strategic independence of some sort?
08:01 < kanzure> is this what tmplab turned into? http://www.lapaillasse.org/
08:01 < ParahSailin> whether it's safety from thugs etc?
08:01 < kanzure> it's sometimes strategic independence, sure
08:02 < kanzure> btw, did you look at their site?
08:03 < kanzure> http://code.google.com/p/homecmos/
08:05 < ParahSailin> hm thats pretty good id say
08:13 < mag1strate> It will only have cheaper per-unit cost until you make your process cheaper. Then it is just the resources needed to make it
08:16 < ParahSailin> average cost is really what matters
08:16 < ParahSailin> cost of your time, cost of physical capital
08:17 < mag1strate> that is the per unit cost I believe
08:17 < kanzure> do you know a chip foundry that will let non-institutional groupies send in masks?
08:17 < mag1strate> the per-unit cost should take into account all those you listed
08:17 < kanzure> i haven't checked in a while :x
08:17 < ParahSailin> i was interpreting per-unit cost as marginal cost
08:18 < ParahSailin> ok
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08:28 < mag1strate> I co-oped at a company that made toys
08:28 < mag1strate> we usually took the per-unit cost to include labor, materials, process, tooling, etc.
08:28 < mag1strate> I thought it might be the same with most other industries
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08:35 < ParahSailin> im not that experienced with finance, so was not sure which cost per-unit typically refers to
08:36 < ParahSailin> per-unit cost there included to price of the machines and buildings that made the units?
08:39 < chris_99> you guys seen this http://www.inscentinel.com/InscentinelLtd/Pages/Science%20and%20technology/technology.html
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08:45 < ParahSailin> i bet you could use that to diagnose/detect cancer
08:45 < chris_99> does cancer have a smell?
08:46 < ParahSailin> there are probably some volatile biomarkers, supposedly some dogs can detect
08:46 < chris_99> yeah "Canine cancer detection is an approach to cancer screening that relies upon the olfactory ability of dogs to detect very low concentrations of the alkanes and aromatic compounds generated by tumors."
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08:46 < chris_99> so i'm sure you're right that the bees could do it too
08:47 < chris_99> its the sort of thing you could DIY i reckon with a camera and some image detection
08:47 < chris_99> and of course a bee
08:48 < kanzure> huh, alex is raising on kickstarter.. http://www.kickstarter.com/projects/primerist/code-hero-a-game-that-teaches-you-to-make-games-he?ref=category
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08:53 < chris_99> http://blog.makezine.com/2009/07/18/chia-keyboard/
08:53 < kanzure> chris_99: that will severely slow down my typing. http://www.seanwrona.com/typeracer/profile.php?username=kanzure
08:54 < chris_99> heh nice, not seen that before
08:55 < kanzure> 196wpm
08:55 < ParahSailin> so that would compost all the human detritus that gets in the keyboard, leaving it fresh and nice smelling?
08:55 < chris_99> exactly :)
08:56 < kanzure> who the heck smells their keyboard
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09:06 < kanzure> i really don't understand all of pyjamas' components
09:06 < kanzure> really really confused.
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09:16 < chris_99> i'm collating a list of DIY bio projects, to make a little pdf out of, does anyone have any suggestions: i've currently got dremelfuge, spectrophotometer,open pcr, posam, 'make' electrophoresis cell
09:20 < kanzure> chris_99: http://diyhpl.us/~bryan/papers2/diytranshuman_projects.v4.html
09:20 < kanzure> chris_99: http://diyhpl.us/cgit/skdb/plain/doc/BOMs/diybio-equipment.yaml
09:20 < kanzure> http://diyhpl.us/cgit/skdb/plain/doc/BOMs/comparison/fablab.yaml
09:20 < kanzure> http://diyhpl.us/cgit/skdb/plain/doc/BOMs/comparison/techshop.yaml
09:20 < kanzure> http://diyhpl.us/cgit/skdb/plain/doc/BOMs/ultimate-tool-buying-guide.yaml
09:20 < chris_99> ooh, thanks a lot! :)
09:21 < chris_99> i'm planning on getting it printed at lulu, to make it easier to read
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09:29 < chris_99> kanzure, how come theres a geiger counter in the bio list out of interest?
09:30 < kanzure> most molecular biology labs use radioactive phosphorous
09:31 < kanzure> p33?
09:31 < chris_99> aha interesting, what for?
09:31 < kanzure> p32
09:31 < kanzure> http://en.wikipedia.org/wiki/Phosphorus-32#Biochemistry_and_molecular_biology
09:32 < kanzure> "DNA contains a large quantity of phosphorus in the phosphodiester linkages between bases in the oligonucleotide chain. DNA can therefore be tracked by replacing the phosphorus with phosphorus-32. This technique is extensively used in Southern blot analysis of DNA samples. In this case a phosphorus-32-containing DNA probe hybridises to its complementary sequence where it appears in a gel. Its location can then be detected by photographic film."
09:32 < kanzure> when you have radioactive materials around, it's a good idea to have a geiger counter
09:33 < chris_99> so its like Electrophoresis?
09:33 < chris_99> and yeah thats a sensible idea
09:33 < kanzure> sorta.. it also has some filtering/hybridization steps iirc
09:34 < kanzure> http://en.wikipedia.org/wiki/Southern_blot#Method
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10:07 < kanzure> something something about being better than anki/supermemo http://news.ycombinator.com/item?id=3598676
10:07 < kanzure> "memrise"
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10:41 < kanzure> beep boop
10:45 < delinquentme> kanzure,
10:45 < delinquentme> THEY SAID NO
10:45  * delinquentme weeps!
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10:45 < delinquentme> something between overqualified and wanting someone whos done enterprise before
10:46 < kanzure> who said no
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10:46 < kanzure> delinquentme: ?
10:48 < delinquentme> badgeviller
10:48 < delinquentme> henceforth known as badgerville
10:48 < delinquentme> Its cool though I've got another call in a few hours ha
10:49 < kanzure> badgebadger
10:52 < delinquentme> kanzure, thoughts on the payrate for a dev in SV?
10:52 < delinquentme> on rails and js
10:52 < delinquentme> that should be like 100 right?
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10:53 < kanzure> delinquentme: $90K/year for a newbie
10:54 < kanzure> well, for a good newbie
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11:24 < delinquentme> ha
11:24 < delinquentme> ahhhhah
11:24 < delinquentme> annnd LBL just contacted me
11:31 < chris_99> is electroporation and a gene gun similar in some ways?
11:34 < ParahSailin> avoid gene gun
11:35 < chris_99> why so?
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11:37 < ParahSailin> expensive
11:38 < chris_99> i thought ou could make one
11:38 < chris_99> from a bb gun
11:38 < ParahSailin> something that accelerates microscopic gold balls at high speed?
11:38 < chris_99> yeah
11:39 < chris_99> thats what the orih
11:39 < chris_99> the original one was
11:39 < chris_99> just a normal gun
11:39 < ParahSailin> we have agrobacterium for plant transduction
11:39 < ParahSailin> thats easy method
11:41 < kanzure> also, you can go hunting for agrobacterium in forests
11:42 < kanzure> and then culture it if you want heh
11:42 < chris_99> haha cool
11:42 < ParahSailin> i have agrobacterium
11:42 < kanzure> http://superkuh.com/library/Biology/Agrobacterium/
11:42 < kanzure> ParahSailin: most places won't ship us agrobacterium
11:42 < chris_99> oh thanks
11:42 < ParahSailin> ill ship you agro
11:42 < kanzure> ParahSailin: thanks
11:42 < kanzure> chris_99: http://superkuh.com/library/Biology/Agrobacterium/YEB%20medium%20for%20Agrobacterium.txt
11:43 < chris_99> cool
11:44 < kanzure> superkuh: hopefully you don't mind.
11:49 < chris_99> could you use electroporation instead of agrobacterium
11:50 < kanzure> Expression of genes transferred into monocot and dicot plant cells by electroporation http://www.pnas.org/content/82/17/5824.full.pdf
11:51 < ParahSailin> maybe, but why not agrobacterium?
11:51 < kanzure> Transgenic maize plants by tissue electroporation http://www.plantcell.org/content/4/12/1495.full.pdf
11:51 < chris_99> thanks, no specific reason ParahSailin i'm just curious
11:52 < ParahSailin> with plants selection is more difficult
11:52 < ParahSailin> its not like you can grow clones out
11:52 < ParahSailin> i guess there is suspended cell tissue culture in plants
11:53 < kanzure> "hey mitch, what is a hacker?" http://www.youtube.com/watch?v=hoDOrKZK3Kg
11:53 < kanzure> puppet show by noisebridge
11:56 < chris_99> :)
12:02 < delinquentme> chris_99, yeah thats what the first one was made with
12:03 < chris_99> yup, i was reading the wikipedia article rather interesting
12:04 < chris_99> http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/McCord/electroporation.htm
12:04 < chris_99> doesn't look difficult to make an electroporator
12:05 < delinquentme> chris_99, i think they're cheap?
12:06 < chris_99> oh heh, i'll checkout ebay
12:06 < chris_99> £700 or more for me
12:07 < delinquentme> chris_99, whats your background homeslicer
12:07 < delinquentme> you like liquid handlers??
12:07 < chris_99> i'm a comp. scientist by day
12:07 < delinquentme> https://github.com/delinquentme/LH002/raw/master/images/LH002_full_01.png
12:08 < chris_99> involved in virus detection
12:08 < chris_99> ooh cool
12:08 < delinquentme> virus detection
12:08 < delinquentme> OH like comp virus
12:08 < delinquentme> kaspersky axions
12:09 < chris_99> yeah computer viruses
12:10 < delinquentme> sexy
12:10 < delinquentme> where @
12:10 < chris_99> university in the uk
12:11 < chris_99> i was wondering if i could apply some biology techniques to it just for a side project
12:13 < delinquentme> chris_99, very cool .. have you talked with catha garvey?
12:13 < chris_99> nope
12:13 < delinquentme> hes a biohacker over there in ireland
12:13 < chris_99> ah, i think i read an article on him recently
12:14 < delinquentme> http://www.technologyreview.com/business/39597/?p1=BI
12:14 < delinquentme> ^^
12:14 < delinquentme> http://gizmodo.com/5885295/how-to-dna+hac-$yogurt-into-prozac
12:14 < delinquentme> also cool
12:15 < chris_99> the problem with the prozac thing, is there isn't anything on the parts registr
12:15 < chris_99> registry to do that
12:15 < chris_99> that i could find anyhow
12:21 < chris_99> just looking at http://en.wikipedia.org/wiki/Electroporation the electrodes should be shown inside the curvette right?
12:22 < chris_99> *cuvette
12:22 < chris_99> sorry ignore that
12:22 < chris_99> misread the diagram
12:25 < kanzure> chris_99: you don't need something from the parts registry...
12:25 < kanzure> the parts registry isn't like.. um.
12:25 < kanzure> ParahSailin: see, i used to have this molecular biology advisor
12:26 < kanzure> and he was honestly pissed about biobricks because of the disservice to the public it was doing
12:27 < kanzure> chris_99: the parts registry has some useful things documented, but it's not like they have a patent on lac or promoters or something
12:27 < kanzure> i don't even know if there's a biosynthesis route to make prozac, but if there is, the guy probably just transplanted it into the yogurt genome
12:27 < kanzure> just like any other metabolic copy-paste
12:28 < chris_99> transplanted what sorry/
12:29 < kanzure> some genetic regulatory network from some other species, who knows
12:30 < kanzure> again i'm not sure if prozac is made by an enzymatic process, but if it is, then that might be what he did
12:30 < chris_99> ah, gotcha
12:30 < kanzure> you should start with something more basic
12:30 < kanzure> like an overexpression project
12:30 < kanzure> or gfp whateverface
12:32 < chris_99> yeah that sounds interesting, how hard would that be to do
12:34 < kanzure> there's lots of tutorials about doing a basic gfp insertion
12:34 < kanzure> and lots of cheap kits you can purchase for that.
12:34 < chris_99> awesome, i'll investigate that
12:35 < kanzure> carolina scientific (or whatever?) carries a gfp kit for high schoolers
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13:02 < chris_99> they don't ship to individuals apparently :(
13:03 < chris_99> seems a bit crap
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13:09 < kanzure> chris_99: you can ask genspace or biocurious to ship you a kit
13:10 < chris_99> thats an idea,i've just found another lab which may ship it
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13:40 < fenn> pretty sure caroline scientific ships to individuals, or at least they do a minimum of checking (half of their products are aimed at teachers)
13:40 < chris_99> i may create an account and see what happens
13:41 < fenn> we got a bunch of dead preserved animals from them
13:41 < chris_99> frozen?
13:41 < fenn> formaldehyde
13:41 < chris_99> ah
13:42 < chris_99> do you work for a lab though?
13:42 < fenn> no, but my house is called "langton labs" which may have been used as the ship-to address
13:42 < chris_99> ah, haha
13:42 < chris_99> would they be ok shipping this kind of stuff abroad
13:43 < fenn> there are other places that actually check if you're an institution, like sigma aldrich
13:43 < chris_99> well i could get them to ship to my comp. sci. dept i guess
13:44 < fenn> looks like they ship all over the place http://www.carolina.com/category/customer+service/international+customers.do
13:47 < chris_99> ah, they have a uk distributor, but alas they don't sell the gfp kit
13:49 < chris_99> could you introduce gfp into a plant?
13:57 < Steel> sup y'all
13:58 < chris_99> hello allo
14:11 < kanzure> wow, i've been using phantomjs with this really complicated scheme involving proxies and running it remotely on another server
14:11 < kanzure> because i thought that it didn't run locally on my development machines
14:11 < kanzure> but nope.. it compiles just fine.
14:24 < chris_99> i'm just wondering if i could do any interesting research with bacteria in near-space using a weather balloon
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14:39 < kanzure> chris_99: anaerobic bacteria?
14:41 < chris_99> yeah thats an idea
14:43 < kanzure> chris_99: have you read up on atmospheric bacteria
14:43 < chris_99> nope
14:54 < Mokbortolan_> kanzure: I think your friend isn't interested in any collaboration with me :p
14:54 < Mokbortolan_> that's OK, he looks busy
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15:07 < kanzure> Mokbortolan_: why do you say that
15:07 < kanzure> he can be a little hard to navigate around but he means well
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15:25 < kanzure> Juul: howdy
15:26 < kanzure> delinquentme says lbl did a job interview call with him today
15:26 < kanzure> delinquentme: was it juul who called you o__o
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15:27 < delinquentme> ha nah i just got the email
15:28 < delinquentme> Dr. Dylan & Dr. Paramvir (WOO!)
15:39 < Juul> hey Juul
15:39 < Juul> nice delinquentme
15:40 < Juul> wut
15:40 < Juul> hey kanzure
15:40 < Juul> <-- confused
15:40 < delinquentme> lol
15:40 < delinquentme> Juul, I was contacted today by some of the KBase scientists
15:40 < Juul> i'm glad
15:41 < Juul> i decided not to pursue a job at KBase myself
15:41 < Juul> i'm just gonna hack things and improve the world
15:41 < Juul> be a starving hacker
15:42 < delinquentme> you didn't like working there?
15:42 < Juul> at the BIOFAB?
15:42 < delinquentme> ya
15:42 < delinquentme> thats where you were now / before right?
15:42 < delinquentme> brb gotta drop girly off
15:42 < Juul> that's where i am until it shuts down in march
15:44 < Juul> i'm not doing my best work there
15:44 < Juul> i need to go do my own thing
15:44 < delinquentme> youre looking for something smaller?
15:44 < delinquentme> kanzure, likes the term 'agile'
15:45 < kanzure> hah i do?
15:51 < kanzure> huh.. https://lists.apple.com/mailman/listinfo
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16:06 < delinquentme> :D
16:06 < delinquentme> Juul,
16:06 < delinquentme> is anyone currently working there a life extension kid?
16:06 < delinquentme> derp well . I mean are you?
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16:26 < fenn> i can't be a starving hacker anymore :(
16:26 < kanzure> fenn: what do you need?
16:26 < fenn> gobs of cash
16:27 < fenn> also, i'm not sure if i'm falling behind the times wrt web technology
16:28 < kanzure> what, node.js?
16:28 < fenn> there's a lot of stuff i don't even know what to make of it, like chef, celery, redis,
16:28 < fenn> it sounds important and people are using it but i don't exist in that world
16:28 < fenn> a server configuration server? wtf really?
16:28 < Steel> Hope y'all are signed up for MITx 6.002 if you don't know the shit already
16:29 < kanzure> Steel: go away
16:29 < kanzure> fenn: chef is more like "i have 100 servers and i don't want to ssh into them manually to do shit"
16:29 < kanzure> fenn: celery is more like "i need to maintain a persistent queue of tasks that my workers will eat up"
16:29 < fenn> for i in `cat servers`; do $* ; done
16:30 < fenn> yeah i get it, but it's hard to learn about this stuff if you dont have 100 servers in the first place
16:30 < kanzure> nobody likes bash apparently
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16:31 < kanzure> it might also be due to the chef/ruby background
16:31 < fenn> i think it's the ruby
16:31 < kanzure> http://devopsanywhere.blogspot.com/2011/10/why-chef.html
16:31 < kanzure> fenn: also see pm
16:32 < fenn> maybe they just like duplicating functionality, but it seems like there's a lot of "stuff"
16:37 < delinquentme> what do you call the code that you're sending to actuators to direct movement
16:37 < Juul> delinquentme, nope
16:37 < delinquentme> i want to say "protocol" but thats definitely not it
16:38 < kanzure> delinquentme: pwm?
16:38 < delinquentme> nah higher level than that
16:38 < kanzure> pulse width monkey
16:38 < fenn> movement commands?
16:38 < delinquentme> like i designed the arduino to accept in a binary input
16:38 < fenn> protocol
16:38 < delinquentme> which would determine x y z by what was packaged into those bytes
16:39 < delinquentme> there is an industrial robotics programmer on reddit
16:39 < delinquentme> http://www.reddit.com/r/IAmA/comments/psact/iaman_industrial_robot_programmer_ama/
16:45 < Steel> yay
16:45 < Steel> someone I can talk to
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17:02 < delinquentme> Stee|, me or the designer :D
17:02 < delinquentme> BOTH
17:09 < Stee|> the designer
17:09 < Stee|> I do controls stuff
17:10 < Stee|> (badly)
17:16 < fenn> "Forget IT or Tech consulting. Forget computer programming or web design. Get into mechanical engineering or controls engineering theory. There is such a shortage of knowledgeable people in this field that you can pretty much write your own ticket."
17:16 < kanzure> except all the companies are classic corporations
17:17 < kanzure> well, most of them
17:17 < fenn> if they didn't all have their heads so far up their asses maybe people would manage to penetrate the gauntlet of bureaucracy and actually do something for them
17:17 < kanzure> and the good ones are well hidden
17:17 < fenn> see, tech consulting doesn't require an 8 year MS in controls theory just to configure a robot
17:18 < kanzure> "we describe a simple method for joining the 5'-protruding, single stranded DNA ends generated by restriction enzymes" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC318626/pdf/nar00322-0105.pdf
17:19 < kanzure> their diagram is pretty simple to understand on pg 2
17:19 < kanzure> page 3
17:20 < fenn> "the tooling on this robot is a trade secret"
17:20 < fenn> people are so stupid
17:20 < kanzure> "it's so secret that we burned the documentation"
17:20 < kanzure> "and fired the original engineer"
17:20 < fenn> and memory wiped the intern
17:20 < fenn> then we hired an institutional archaeology team to reassemble the remnants
17:21 < Stee|> that happens sometimes with defense
17:21 < Stee|> but high level controls theory does take a while to learn
17:21 < fenn> oh bullshit
17:22 < fenn> it's no worse than figuring out how to use celery
17:22 < fenn> somewhat less complex, more safety overhead
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17:23 < Stee|> Ehhh, there's very little in the way of standardized education for things like CCILC
17:24 < Stee|> anyway, I gotta get ready for dance lesson and party, so bbl
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17:25 < ParahSailin> howdy
17:26 < kanzure> hi ParahSailin
17:26 < kanzure> ParahSailin: does this look like the ligation scheme i need? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC318626/pdf/nar00322-0105.pdf
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18:05 < fenn> okay i've been putting up with dyndns's bullshit for years because i can't stand godaddy's bullshit, but today's the day i pulled the trigger
18:06 < kanzure> jrayhawk: don't you run a dns server somewhere
18:08 < fenn> i don't need a dns server, just can't remember my godaddy credentials
18:10 < kanzure> fenn: what do you think about all the pneumatics hardware for pneumatic-microvalve-based microfluidics
18:10 < kanzure> it looks like a lot of bulky equipment :/
18:11 < kanzure> quake's lab published some stuff where they claim they keep buying these $400 solenoid switches or something, for controlling the air
18:11 < fenn> i like the laser blood pump idea
18:11 < kanzure> https://sites.google.com/a/lbl.gov/microfluidics-lab/valve-controllers/usb-based-controller
18:12 < fenn> $400 is too much for a valve
18:12 < kanzure> the their solenoids: https://sites.google.com/a/lbl.gov/microfluidics-lab/valve-controllers/solenoid-valves
18:12 < fenn> $4 is about right
18:12 < kanzure> *then their
18:12 < kanzure> "The standard 8-valve manifolds have the following part numbers, and can be bought from www.festo.com for approximately $490.00 each (as of August 2011)."
18:13 < ThomasEgi> may i ask what this is used for and what the requirements for the valves are?
18:14 < kanzure> microfluidics.. urm. microvalves. so usually a channel in pdms over another channel in another layer, where you pump air through
18:14 < kanzure> here's a review paper:
18:14 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/Review%20-%20A%20review%20of%20microvalves%20-%202006.pdf
18:15 < kanzure> for making stuff like http://thebigone.stanford.edu/images/chemostat.jpg
18:16 < ThomasEgi> hehe that one looks neat
18:18 < kanzure> oh neat, haven't seen this one before: http://openwetware.org/wiki/Endy:Microfluidic_Setup
18:18 < kanzure> "The Endy Lab orders their from the Caltech Microfluidic Foundry" lame
18:19 < kanzure> oh this is nifty too
18:19 < kanzure> http://2011.igem.org/Team:EPF-Lausanne/Tools/Microfluidics/HowTo2
18:20 < kanzure> "12-Solenoid manifold (part S08-1557) Pneumadyne 1 245.00"
18:20 < kanzure> $245
18:20 < kanzure> "Pressure Regulator Bellofram 2 $186.00"
18:21 < ThomasEgi> those.. are just valves rigth?
18:21 < kanzure> the stuff on that wiki page is for the macro-world setup like controlling what goes into the chip
18:21 < kanzure> the paper i linked you to is for microvalves on your chip
18:22 < ThomasEgi> i mean the eletronics and usb controlls are pretty much a nobrainer.
18:22 < ThomasEgi> the valves look a lot more interesting to me.
18:22 < kanzure> sure.. i don't see why a manifold should cost $245
18:23 < kanzure> i'd like a way to avoid having to use pneumatic valves, but most people have more experience with pneumatic valves in microchips
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18:24 < kanzure> "Our chips have a second control layer above or below the main flow layer. The layers are separated by a thin membrane of PDMS, and their channels overlap in specific locations. "
18:24 < kanzure> "When channels of the control layer are pressurized, the membrane bends into the flow layer and blocks it. This creates a microfluidic 'on-chip' valve."
18:24 < kanzure> yashgaroth: hi. we're reading http://2011.igem.org/Team:EPF-Lausanne/Tools/Microfluidics/HowTo2
18:24 < kanzure> and http://openwetware.org/wiki/Endy:Microfluidic_Setup
18:24 < ThomasEgi> wouldnt piezo-actors be the choice there?
18:24 < kanzure> how would you manufacture/bake those into the pdms
18:24 < fenn> piezo is not good for maintaining a constant force
18:25 < fenn> i guess you could just vibrate and hope the hysteresis holds the pdms shut
18:25 < kanzure> "chip tunes" get it :(
18:26 < fenn> i think people just like to buy stuff
18:26 < kanzure> aren't labs supposed to be broke
18:26 < fenn> you can make a valve from a piece of nitinol wire and some rubber hose
18:26 < fenn> i wonder if people are rioting outside my house
18:26 < kanzure> those valve manifolds don't look hard to machine
18:26 < kanzure> i just don't understand. $200+.. geeze
18:26 < ThomasEgi> hm. i have no precise idea on how those valves have to be manufactored. but with thin disks of piezos you can get pretty good force
18:26 < fenn> you shouldnt be machining anything
18:27 < ThomasEgi> they are a bit big tho
18:27 < ThomasEgi> they could be made into a thin flat rectangular.bending up and down
18:28 < kanzure> the way pdms pneumatic valves are made is just on the second layer
18:28 < kanzure> one mask has the fluid lines
18:28 < kanzure> the other mask has the air lines
18:28 < kanzure> at the end of this doc are samples of both mask layers: http://diyhpl.us/~bryan/papers2/microfluidics/training-bootcamp.pdf
18:30 < kanzure> page 77
18:31 < ThomasEgi> currently looking at page 35 and 36
18:31 < kanzure> close enough
18:37 < ThomasEgi> what ssize are those lines ? 100μm?
18:38 < kanzure> dna ligase animation http://www.dnalc.org/view/15487-DNA-ligation-3D-animation-with-no-audio.html
18:38 < kanzure> ThomasEgi: yes. 100 microns is a good target.
18:40 < ThomasEgi> adding piezos is a bit tricky. as in placement i guess.
18:40 < ThomasEgi> actual operations might be less difficult
18:40 < kanzure> iirc there's some group that used a pin array and just pressed down with pins -_-
18:42 < ThomasEgi> https://en.wikipedia.org/wiki/File:Piezo_bending_principle.jpg
18:42 < ThomasEgi> theroetically. one could put those cross a line
18:43 < kanzure> i'm familiar with piezos :P
18:44 < ThomasEgi> mhm. well it really introduces some issues if you need to add piezos inbetween the single layers.
18:48 < kanzure> well there's also piezoelectric film. i don't know.
18:49 < ThomasEgi> so creating pneumatic vales seems to be quite ok, but operating them aint?
18:50 < kanzure> well ideally i'd like some electronic-only scheme of course :P
19:08 < ThomasEgi> hm. magnetic sounds a bit tricky on that scale. electrostatic ways too weak, thermic might be a way if the slow reaction time is ok.
19:16 -!- ParahSailin [~parahsail@unaffiliated/parahsailin] has quit [Remote host closed the connection]
19:28 < yashgaroth> ThomasEgi: so I noticed you posting in that biohack thread about the electroporator
19:28 < ThomasEgi> yeah
19:28 < yashgaroth> it seems like everyone there was talking about one for bacteria, even though the original post was about gene therapy
19:29 < yashgaroth> if I gave you parameters for one that was targeted at human muscle tissue and paid you, would you build me one?
19:29 < ThomasEgi> the whole thing?
19:29 < ThomasEgi> or just the electronics?
19:29 < yashgaroth> what is there aside from the electronics?
19:29 < ThomasEgi> the chamber where the stuff goes into?
19:30 < yashgaroth> oh, that's separate; we attach the electrodes to two needles, which are delivering the DNA already
19:30 < yashgaroth> people seem to convolute bacteria in a cuvette, and someone's bicep, for some reason
19:31 < yashgaroth> but the voltage etc. settings are much different
19:33 < yashgaroth> like 100V and 0.5amps at most
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19:35 < kanzure> hrmm i don't think i've seen electroporation in vivo on a mammal before
19:35 < yashgaroth> it's been done in livestock, just not humans much
19:36 < yashgaroth> most of the research is for DNA vaccine applications, since antigen-coding DNA is far easier to make than the actual antigen
19:36 < kanzure> can you show me a livestock electroporation paper
19:37 < yashgaroth> they're mostly paywalled, but http://online.liebertpub.com/doi/pdfplus/10.1089/dna.2005.24.810 for example
19:38 < kanzure> also, i've scraped protocol-online.org many times in the past, how should i reformat all this horrible info
19:38 < yashgaroth> oh here's a good review paper, and it's free http://docstore.ingenta.com/cgi-bin/ds_deliver/1/u/d/ISIS/67256495.1/ben/cgt/2006/00000006/00000002/art00006/3F0ED4E224CD2FCB13294498800C2C7E430DEDF2CC.pdf?link=http://www.ingentaconnect.com/error/delivery&format=pdf
19:38 < delinquentme> <3
19:39 < kanzure> "We delivered plasmid DNA locally into the brain of adult C57BL/6 mice in vivo by voltage- and current-controlled electroporation. The low current-controlled delivery of unipolar square wave pulses of 125 µA with microstimulation electrodes at the injection site gave 16 times higher transfection rates than a voltage-controlled electroporation protocol with plate electrodes resulting in currents of about 400 mA."
19:39 < kanzure> "Transfection was restricted to the target region and no damage due to the electric pulses was found. Our current-controlled electroporation protocol indicated that the use of very low currents resulting in applied voltages within the physiological range of the membrane potential, allows efficient transfection of nonviral plasmid DNA. "
19:39 < kanzure> "In conclusion, low current-controlled electroporation is an excellent approach for electroporation in the adult brain, i.e., gene function can be influenced locally at a high level with no mortality and minimal tissue damage."
19:39 < kanzure> welp ok
19:39 < kanzure> sounds like a plan to me
19:39 < yashgaroth> yeah I'm mostly looking at muscle since, you know, brain electrocution
19:39 < kanzure> pussy
19:40 < yashgaroth> I'm still expressing a transgene, yeesh
19:41 < yashgaroth> anyway, general parameters are: 0.1-1.0 amps adjustable, unipolar square wave pulses with adjustable duty cycle and number, 10-50milliseconds long
19:41 < yashgaroth> constant current, but the voltage shouldn't be going about 200
19:42 < yashgaroth> above 200*
19:45 < yashgaroth> but I am not an EE so I have no idea what part(s) make that complicated/expensive
19:45 < kanzure> fenn might be able to help
19:46 < kanzure> jonathan cline in the diybio community also does schematics for random projects
19:46 < kanzure> i think he did the original openpcr power supply
19:46 < kanzure> and the ewod microfluidics stuff
19:46 < yashgaroth> I've been discussing it a bit with baslisks on That Forum that kanzure dislikes
19:47 < kanzure> i just dislike stee| for poaching users
19:47 < ThomasEgi> doesnt sound very fancy, electriaclly
19:47 < kanzure> yashgaroth: i've never even commented about that forum
19:47 < kanzure> so i think either you're making up a lie or stee| is spreading bullshit
19:47 < yashgaroth> that's all my own extrapolation
19:48 < yashgaroth> it was easier to type than "the forum kanz dislikes the recruiting practices of"
19:49 < ThomasEgi> yashgaroth, using a microcontroller, you can get very precise and repitive timing, limiting the maximum voltage is pretty easy, an adjustable constant current source is nothing difficult either
19:50 < ThomasEgi> can be done without i microcontroller,too.
19:50 < ThomasEgi> but invokes a few more parts
19:50 < yashgaroth> I can invoke a few more money then
19:51 < ThomasEgi> how many pulses are we talking bout?
19:51 < kanzure> microcontrollers are fine to include in such a project, and in fact probably preferred
19:51 < kanzure> why would that be a problem?
19:51 < yashgaroth> maybe 4-20ish, between once per second and all within one second
19:51 < ThomasEgi> kanzure, cause they require a toolchain to programm
19:51 < kanzure> programming is not an issue around here
19:52 < ThomasEgi> then i recommend a microcontroller.
19:52 < kanzure> haha
19:52 < kanzure> we have more code flowing out of noses than mucus
19:52 < yashgaroth> I'd imagine the medical electroporators use microcontrollers anyway
19:53 < ThomasEgi> it is rather easy to parse a few numbers via usb-serial adapters to the microcontroller, which in turn starts the timing based on the given inputs
19:53 < ThomasEgi> so all you have to do is taking care of the current and voltage limits, but those are just 2 knobs to turn
19:54 < yashgaroth> that works for me
19:58 < ThomasEgi> then there is very little to add, other than a step-up converter to get to the desired maximum voltage, few zener diodes to limite that voltage,  the constant current source pretty much is only a high voltage transistor and a poti.
19:58 < ThomasEgi> neiter expensive, nor complex
20:01 < yashgaroth> okay how much shall I paypal you to motivate a schematic? I'll start the offer at 200usd
20:01 < ThomasEgi> u kidding me? that circuit has bout 10 parts
20:01 < ThomasEgi> it would hardly be worth a fraction of that money
20:02 < kanzure> yeah.. you can get a batch of the pcbs made for $200 heh
20:02 < ThomasEgi> especially not when using a microcontroler
20:02 < kanzure> do you use eagle or kicad or geda or what
20:02 < yashgaroth> okay fine, well price it out and I'll cover it and your time or something
20:03 < ThomasEgi> kicad
20:04 < ThomasEgi> i could even build you a prototype with a usb-serial converter onboard
20:06 < yashgaroth> awesome
20:07 < yashgaroth> wait so you're plugging a PCB in a mains power socket? or is the power supply separate
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20:10 < yashgaroth> actually I have no idea what any of that entails, so you don't need to answer that, I'm just being dumb
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20:15 < ThomasEgi> it can operate on battery power if you need it to.
20:16 < klafka> hey
20:16 < yashgaroth> nah, we can stick with mains for now
20:16 < ThomasEgi> if you hard-code the timing of the pulses into the microcontroller (or if you use some of the microcontrollers analog inputs to set hem)
20:17 < ThomasEgi> i guess i can leave the task of programnning a square-wave genarator up to the software guys^
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20:17 < kanzure> hi Adifex
20:17 < Adifex> ay
20:17 < ThomasEgi> yashgaroth, http://home.arcor.de/positiveelectron/files/analog-frontent-dna-transfer.png
20:18 < ThomasEgi> that's about it
20:18 < kanzure> wait why not transfer the file
20:18 < kanzure> instead of the png
20:18 < ThomasEgi> cause i drew it in an existing project and have no intention of messing that one up by saving :D
20:19 < ThomasEgi> besides it is still lacking the actual values for the parts
20:19 < ThomasEgi> i dont feel like adding them right now as it is just past 5am here
20:19 < klafka> arrgh why must bart stop running at midnight
20:20 < ThomasEgi> there pretty much are 2 inputs required to make it work. a continuous square wave at the input of the boost converter (just noticed i am lacking a resistor there)
20:21 < ThomasEgi> and the pulse-control, pulling that pin to 5V will make a constant current flow through the 2 connectors in the upright, given there is any connection
20:21 < ThomasEgi> the maximum voltage is limited by the zener diode next to the capacitor
20:22 < yashgaroth> p.s. we can discuss it more over the weekend, when I'll be on at a reasonable hour; didn't realize you were in germany
20:23 < ThomasEgi> yeah.
20:23 < Adifex> what are you discussing?
20:24 < yashgaroth> guten morgen I guess :D
20:24 < ThomasEgi> well that circuit is pretty much all there is , power supply and microcontroller are not included atm. but those are pretty standard
20:24 < ThomasEgi> yashgaroth, i am noctural :p so it is late evening for me
20:24 < yashgaroth> heh, okay then
20:25 < ThomasEgi> do you guys have arduinos around?
20:25 < kanzure> some of us do
20:25 < kanzure> i'm p. sure yashgaroth does not
20:25 < yashgaroth> correct
20:25 < ThomasEgi> would be a piece of cake to build with an arduino.
20:26 < ThomasEgi> if you give me some time i can do a few prototypes
20:26 < yashgaroth> arduinos can handle that kind of wattage? I never knew, would make it easier though
20:26 < kanzure> would you be willing to breed mice and test
20:26 < ThomasEgi> what wattage? there are just a few miliseconds of milliamps flowing
20:26 < yashgaroth> where the hell am I gonna put mice
20:26 < ybit> in a cage
20:27 < kanzure> lots of cages
20:27 < yashgaroth> like I say, no EE experience thomas
20:27 < yashgaroth> where the hell am I gonna put [lots of cages]
20:27 < delinquentme> http://www.huffingtonpost.com/2011/01/20/two-suns-twin-stars_n_811864.html
20:27 < ThomasEgi> ybit, how about suspending the mice in magnetic levitation
20:27 < delinquentme> @_@_@_@_@_@_@_@_@_@_@_@_@_@_@
20:28 < yashgaroth> I've got perfectly good muscles, you know "muscle" was named after mice so basically we're good to go
20:28 < ybit> ThomasEgi: i haven't seen a study on that
20:28 < ThomasEgi> magnetic levitation ?
20:28 < ybit> of mice
20:28 < ThomasEgi> they are made from mostly water
20:28 < yashgaroth> it worked with frogs, no?
20:28 < ybit> yashgaroth: link
20:28 < ThomasEgi> water is diamagnetic, and levitates in mindblowingstrong magnetic fields
20:28 < ThomasEgi> yeah
20:28 < ThomasEgi> frog, wood, strawberries, spiders
20:28 < ThomasEgi> water.
20:28 < yashgaroth> um http://www.youtube.com/watch?v=A1vyB-O5i6E
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20:29 < kanzure> hi nmz787
20:29 < kanzure> https://picasaweb.google.com/lh/photo/tp2tKRvgmsixzWt7jpMAu48Zjm_dlgeSl51CJZW3KYU?feat=directlink
20:29 < nmz787> figured you would disperse the link if anyone was here
20:29 < kanzure> OH GOD there's no zoom?
20:29 < nmz787> ?
20:29 < nmz787> says its a big image
20:30 < ThomasEgi> use the browsers zoom function?
20:30 < ybit> that just made my night
20:30 < ybit> hadn't seen that
20:30 < yashgaroth> ^of course you need a 10 tesla magnet, but still
20:30 < nmz787> 10 tesla magnet?
20:31 < kanzure> nmz787: SCIENCE is happening in here
20:31 < nmz787> i have magnets from NEB that came with an mRNA extraction kit
20:31 < yashgaroth> for levitating frogs
20:31 < nmz787> oh
20:31 < kanzure> when you get up past 2 teslas you know shit is giong down
20:31 < yashgaroth> yeah, we got on a tangent somehow
20:31 < nmz787> hmm
20:31 < nmz787> tangerine
20:31 < nmz787> more like it
20:31 < kanzure> your diagram is not powerpoint
20:31 < nmz787> picasa kinda sucks
20:31 < nmz787> no
20:31 < kanzure> can you explain what the colors mena
20:31 < kanzure> *mean
20:31 < nmz787> it is hand drawn
20:31 < kanzure> also, yes picasa sucks
20:31 < nmz787> umm
20:32 < ThomasEgi> anyway, will be in bed for a couple of hours.
20:32 < nmz787> blue lines show hybridization
20:32 < ThomasEgi> btw. any idea how many of those circuits would be requested?
20:32 < nmz787> red shows progression to next step
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20:32 < yashgaroth> thomasegi - one, for now
20:33 < ThomasEgi> kk
20:33 < yashgaroth> p.s. thanks for the help, it's been very informative
20:33 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/enzymaticSynthesisCycle.png
20:34 < nmz787> that is smaller than orig
20:34 < nmz787> lemme just email you the damn file
20:34 < kanzure> oops refresh
20:34 < kanzure> the bigger one is up
20:34 < nmz787> ahh
20:34 < nmz787> kewl
20:34 < yashgaroth> looks good to me
20:35 < kanzure> blue means hybridization
20:35 < kanzure> red is step incrementer
20:35 < kanzure> ?
20:35 < nmz787> ya
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20:36 < nmz787> the phosphatase and kinase make it so even if you're ligating AAAAAA... you won't have repeat ligations (you may have repeat hybridizations... but they won't last past the wash)
20:36 < nmz787> i didn't show washes
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20:37 < nmz787> we would be washing away enzyme too if we don't figure out some way to sieve it with a silicon nanopore membrane, or some sort of recycling circuit that relies on a protein sorter
20:37 < yashgaroth> or some way of de/activating it when we want
20:38 < kanzure> i'm fine with losing enzyme as long as we don't lose library
20:38 < nmz787> (3 proteins for phos, kinase, ligase... 4 if we want to do PCR at the very end to amplify a bunch)
20:38 < nmz787> oh?
20:38 < nmz787> why is enzyme less important?
20:38 < nmz787> i would think its more expensive
20:38 < nmz787> but I could be wrong
20:38 < nmz787> at these scales we won't waste nearly as much as in macro lab
20:39 < nmz787> per step
20:39 < yashgaroth> if we can produce it ourselves, it's pretty cheap
20:39 < nmz787> hmm
20:39 < nmz787> ok
20:39 < yashgaroth> especially if it's bacterial production, no problem
20:39 < kanzure> i have this irrational confidence in enzyme purification being easier than an organic chemistry lab for dillutions and vaporizations and shit
20:40 < nmz787> the polymerase for amplification PCR could be substituted by a transformation circuit where it just goes into yeast or ecoli
20:40 < kanzure> cloning should be a last step :x no?
20:40 < yashgaroth> trust me, I do protein purification for a living :V
20:40 < kanzure> yeah on fancypants $80k hplc columns
20:40 < nmz787> i've done it with lys tags and some sort of agarose beads... i can't remember exactly, its standard though, and easy... and the capture beads are refreshable
20:41 < yashgaroth> ehh it's basically just a peristaltic pump and a controller, and we can do gravity columns anyway
20:41 < nmz787> it was poly some AA
20:41 < yashgaroth> poly histidine, probably
20:41 < nmz787> ya
20:41 < yashgaroth> nickel-nta beads, wash with imidazole, it works good
20:41 < nmz787> yup
20:41 < yashgaroth> elute*, not wash
20:42 < yashgaroth> but yeah, easy, no worries
20:42 < nmz787> the nickel agarose beads were refresable until the agarose bead itself dissolved i think
20:42 < nmz787> i was thinking
20:42 < yashgaroth> yep, I never bothered recycling them but if we're being cheap it's fine
20:42 < nmz787> we might be able to get away with 2 or 4mer library
20:43 < yashgaroth> depends on the minimal site for the ligase, but a 4 mer might be safe
20:43 < nmz787> it depends how much room ligase needs to sit down
20:43 < nmz787> yeah
20:43 < nmz787> but it was just a thought
20:43 < nmz787> not sure which would be faster, I guess 6mer
20:44 < yashgaroth> depends whether we can actually control 4000 droplets
20:44 < nmz787> and then there's what the optimal oligo length on the library production/nick side is
20:44 < kanzure> 4000 droplets.. sure. library access times might suck though ;)
20:45 < kanzure> i guess suck is a relative thing, you can probably queue/sort droplets ahead of time
20:45 < yashgaroth> production is scalable
20:45 < nmz787> i forgot to add "remove polynucleotide kinase"
20:45 < nmz787> to that graph
20:45 < nmz787> i'll update it
20:46 < yashgaroth> I'm perfectly fine with an overnight synthesis
20:47 < nmz787> i suspect not more than 5-30secs / nt
20:48 < kanzure> you mean, not better than?
20:48 < kanzure> or not worse than
20:48 < nmz787> (12 hours) / (5 seconds) = 8640
20:48 < kanzure> you're expecting 5 seconds per nt? hahah
20:48 < kanzure> alright
20:48 < nmz787> slowest would be no more than 5-30 secs/nt
20:48 < nmz787> oh
20:48 < kanzure> that's fine with me
20:48 < nmz787> wait
20:48 < nmz787> that's not ny
20:48 < nmz787> nt
20:48 < nmz787> that's per 6mer
20:49 < nmz787> per ligation
20:49 < nmz787> cycle
20:49 < nmz787> 12 hrs at 5sec / 6mer is 51.84kb
20:50 < kanzure> that seems unlikely, but i like it anyway
20:50 < nmz787> and if we scale it, then do gibson synthesis
20:50 < nmz787> on those
20:50 < yashgaroth> better to give the enzymes plenty of time just to make sure
20:50 < nmz787> etc
20:50 < yashgaroth> oh parahsailin was talking about vaccinia pol instead of gibson assembly
20:50 < nmz787> yeah, the conservative estimate even of 10sec / cycle is still OK
20:50 < nmz787> oh
20:51 < nmz787> whats the benefit?
20:51 < yashgaroth> basically it merges any two blunt ended sequences with the same 15bp ends to each other
20:51 < nmz787> oh
20:51 < nmz787> cool
20:51 < kanzure> ssdna?
20:51 < nmz787> well whatever
20:51 < yashgaroth> dsDNA I thought, which is what we'll be making
20:51 < nmz787> its been done
20:52 < kanzure> alright, so let's draw up the lsit of reagents
20:52 < kanzure> and who has the protocol for attaching all this shit to beads?
20:52 < nmz787> got it
20:52 < nmz787> the bead DNA needs to be special order
20:53 < kanzure> what.
20:53 < nmz787> as the 5' end needs to have an amino added
20:53 < kanzure> do you mean library dna, or any polystre-- oh
20:53 < yashgaroth> what was the problem with permanent substrates? we're not moving the beads are we?
20:53 < kanzure> hell yeah we're moving beads
20:53 < yashgaroth> oh fine then
20:53 < kanzure> unless you can convince us
20:53 < yashgaroth> let me get an idea of your method first
20:53 < nmz787> i thought it was needed to keep the growing DNA in place
20:54 < kanzure> the idea of beads is to have a 'macroscopic' object that we know has dna on it
20:54 < nmz787> attach a restriction site to the fluorescent magnetic beads
20:54 < kanzure> so as long as we move those beads around, we'er fine
20:54 < yashgaroth> ah, that works
20:54 < nmz787> inject these beads into the reaction center, magnetize.. do cycling, while cycling washes don't take away DNA
20:54 < yashgaroth> please ignore my mention of permanence and continue
20:55 < kanzure> erm we still need to confirm the "keeping a magnetic bead in place" thing
20:55 < nmz787> that works
20:55 < nmz787> i have a kit that uses it in an eppendorf
20:55 < nmz787> I think the PDMS will be thinner or as thick as an eppendorf
20:56 < kanzure> storage of drops:
20:56 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/Simple,%20robust%20storage%20of%20drops%20and%20fluids%20in%20a%20microfluidic%20device.pdf
20:56 < kanzure> although i liked my idea better (capillary tube of drops)
20:57 < nmz787> there are also the nanopore sieves that is right down the road from me: http://www.simpore.com/
20:57 < nmz787> (the company is right by my school)
20:58 < kanzure> ParahSailin: hey
20:58 < yashgaroth> that's what I like about living in SD - "oh that's a cool company; oh hey they're five minutes from me" every day
20:59 < nmz787> san diego?
20:59 < yashgaroth> yeah
20:59 < nmz787> first i though south dakota
20:59 < nmz787> it was a brief thought
21:00 < yashgaroth> that would have been my first thought were I not living here
21:00 < nmz787> i don't like that drop storage method
21:00 < kanzure> hooray me either
21:00 < nmz787> too high-class for what we need i think
21:00 < nmz787> fancy pants
21:00 < nmz787> have i met you yash?
21:01 < yashgaroth> not officially I don't think
21:01 < nmz787> NYC FBI-DIYbio?
21:01 < kanzure> hah no
21:01 < yashgaroth> Seattle FBI-DIYbio
21:01 < nmz787> ok
21:01 < nmz787> different guy from SD
21:01 < nmz787> lol
21:01 < nmz787> i guess a lot of people live down there
21:02 < yashgaroth> it's big for biotech
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21:04 < kanzure> nmz787: what's the extra molecule we'd need on the dna you said? an amino acid?
21:04 < nmz787> section IV
21:04 < nmz787> http://bangslabs.com/sites/default/files/bangs/docs/pdf/302.pdf
21:05 < nmz787> 5' amino modified
21:05 < nmz787> pg 5 of 11 here: http://bangslabs.com/sites/default/files/bangs/docs/pdf/205.pdf
21:05 < yashgaroth> oh btw nmz I just sent you a request on FB if you're wondering who I am
21:06 < nmz787> "ligand with available amine"
21:06 < nmz787> its easy to do
21:06 < nmz787> i've done it before
21:06 < nmz787> albeit i was attaching biotin (protein)
21:07 < yashgaroth> ya I've done that with proteins, it is easy
21:07 < nmz787> with the 5' amino mod, it looks the same to the linker as a protein N terminal end
21:09 < kanzure> i'm looking at your graph and i don't know where the ATGCAC comes from
21:09 < Mokbortolan_> is that a valid sequence?
21:09 < kanzure> or why ATGCAC's arrow points to TCTTAC
21:10 < yashgaroth> ATG pairs there to TAC
21:10 < kanzure> Mokbortolan_: as long as it's A's and C's and T's and G's
21:10 < Mokbortolan_> I always thought they paired up like AT and GC
21:10 < kanzure> you're thinking of base pairing rules
21:10 < Mokbortolan_> right
21:11 < Mokbortolan_> err, yes :)
21:11 < Mokbortolan_> what other rules are there?
21:11 < kanzure> so ATT hybridizes to TAA
21:11 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Quit: Computer has gone to sleep.]
21:12 < nmz787> almost
21:12 < nmz787> 5' ATT 3' hybridizes with 3' TAA 5'
21:13 < nmz787> what other rules? polymerase extends from 3' OH
21:13 < yashgaroth> man there's dozens of rules
21:13 < nmz787> yeah
21:13 < nmz787> i got a bookshelf full of em
21:13 < kanzure> the number one rule is that it will take at least 10 tries
21:14 < nmz787> you may not pass Go, you may not collect #$200
21:14 < nmz787> oh man, script injection is pretty fun
21:14 < nmz787> that django site i was working on the other night
21:14 < kanzure> trusty %00
21:14 < yashgaroth> brb 10 mins
21:14 < nmz787> we tested some text inputs and image hover-over comments
21:14 < kanzure> ' OR 1='1' ;--%00
21:15 < nmz787> and they both weren't being sanitized
21:15 < nmz787> they were easy fixes though
21:15 < nmz787> django is pretty good stuff
21:15 < kanzure> that's odd.. that's like the number one reason to be using a framework
21:15 < kanzure> i was hesitant to ever try rails since i liked django so much
21:15 < kanzure> but rails has such a tremendously big library of gems :(
21:16 < nmz787> well we weren't saintizing what we stored in the DB, then in the template we were calling it |safe
21:16 < nmz787> so it wasnt sanitizing on the way out either, lol
21:16 < kanzure> we?
21:16 < nmz787> we were specifically telling it not to
21:16 < nmz787> my roommate
21:16 < nmz787> and i
21:18 < kanzure> i wonder if we should just throw this method up on scienceexchange to verify it first
21:18 < nmz787> so i installed cyanogen mod on that evo i have
21:18 < nmz787> 3G started working, as i said it hadn't been
21:19 < nmz787> then about 2 or 3 days later it stopped
21:19 < kanzure> oh good, i thought cyanogenmod was still borked?
21:19 < kanzure> hrm
21:19 < nmz787> and I haven't been able to get it to come back
21:19 < nmz787> it seems like its some AAA secret password
21:19 < nmz787> which I can't read from the 'donor' phone
21:19 -!- Charlie_ is now known as poptire
21:19 < kanzure> btw there's tons of helpful people in #android
21:19 < nmz787> getting a denied message when i try to dump that mem location
21:20 < kanzure> but they usually only show up during the waking hours because they're lame
21:20 < nmz787> whats the chance someone will see it and beat us to building it by a few months?
21:21 < kanzure> see what
21:21 < kanzure> oh on science exchange?
21:21 < kanzure> no we can keep shit hidden
21:21 < nmz787> how would we verify it without showing others>?
21:22 < nmz787> oh youre sayin keep it hidden by not puttin git up?
21:22 < nmz787> putting it up*
21:22 < kanzure> i mean we get someone to do the molecular biology tests for us through that service
21:22 < kanzure> it's just a hiring thing
21:22 < nmz787> oh, hmm
21:22 < kanzure> just an idle thought
21:23 < nmz787> if i don't have a fulltime job come June, I could be that person
21:23 < nmz787> oh man
21:23 < nmz787> i trapped a squirrel
21:23 < nmz787> its been in the back yard for at least 6-9 hours
21:24 < ParahSailin> trapped it?
21:24 < kanzure> are you a dog
21:24 < nmz787> hmm, i really need to drive it away from the house to let it go... it might freeze if i leave it out overnight
21:24 < nmz787> which i don't want to do to it
21:24 < nmz787> no
21:24 < nmz787> not a dog
21:24 < nmz787> but my landlord has holes in his house
21:24 < nmz787> and squirrels live in the walls
21:25 < nmz787> so we've just been trapping and releasing 4 miles away on campus
21:25 < nmz787> (not in the buildings)
21:25 < nmz787> though we've joked about doing that
21:25 < Adifex> nmz787, what school?
21:25 < nmz787> Rochester Institute of Technology
21:25 < Adifex> ah you and kanzure?
21:25 < nmz787> hah
21:26 < nmz787> kanzure is in sunshine ville
21:26 < nmz787> i am in overcast pergatory
21:26 < ParahSailin> nmz787, benefit of "in-fusion" kit, the trade name for vaccinia pol: much more reliable for cloning assemblies with up to 5 parts in my experience
21:26 < nmz787> no he is ~2000 miles from me
21:27 < Adifex> ah k nvm
21:27 < nmz787> yashagaroth said vaccinia pol did some recombination like thing
21:27 < ParahSailin> i trap and release rats
21:28 < nmz787> 15bp similars get ligated
21:28 < nmz787> or something
21:28 < ParahSailin> right
21:28 < nmz787> clontech doesnt mention that
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21:28 < ParahSailin> well not ligated, but it definitely chews off 15nt leaving overhang
21:28 < nmz787> in-fusion looks like an overyhyped pol + buffer kit
21:28 < ParahSailin> not
21:28 < nmz787> not to say its bad
21:28 < kanzure> i was thinking of doing a site called adopt a lab rat, where lab mice/rats are sent to adoption after their "use"
21:28 < nmz787> but it doesn't look much different on the surface
21:29 < kanzure> instead of capturing heh'
21:29 < kanzure> (or instead of a breeding farm)
21:29 < Mokbortolan_> I want one of those high-intelligence rats
21:29 < nmz787> or, donatesothisrodentdoesntdie.com
21:29 < ParahSailin> not at all, vaccinia pol has pretty powerful recombinase activity
21:29 < kanzure> Mokbortolan_: they look like this http://3.bp.blogspot.com/_AcBUSVxs82w/TDTFxGbUzSI/AAAAAAAAfUg/PbGCFK4O5t0/s1600/Pinky-And-The-Brain-Wallpapers.jpg
21:29 < Mokbortolan_> you've heard of save toby, right?
21:29 < nmz787> was that a rabbit?
21:29 < Mokbortolan_> yeah
21:30 < ParahSailin> it has ssbinding activity and dimerizes with itself, catalyzing the hybridization of stuff
21:30 < nmz787> have y'all seen this: http://www.youtube.com/watch?v=8bhq_NL6jL0
21:30 < ParahSailin> in-fusion saves a lot of time cloning
21:30 < ParahSailin> thats why i wanna produce it cheap
21:31 < nmz787> hmm
21:33 < kanzure> nmz787: i'll one up you.. http://www.youtube.com/watch?v=akaos1U8Rto
21:33 < kanzure> or http://www.youtube.com/watch?v=jdERgfgB9Yc
21:33 < kanzure> random commercials.
21:34 -!- Adifex [~Adifex@rrcs-97-77-55-27.sw.biz.rr.com] has quit [Quit: Adifex]
21:35 < kanzure> oh speaking of bad commercials does anyone remember the old biorad commercial
21:35 < kanzure> http://www.youtube.com/watch?v=CQEaX3MiDow
21:35 < yashgaroth> ugh
21:35 < kanzure> oh come on
21:36 < kanzure> until you replace bio-rad as a supplier, suck it
21:36 < yashgaroth> they do make good gels
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21:41 < nmz787> first one was pretty good
21:41 -!- marainein [~marainein@114-198-65-190.dyn.iinet.net.au] has joined ##hplusroadmap
21:44 < nmz787> loving the biorad
21:44 < nmz787> G T C A
21:44 < nmz787> !!!
21:44 < kanzure> gah what have i done
21:48 < nmz787> this was linked from the biorad one, but it gets my approval
21:48 < nmz787> http://www.youtube.com/watch?v=XViCOAu6UC0&feature=endscreen&NR=1
21:49 < roksprok> is the synthesizer you were talking about using phosphoramidites?
21:50 < nmz787> no
21:50 < nmz787> good old natural style oligonucleotides
21:51 < yashgaroth> what about generating the library templates?
21:52 < nmz787> you had that image
21:52 < nmz787> of the cycle with the pol and nicking enzyme
21:52 < yashgaroth> yeah, but we still need to make the initial backbones with pamidites
21:52 < nmz787> well yeah
21:52 < nmz787> chicken and the egg
21:53 < yashgaroth> pretty much, but I do love semantics; beyond the initial setup, we won't need pamidites no
21:53 < nmz787> we can probably think up something where we restriction digest or shear a genome/plasmid with the library in it
21:53 < nmz787> if it was a 4mer
21:53 < nmz787> that's only 16 oligos
21:54 < nmz787> plus the 5' mod one for attaching to the main work bead
21:54 < nmz787> the magnetic one
21:54 < kanzure> we will probably also do an oligo synthesizer anyway
21:54 < kanzure> because fuck ordering oligos
21:54 < nmz787> lol
21:54 < yashgaroth> shorter sequences mean a higher % that will bind to themselves
21:55 < kanzure> hmm.. i don't see how we would recover the library items from a genome
21:55 < kanzure> but yeah it would be great to clone it in culture or distribute it in culture
21:55 < nmz787> plasmid
21:55 < nmz787> ?
21:55 < yashgaroth> you still need to divvy up the individual oligos, without any way to separate them
21:55 < kanzure> :/
21:55 < nmz787> hmm
21:56 < nmz787> i'm sure theres a crazy way to do it
21:56 < nmz787> or a stupid simple way
21:56 < nmz787> that we're too smart to realize
21:56 < kanzure> yes..
21:56 < kanzure> each cell has a custom plasmid
21:56 < nmz787> bryan, hire a good ole boy
21:56 < kanzure> with a custom marker on the surface
21:56 < kanzure> then bind to that marker. caveat: must distribute markers
21:57 < kanzure> erm, not markes but binders
21:57 < yashgaroth> oh god 4000 different markers
21:57 < kanzure> you still have to distribute markers for each cell heh
21:57 < kanzure> *binders for each cell
21:57 < kanzure> i'm really interested in the one-cell-per-drop cultures
21:57 < kanzure> i wonder how much volume of water around a cell is absolutely necessary
21:58 < nmz787> wait earlier i said a 16 item lib would be 4mer, but it would only be 2mer
21:58 < nmz787> i was doing binary or something
21:58 < kanzure> 4^n
21:58 < nmz787> yeah 2^4=16
21:58 < nmz787> my fault
21:59 < yashgaroth> once you have the initial library templates they should last a long time, even if that means ordering and placement of all 4000 of them
21:59 < nmz787> 8 mer is 65535
21:59 < nmz787> i can remeber when 16 bit color was hot shit
22:00 < nmz787> yeah i wonder /how/ long
22:00 < nmz787> what are the half-lives of the constituent atoms???
22:00 < nmz787> is that how to approach this?
22:00 < yashgaroth> DNA lasts forever
22:01 < yashgaroth> minus the nicking enzyme spazzing out during production, it'll be stable
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22:01 < nmz787> 4096*6*0.3=7372.8
22:01 < yashgaroth> *spazzing out is the technical term for star activity
22:01 < nmz787> 30 cents /bp is advertised to Joe Public
22:01 < nmz787> but i last paid 0.15/bp
22:02 < nmz787> a year ago
22:02 < nmz787> that was for 25nMol too
22:02 < nmz787> buying more mols makes it cheaper i think
22:02 < yashgaroth> 6 plus the nicking enzyme recognition site and a spacer for the bead attachment
22:03 < nmz787> ahh
22:03 < nmz787> rigt
22:03 < nmz787> 4096*26*0.15=15974.4
22:03 < nmz787> if we can modify the 5' end ourselves
22:03 < nmz787> then we can buy once
22:03 < nmz787> also
22:04 < nmz787> to test we don't need a full library
22:04 < yashgaroth> how are we selecting for only the correct 5' end? since the template strand has one too
22:04 < nmz787> we'll need to write software to break input DNA seq into the steps
22:04 < nmz787> oligos come ssDNA
22:05 < yashgaroth> oh yeah n/m then
22:05 < nmz787> teh nicking enzyme should produce ssDNA too
22:05 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Client Quit]
22:06 < nmz787> ok i'm out for the night
22:06 < nmz787> ttyl
22:06 < yashgaroth> cya
22:07 < ParahSailin> im not real clear on the scheme still
22:07 < ParahSailin> you want nicking RE to make 6mer with some overhang?
22:08 < nmz787> uh oh, we need to learn how to make 3D animations of these proteins and shit
22:09 < nmz787> that would be sweet
22:09 < nmz787> lata
22:09 -!- nmz787 [43f2b117@gateway/web/freenode/ip.67.242.177.23] has quit [Quit: Page closed]
22:09 < yashgaroth> parahsailin: did you see http://diyhpl.us/~bryan/papers2/DNA/nicking-library-method.jpg ?
22:09 < ParahSailin> yah
22:09 < yashgaroth> there shouldn't be any overhang
22:10 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection]
22:10 < yashgaroth> the pol and the nicking enzyme alternate to churn out 6mers
22:13 < ParahSailin> the green strand is the oligo you are making?
22:13 < yashgaroth> yes
22:13 < ParahSailin> ohhhh
22:13 < ParahSailin> that was fairly nonobvious
22:13 < yashgaroth> yeah I suck at making diagrams
22:17 < ParahSailin> im not sure how green sticks backs on and gets extended
22:17 < kanzure> i guess we could dump pdb models into blender and do animations that way?
22:17 < yashgaroth> green is supposed to melt off, you don't need to extend it
22:17 < ParahSailin> how does it get bigger
22:18 < yashgaroth> http://diyhpl.us/~bryan/papers2/DNA/enzymaticSynthesisCycle.png
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22:18 < yashgaroth> we're just adding those 6mers onto a growing strand, somewhere else
22:22 < roksprok> so is the idea that you have 4096 of the beads, with every possible 6mer?
22:22 < kanzure> yes
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22:26 < yashgaroth> re: nmz's diagram, it doesn't seem like we need to grow this double-stranded
22:26 < yashgaroth> after you ligate the top strand, you wash off the bottom strand, then add the new correct top & bottom strand
22:27 < yashgaroth> bottom strand then allows the ligation of the top ones together
22:29 < yashgaroth> then you can skip the PNK enzyme step altogether
22:31 < kanzure> we should consolidate the diagrams into a similar style
22:31 < kanzure> or else my eyes are going to bleed
22:31 < yashgaroth> I can draw mine, but I warn you my handwriting's far shittier than his
22:31 < kanzure> that's what the text box is for?
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22:32 < yashgaroth> fuck it I'll do my modification of his diagram in powerpoint tomorrow, it'll be a lazy friday anyway
22:43 < Mokbortolan_> how can I get an NR2B transgenic rat?
22:45 < yashgaroth> like, nr2b knockout?
22:45 < Mokbortolan_> no, over-expressed
22:46 < kanzure> i think some universities just run a lab for doing transgenic mice for whoever needs them on campus
22:46 -!- nchaimov_ [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has joined ##hplusroadmap
22:46 < Mokbortolan_> "knock-in"
22:47 < kanzure> http://www.nih.gov/science/models/mouse/deltagenlexicon/list.html
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22:47 < yashgaroth> I'm assuming brain-specific expression?
22:47 < Mokbortolan_> yes
22:48 < kanzure> "Beginning January 1, 2012, the Knockout Mouse Project (KOMP) Repository is now fully self-supporting. Therefore, costs to distribute products (vectors, ES cells, mice, germplasm) and offer services (microinjection, cryopreservation and recovery, germline transmission testing, genotyping, etc.) will no longer be subsidized by the NIH."
22:48 < Mokbortolan_> it'd be nice to get a breeding pair
22:48 < kanzure> http://www.komp.org/
22:48 < kanzure> hmm you don't usually do your own breeding
22:48 < Mokbortolan_> No, I mean, I'd want to breed one into an existing pet rat line
22:49 < kanzure> "Parental ES cells, Ultra low passage for multiple electroporations	$ 1,296.00
22:49 < Mokbortolan_> and also keep the line separate
22:49 < kanzure> "Live mice - Conventional Facility (per mouse) $348"
22:49 < yashgaroth> well you only need one for that until you get a homozygous pair
22:49 < kanzure> "Recombination services (in vivo, Cre or FLPe) $5,940.00"
22:49 < kanzure> the hell?
22:49 < kanzure> someone should go undercut their prices
22:50 < Mokbortolan_> if you're going to buy a pet rat, why not the smartest rat?
22:50 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has quit [Ping timeout: 244 seconds]
22:50 < yashgaroth> buy a higher animal instead
22:50 < Mokbortolan_> rats are nice
22:50 < kanzure> most of the "intelligence" gene research stuff is not.. all at once..
22:50 < Mokbortolan_> small carbon footprint
22:50 < kanzure> it's more like.. piecewise research
22:51 < Mokbortolan_> you could accumulate them and breed them in
22:51 < Mokbortolan_> evaluate different combinations
22:51 < yashgaroth> try contacting whoever did the research that these mice are smarter, they usually keep them
22:51 < kanzure> don't most lab mice stranis get cancer like immediately?
22:51 < kanzure> *strains
22:51 < yashgaroth> tell them you have a "lab" for "research"
22:51 < yashgaroth> only the ones that are bred to get cancer^
22:51 < kanzure> hrmm
22:51 < yashgaroth> otherwise that would be annoying
22:52 < Mokbortolan_> I'm sure it happens at a certain rate
22:52 < yashgaroth> interesting results...oh it's got cancer damnit
22:52 < kanzure> yashgaroth: do you remember the hubbub about the longevity mice stuff that john schloendorn was trying to sponsor for a while
22:52 < kanzure> i guess ParahSailin would be the better person to ask
22:53 < yashgaroth> yeah we've pretty much cured every disease in mice already anyway
22:53 < yashgaroth> isn't that what their prize is about?
22:53 < kanzure> they were trying to raise money to sequence some genomes, but people were skeptical about one of the researchers' record
22:53 < kanzure> no this was not related to m-prize
22:53 < yashgaroth> ah, then I don't know any specifics
22:53 < kanzure> oh well. it's in the logs somewhere. we were all complaining about it.
22:54 < yashgaroth> Mok - did you have a specific paper with this nr2b research?
22:55 < kanzure> i always wanted a beta-catenin mouse
22:55 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Increased%20neuronal%20production,%20enlarged%20forebrains%20and%20cytoarchitectural%20distortions%20in%20beta-catenin%20overexpressing%20transgenic%20mice.pdf
22:55 < kanzure> page 2 figure 1b
22:56 < yashgaroth> there is some promise to sperm-mediated gene transfer with plasmids if you wanted to try it yourself, but your best bet would be to beg for mice from the PI
22:58 < yashgaroth> kanzure: did they test those mice for enhanced mental function or do they just have big brains
22:59 < kanzure> haha those things? dead
22:59 < yashgaroth> oh yeah I just saw "We found that transgenic mice generated using this construct
22:59 < yashgaroth> occasionally (n = 5) survived to adulthood"
22:59 < kanzure> oh
22:59 < kanzure> i don't remember that part. alright.
22:59 < kanzure> that's great :)
23:00 < yashgaroth> but no I don't think they went on to live healthy lives
23:02 < kanzure> "Recently-derived variants of brain-size genes ASPM, MCPH1, CDK5RAP and BRCA1 not associated with general cognition, reading or language"
23:02 < kanzure> i'm reading the file list in that directory.
23:02 < kanzure> Reconstruction of natural scenes from ensemble responses in cat visual cortex - Stanley - 1999.pdf
23:03 < yashgaroth> I thought there was some awesomely smart rat created recently, fuck if I know where I read it
23:03 < kanzure> ^a favorite. http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20of%20natural%20scenes%20from%20ensemble%20responses%20in%20cat%20visual%20cortex%20-%20Stanley%20-%201999.pdf
23:03 < yashgaroth> yeah that one's pretty terrifying/amazing
23:05 < kanzure> Structure of the cerebral cortex of the humpback whale, Megaptera novaeangliae (Cetacea, Mysticeti, Balaenopteridae).pdf
23:05 < rdb> *yawn* morning all
23:06 < kanzure> sleep is for the weak
23:06 < kanzure> there will be no more of this, sleep, thing.
23:07 < rdb> mk
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23:20 < kanzure> http://www.piccolo.cc/ well, the autonomously-draw-random-forests is a nice feature i guess
23:21 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has joined ##hplusroadmap
23:21 < kanzure> but why not just use the drawstring-whiteboard-drawing-bots instead
23:22 < yashgaroth> that's the cutest robot I've seen since that one that spews ketchup
23:22 < kanzure> what was it called.. huxbee?
23:23 < rdb> it doesn't look too sturdy to me
23:23 < yashgaroth> automato :D
23:24 < kanzure> you know.. this thing http://www.youtube.com/watch?v=FmCWx30g7Ks
23:25 < kanzure> geeze it needs to use another string for stabilization i think
23:26 < kanzure> maybe not http://www.youtube.com/watch?v=i5rxxGuWUo8
23:36 -!- nchaimov [~nchaimov@c-67-171-214-94.hsd1.or.comcast.net] has quit [Quit: nchaimov]
23:37 < yashgaroth> time for sleep
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--- Log closed Fri Feb 17 00:00:14 2012