| --- Log opened Thu Feb 16 00:00:12 2012 | ||
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| 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 | 00:42 |
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| rdb | morning all | 02:40 |
| Steel2_ | almost everyone is asleep, I'd say :P | 02:40 |
| Steel2_ | I'm up late running simulations | 02:40 |
| rdb | ah, are most of you in the US? | 02:41 |
| Steel2_ | east coast us | 02:41 |
| Steel2_ | you? | 02:41 |
| rdb | EU, netherlands | 02:41 |
| Steel2_ | cool | 02:42 |
| Steel2_ | gamedev? | 02:42 |
| rdb | 3d engine developer, I'm trying to get into electrical engineering too | 02:42 |
| Steel2_ | cool, I just got an EE job | 02:43 |
| Steel2_ | what's your interest in H+? | 02:43 |
| rdb | I've always been interested in biohacking | 02:44 |
| rdb | I've been researching and developing cheap biometrics solutions | 02:45 |
| rdb | sensitive ekg and eeg for low price, if you will | 02:45 |
| 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 | 02:47 |
| chris_99 | have you seen the emokit rdb? | 02:58 |
| chris_99 | Emotive Epoc | 02:58 |
| 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 | 02:59 |
| 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 | 03:00 |
| 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 | 03:01 |
| 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? | 03:02 |
| rdb | hasn't been updated in quite a while, they seem to rely on outdated components whereas nowadays you can get much better quality componetns for the same price, but I'm mostly discouraged by the fact that they have a really fancy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. | 03:04 |
| 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 | 03:05 |
| 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 | 03:06 |
| 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 | 03:07 |
| chris_99 | ADS1x9x is an ADC? | 03:08 |
| rdb | it is, particularly aimed at biopotential measurements | 03:08 |
| rdb | Steel2_, I'll sign up | 03:08 |
| 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' | 03:09 |
| chris_99 | what pcb fab lab are you using btw? | 03:10 |
| rdb | I'm using seeedstudio for this batch, which is cheap for prototypes | 03:11 |
| 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 | 03:12 |
| 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 | 03:13 |
| 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 | 03:15 |
| 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 | 03:16 |
| 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 | 03:17 |
| 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 | 03:18 |
| 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 | 03:19 |
| rdb | understandable | 03:20 |
| Steel2_ | I think our setup has 2nm error bars | 03:20 |
| rdb | that's impressive! | 03:21 |
| Steel2_ | it's expensive is what it is | 03:22 |
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| rdb | looks like ThomasEgi already introduced the ads119x/129x chip range on the biohack.me forums | 03:29 |
| chris_99 | whats your thesis on Steel2_? | 03:56 |
| Steel2_ | electrohydrodynamic jet nanoprinting | 03:56 |
| chris_99 | sounds complex :) | 03:57 |
| Steel2_ | ehhhh | 03:59 |
| Steel2_ | lots of scanning papers | 03:59 |
| Steel2_ | not so much intuition needed | 03:59 |
| chris_99 | ah heh | 04:02 |
| 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 | 04:10 |
| rdb | it seems to me like it'd be very useful for hacking up devices to hook up to your body | 04:11 |
| 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? | 04:12 |
| 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 | 04:13 |
| 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 | 04:14 |
| 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 | 04:15 |
| 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 | 04:16 |
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| 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 | 04:18 |
| chris_99 | i'm a bit confused how you can get electrocuted, if these are passive things? | 04:19 |
| 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) | 04:20 |
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| chris_99 | oh scary!, how do you stop that | 04:21 |
| 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 | 04:22 |
| 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 | 04:23 |
| 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 | 04:24 |
| 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 | 04:25 |
| 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 | 04:26 |
| 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 | 04:27 |
| 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 | 04:28 |
| 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 | 04:29 |
| chris_99 | cool, are you planning on using a microcontroller too | 04:30 |
| 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. | 04:31 |
| chris_99 | nice, i've only got experience with PIC chips atm | 04:32 |
| 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 | 04:33 |
| 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 | 04:34 |
| * rdb goes to grab some lunch. | 04:37 | |
| rdb | By the way, when I get these fabbed, I'll have a few spare (very simple) ads1192 breakouts, if anyone is interested | 04:38 |
| chris_99 | ooh yeah i'm interested | 04:41 |
| rdb | back | 04:50 |
| rdb | where do you live? | 04:50 |
| 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 | 04:55 |
| Steel2_ | jesus christ | 04:58 |
| Steel2_ | I can finally go to bed | 04:58 |
| rdb | have a pleasant rest :-) | 04:59 |
| Steel2_ | thanks :P | 04:59 |
| Steel2_ | I look forward to talking with you in the future | 04:59 |
| rdb | same here :-) | 05:00 |
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| 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 | 07:38 |
| 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 | 07:39 | |
| 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 | 07:40 |
| 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 | 07:41 |
| 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 | 07:43 |
| ParahSailin | but whats the benefit of doing it at home? saving money or just fun? | 07:44 |
| 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 | 07:45 |
| 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 | 07:47 |
| 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... | 07:48 |
| 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 | 07:49 |
| kanzure | well obv. nobody is doing 22nm features at home | 07:51 |
| mag1strate | That would be really expensive wouldn't it? | 07:52 |
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| ParahSailin | i would like to see an explanation of how doing whatever sized features they do has some benefit over buying a commercial product | 07:56 |
| mag1strate | well you would have control over the quality | 07:57 |
| mag1strate | unless the quality of what you buy is really good | 07:57 |
| ParahSailin | can one make a custom asic for cheaper than an fpga would be? | 07:58 |
| kanzure | i don't think cost is the point | 07:59 |
| kanzure | commercial large-scale production will always have cheaper per-unit costs | 08:00 |
| 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 | 08:01 |
| kanzure | btw, did you look at their site? | 08:02 |
| kanzure | http://code.google.com/p/homecmos/ | 08:03 |
| ParahSailin | hm thats pretty good id say | 08:05 |
| 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 | 08:13 |
| ParahSailin | average cost is really what matters | 08:16 |
| ParahSailin | cost of your time, cost of physical capital | 08:16 |
| 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 | 08:17 |
| ParahSailin | ok | 08:18 |
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| 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 | 08:28 |
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| ParahSailin | im not that experienced with finance, so was not sure which cost per-unit typically refers to | 08:35 |
| ParahSailin | per-unit cost there included to price of the machines and buildings that made the units? | 08:36 |
| chris_99 | you guys seen this http://www.inscentinel.com/InscentinelLtd/Pages/Science%20and%20technology/technology.html | 08:39 |
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| ParahSailin | i bet you could use that to diagnose/detect cancer | 08:45 |
| chris_99 | does cancer have a smell? | 08:45 |
| 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." | 08:46 |
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| chris_99 | so i'm sure you're right that the bees could do it too | 08:46 |
| 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 | 08:47 |
| 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 | 08:48 |
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| 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 | 08:53 |
| chris_99 | heh nice, not seen that before | 08:54 |
| 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 :) | 08:55 |
| kanzure | who the heck smells their keyboard | 08:56 |
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| kanzure | i really don't understand all of pyjamas' components | 09:06 |
| kanzure | really really confused. | 09:06 |
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| 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 | 09:16 |
| 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! :) | 09:20 |
| chris_99 | i'm planning on getting it printed at lulu, to make it easier to read | 09:21 |
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| chris_99 | kanzure, how come theres a geiger counter in the bio list out of interest? | 09:29 |
| kanzure | most molecular biology labs use radioactive phosphorous | 09:30 |
| 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 | 09:31 |
| 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 | 09:32 |
| 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 | 09:33 |
| kanzure | http://en.wikipedia.org/wiki/Southern_blot#Method | 09:34 |
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| kanzure | something something about being better than anki/supermemo http://news.ycombinator.com/item?id=3598676 | 10:07 |
| kanzure | "memrise" | 10:07 |
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| kanzure | beep boop | 10:41 |
| delinquentme | kanzure, | 10:45 |
| delinquentme | THEY SAID NO | 10:45 |
| * delinquentme weeps! | 10:45 | |
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| delinquentme | something between overqualified and wanting someone whos done enterprise before | 10:45 |
| kanzure | who said no | 10:46 |
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| kanzure | delinquentme: ? | 10:46 |
| 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 | 10:48 |
| kanzure | badgebadger | 10:49 |
| 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? | 10:52 |
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| kanzure | delinquentme: $90K/year for a newbie | 10:53 |
| kanzure | well, for a good newbie | 10:54 |
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| delinquentme | ha | 11:24 |
| delinquentme | ahhhhah | 11:24 |
| delinquentme | annnd LBL just contacted me | 11:24 |
| chris_99 | is electroporation and a gene gun similar in some ways? | 11:31 |
| ParahSailin | avoid gene gun | 11:34 |
| chris_99 | why so? | 11:35 |
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| ParahSailin | expensive | 11:37 |
| 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 | 11:38 |
| 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 | 11:39 |
| kanzure | also, you can go hunting for agrobacterium in forests | 11:41 |
| 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 | 11:42 |
| chris_99 | cool | 11:43 |
| kanzure | superkuh: hopefully you don't mind. | 11:44 |
| chris_99 | could you use electroporation instead of agrobacterium | 11:49 |
| kanzure | Expression of genes transferred into monocot and dicot plant cells by electroporation http://www.pnas.org/content/82/17/5824.full.pdf | 11:50 |
| 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 | 11:51 |
| 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 | 11:52 |
| kanzure | "hey mitch, what is a hacker?" http://www.youtube.com/watch?v=hoDOrKZK3Kg | 11:53 |
| kanzure | puppet show by noisebridge | 11:53 |
| chris_99 | :) | 11:56 |
| delinquentme | chris_99, yeah thats what the first one was made with | 12:02 |
| chris_99 | yup, i was reading the wikipedia article rather interesting | 12:03 |
| 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 | 12:04 |
| delinquentme | chris_99, i think they're cheap? | 12:05 |
| chris_99 | oh heh, i'll checkout ebay | 12:06 |
| chris_99 | £700 or more for me | 12:06 |
| 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 | 12:07 |
| 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 | 12:08 |
| chris_99 | yeah computer viruses | 12:09 |
| delinquentme | sexy | 12:10 |
| delinquentme | where @ | 12:10 |
| chris_99 | university in the uk | 12:10 |
| chris_99 | i was wondering if i could apply some biology techniques to it just for a side project | 12:11 |
| 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 | 12:13 |
| 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 | 12:14 |
| 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 | 12:15 |
| chris_99 | just looking at http://en.wikipedia.org/wiki/Electroporation the electrodes should be shown inside the curvette right? | 12:21 |
| chris_99 | *cuvette | 12:22 |
| chris_99 | sorry ignore that | 12:22 |
| chris_99 | misread the diagram | 12:22 |
| 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 | 12:25 |
| kanzure | and he was honestly pissed about biobricks because of the disservice to the public it was doing | 12:26 |
| 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 | 12:27 |
| chris_99 | transplanted what sorry/ | 12:28 |
| kanzure | some genetic regulatory network from some other species, who knows | 12:29 |
| 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 | 12:30 |
| chris_99 | yeah that sounds interesting, how hard would that be to do | 12:32 |
| 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 | 12:34 |
| kanzure | carolina scientific (or whatever?) carries a gfp kit for high schoolers | 12:35 |
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| chris_99 | they don't ship to individuals apparently :( | 13:02 |
| chris_99 | seems a bit crap | 13:03 |
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| kanzure | chris_99: you can ask genspace or biocurious to ship you a kit | 13:09 |
| chris_99 | thats an idea,i've just found another lab which may ship it | 13:10 |
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| 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 | 13:40 |
| 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 | 13:41 |
| 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 | 13:42 |
| 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 | 13:43 |
| fenn | looks like they ship all over the place http://www.carolina.com/category/customer+service/international+customers.do | 13:44 |
| chris_99 | ah, they have a uk distributor, but alas they don't sell the gfp kit | 13:47 |
| chris_99 | could you introduce gfp into a plant? | 13:49 |
| Steel | sup y'all | 13:57 |
| chris_99 | hello allo | 13:58 |
| 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. | 14:11 |
| chris_99 | i'm just wondering if i could do any interesting research with bacteria in near-space using a weather balloon | 14:24 |
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| kanzure | chris_99: anaerobic bacteria? | 14:39 |
| chris_99 | yeah thats an idea | 14:41 |
| kanzure | chris_99: have you read up on atmospheric bacteria | 14:43 |
| chris_99 | nope | 14:43 |
| Mokbortolan_ | kanzure: I think your friend isn't interested in any collaboration with me :p | 14:54 |
| Mokbortolan_ | that's OK, he looks busy | 14:54 |
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| kanzure | Mokbortolan_: why do you say that | 15:07 |
| kanzure | he can be a little hard to navigate around but he means well | 15:07 |
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| kanzure | Juul: howdy | 15:25 |
| kanzure | delinquentme says lbl did a job interview call with him today | 15:26 |
| kanzure | delinquentme: was it juul who called you o__o | 15:26 |
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| delinquentme | ha nah i just got the email | 15:27 |
| delinquentme | Dr. Dylan & Dr. Paramvir (WOO!) | 15:28 |
| Juul | hey Juul | 15:39 |
| Juul | nice delinquentme | 15:39 |
| 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 | 15:40 |
| 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 | 15:41 |
| 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 | 15:42 |
| 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' | 15:44 |
| kanzure | hah i do? | 15:45 |
| kanzure | huh.. https://lists.apple.com/mailman/listinfo | 15:51 |
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| 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? | 16:06 |
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| fenn | i can't be a starving hacker anymore :( | 16:26 |
| kanzure | fenn: what do you need? | 16:26 |
| fenn | gobs of cash | 16:26 |
| fenn | also, i'm not sure if i'm falling behind the times wrt web technology | 16:27 |
| 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 | 16:28 |
| 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 | 16:29 |
| 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 | 16:30 |
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| 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 | 16:31 |
| fenn | maybe they just like duplicating functionality, but it seems like there's a lot of "stuff" | 16:32 |
| 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 | 16:37 |
| 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 | 16:38 |
| 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/ | 16:39 |
| Steel | yay | 16:45 |
| Steel | someone I can talk to | 16:45 |
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| delinquentme | Stee|, me or the designer :D | 17:02 |
| delinquentme | BOTH | 17:02 |
| Stee| | the designer | 17:09 |
| Stee| | I do controls stuff | 17:09 |
| Stee| | (badly) | 17:10 |
| 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 | 17:16 |
| 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 | 17:17 |
| 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 | 17:18 |
| kanzure | their diagram is pretty simple to understand on pg 2 | 17:19 |
| kanzure | page 3 | 17:19 |
| 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 | 17:20 |
| 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 | 17:21 |
| fenn | it's no worse than figuring out how to use celery | 17:22 |
| fenn | somewhat less complex, more safety overhead | 17:22 |
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| Stee| | Ehhh, there's very little in the way of standardized education for things like CCILC | 17:23 |
| Stee| | anyway, I gotta get ready for dance lesson and party, so bbl | 17:24 |
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| ParahSailin | howdy | 17:25 |
| 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 | 17:26 |
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| 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 | 18:05 |
| kanzure | jrayhawk: don't you run a dns server somewhere | 18:06 |
| fenn | i don't need a dns server, just can't remember my godaddy credentials | 18:08 |
| 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 :/ | 18:10 |
| 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 | 18:11 |
| 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)." | 18:12 |
| ThomasEgi | may i ask what this is used for and what the requirements for the valves are? | 18:13 |
| 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 | 18:14 |
| kanzure | for making stuff like http://thebigone.stanford.edu/images/chemostat.jpg | 18:15 |
| ThomasEgi | hehe that one looks neat | 18:16 |
| 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 | 18:18 |
| kanzure | oh this is nifty too | 18:19 |
| kanzure | http://2011.igem.org/Team:EPF-Lausanne/Tools/Microfluidics/HowTo2 | 18:19 |
| kanzure | "12-Solenoid manifold (part S08-1557) Pneumadyne 1 245.00" | 18:20 |
| kanzure | $245 | 18:20 |
| kanzure | "Pressure Regulator Bellofram 2 $186.00" | 18:20 |
| 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 | 18:21 |
| 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 | 18:22 |
| kanzure | i'd like a way to avoid having to use pneumatic valves, but most people have more experience with pneumatic valves in microchips | 18:23 |
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| 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 | 18:24 |
| fenn | i guess you could just vibrate and hope the hysteresis holds the pdms shut | 18:25 |
| kanzure | "chip tunes" get it :( | 18:25 |
| 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 | 18:26 |
| ThomasEgi | they are a bit big tho | 18:27 |
| ThomasEgi | they could be made into a thin flat rectangular.bending up and down | 18:27 |
| 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 | 18:28 |
| kanzure | page 77 | 18:30 |
| ThomasEgi | currently looking at page 35 and 36 | 18:31 |
| kanzure | close enough | 18:31 |
| ThomasEgi | what ssize are those lines ? 100μm? | 18:37 |
| 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. | 18:38 |
| 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 -_- | 18:40 |
| ThomasEgi | https://en.wikipedia.org/wiki/File:Piezo_bending_principle.jpg | 18:42 |
| ThomasEgi | theroetically. one could put those cross a line | 18:42 |
| kanzure | i'm familiar with piezos :P | 18:43 |
| ThomasEgi | mhm. well it really introduces some issues if you need to add piezos inbetween the single layers. | 18:44 |
| kanzure | well there's also piezoelectric film. i don't know. | 18:48 |
| ThomasEgi | so creating pneumatic vales seems to be quite ok, but operating them aint? | 18:49 |
| kanzure | well ideally i'd like some electronic-only scheme of course :P | 18:50 |
| 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. | 19:08 |
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| 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 | 19:28 |
| 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? | 19:29 |
| 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 | 19:30 |
| yashgaroth | but the voltage etc. settings are much different | 19:31 |
| yashgaroth | like 100V and 0.5amps at most | 19:33 |
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| 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 | 19:35 |
| 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 | 19:36 |
| yashgaroth | they're mostly paywalled, but http://online.liebertpub.com/doi/pdfplus/10.1089/dna.2005.24.810 for example | 19:37 |
| 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 | 19:38 |
| 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 | 19:39 |
| yashgaroth | I'm still expressing a transgene, yeesh | 19:40 |
| 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 | 19:41 |
| yashgaroth | above 200* | 19:42 |
| 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 | 19:45 |
| 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 | 19:46 |
| 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 | 19:47 |
| yashgaroth | it was easier to type than "the forum kanz dislikes the recruiting practices of" | 19:48 |
| 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 | 19:49 |
| 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 | 19:50 |
| 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 | 19:51 |
| 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 | 19:52 |
| 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 | 19:53 |
| yashgaroth | that works for me | 19:54 |
| 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 | 19:58 |
| 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 | 20:01 |
| 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 | 20:02 |
| ThomasEgi | kicad | 20:03 |
| ThomasEgi | i could even build you a prototype with a usb-serial converter onboard | 20:04 |
| yashgaroth | awesome | 20:06 |
| yashgaroth | wait so you're plugging a PCB in a mains power socket? or is the power supply separate | 20:07 |
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| yashgaroth | actually I have no idea what any of that entails, so you don't need to answer that, I'm just being dumb | 20:10 |
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| ThomasEgi | it can operate on battery power if you need it to. | 20:15 |
| 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) | 20:16 |
| ThomasEgi | i guess i can leave the task of programnning a square-wave genarator up to the software guys^ | 20:17 |
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| kanzure | hi Adifex | 20:17 |
| Adifex | ay | 20:17 |
| ThomasEgi | yashgaroth, http://home.arcor.de/positiveelectron/files/analog-frontent-dna-transfer.png | 20:17 |
| 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 | 20:18 |
| 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 | 20:19 |
| 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) | 20:20 |
| 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 | 20:21 |
| 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 | 20:22 |
| ThomasEgi | yeah. | 20:23 |
| Adifex | what are you discussing? | 20:23 |
| 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 | 20:24 |
| 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. | 20:25 |
| 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 | 20:26 |
| 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 | @_@_@_@_@_@_@_@_@_@_@_@_@_@_@ | 20:27 |
| 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 | 20:28 |
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| 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 | 20:29 |
| 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? | 20:30 |
| 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 | 20:31 |
| 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 | 20:32 |
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| yashgaroth | thomasegi - one, for now | 20:32 |
| 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 | 20:33 |
| 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 | 20:34 |
| kanzure | blue means hybridization | 20:35 |
| kanzure | red is step incrementer | 20:35 |
| kanzure | ? | 20:35 |
| nmz787 | ya | 20:35 |
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| 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 | 20:36 |
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| 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 | 20:37 |
| 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 | 20:38 |
| 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 | 20:39 |
| 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 | 20:40 |
| 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 | 20:41 |
| 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 | 20:42 |
| 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 | 20:43 |
| 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 ;) | 20:44 |
| 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 | 20:45 |
| yashgaroth | I'm perfectly fine with an overnight synthesis | 20:46 |
| nmz787 | i suspect not more than 5-30secs / nt | 20:47 |
| 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 | 20:48 |
| nmz787 | per ligation | 20:49 |
| nmz787 | cycle | 20:49 |
| nmz787 | 12 hrs at 5sec / 6mer is 51.84kb | 20:49 |
| 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 | 20:50 |
| 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 | 20:51 |
| 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 | 20:52 |
| 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 | 20:53 |
| 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 | 20:54 |
| 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 | 20:55 |
| 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) | 20:56 |
| 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) | 20:57 |
| 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 | 20:58 |
| nmz787 | san diego? | 20:59 |
| yashgaroth | yeah | 20:59 |
| nmz787 | first i though south dakota | 20:59 |
| nmz787 | it was a brief thought | 20:59 |
| 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? | 21:00 |
| 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 | 21:01 |
| yashgaroth | it's big for biotech | 21:02 |
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| 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 | 21:04 |
| 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 | 21:05 |
| 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) | 21:06 |
| 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 | 21:07 |
| 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 | 21:09 |
| 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 | 21:10 |
| Mokbortolan_ | err, yes :) | 21:11 |
| Mokbortolan_ | what other rules are there? | 21:11 |
| kanzure | so ATT hybridizes to TAA | 21:11 |
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| nmz787 | almost | 21:12 |
| nmz787 | 5' ATT 3' hybridizes with 3' TAA 5' | 21:12 |
| 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 | 21:13 |
| 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 | 21:14 |
| 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 :( | 21:15 |
| 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 | 21:16 |
| 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 | 21:18 |
| 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 |
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| 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 | 21:19 |
| 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? | 21:20 |
| 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>? | 21:21 |
| 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 | 21:22 |
| 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 | 21:23 |
| 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 | 21:24 |
| 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 | 21:25 |
| 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 | 21:26 |
| Adifex | ah k nvm | 21:27 |
| nmz787 | yashagaroth said vaccinia pol did some recombination like thing | 21:27 |
| ParahSailin | i trap and release rats | 21:27 |
| nmz787 | 15bp similars get ligated | 21:28 |
| nmz787 | or something | 21:28 |
| ParahSailin | right | 21:28 |
| nmz787 | clontech doesnt mention that | 21:28 |
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| 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 | 21:28 |
| 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 | 21:29 |
| 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 | 21:30 |
| nmz787 | hmm | 21:31 |
| 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. | 21:33 |
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| 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 | 21:35 |
| kanzure | until you replace bio-rad as a supplier, suck it | 21:36 |
| yashgaroth | they do make good gels | 21:36 |
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| nmz787 | first one was pretty good | 21:41 |
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| nmz787 | loving the biorad | 21:44 |
| nmz787 | G T C A | 21:44 |
| nmz787 | !!! | 21:44 |
| kanzure | gah what have i done | 21:44 |
| 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 | 21:48 |
| roksprok | is the synthesizer you were talking about using phosphoramidites? | 21:49 |
| nmz787 | no | 21:50 |
| nmz787 | good old natural style oligonucleotides | 21:50 |
| yashgaroth | what about generating the library templates? | 21:51 |
| 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 | 21:52 |
| 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 | 21:53 |
| 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 | 21:54 |
| 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 | 21:55 |
| 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 | 21:56 |
| 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 | 21:57 |
| 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 | 21:58 |
| 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 | 21:59 |
| 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 | 22:00 |
| yashgaroth | minus the nicking enzyme spazzing out during production, it'll be stable | 22:01 |
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| 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 | 22:01 |
| 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 | 22:02 |
| 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 | 22:03 |
| 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 | 22:04 |
| yashgaroth | oh yeah n/m then | 22:05 |
| nmz787 | teh nicking enzyme should produce ssDNA too | 22:05 |
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| nmz787 | ok i'm out for the night | 22:06 |
| nmz787 | ttyl | 22:06 |
| yashgaroth | cya | 22:06 |
| ParahSailin | im not real clear on the scheme still | 22:07 |
| ParahSailin | you want nicking RE to make 6mer with some overhang? | 22:07 |
| nmz787 | uh oh, we need to learn how to make 3D animations of these proteins and shit | 22:08 |
| nmz787 | that would be sweet | 22:09 |
| nmz787 | lata | 22:09 |
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| 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 | 22:09 |
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| yashgaroth | the pol and the nicking enzyme alternate to churn out 6mers | 22:10 |
| 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 | 22:13 |
| 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 | 22:17 |
| yashgaroth | http://diyhpl.us/~bryan/papers2/DNA/enzymaticSynthesisCycle.png | 22:18 |
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| yashgaroth | we're just adding those 6mers onto a growing strand, somewhere else | 22:18 |
| roksprok | so is the idea that you have 4096 of the beads, with every possible 6mer? | 22:22 |
| kanzure | yes | 22:22 |
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| 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 | 22:26 |
| yashgaroth | bottom strand then allows the ligation of the top ones together | 22:27 |
| yashgaroth | then you can skip the PNK enzyme step altogether | 22:29 |
| 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? | 22:31 |
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| yashgaroth | fuck it I'll do my modification of his diagram in powerpoint tomorrow, it'll be a lazy friday anyway | 22:32 |
| Mokbortolan_ | how can I get an NR2B transgenic rat? | 22:43 |
| yashgaroth | like, nr2b knockout? | 22:45 |
| Mokbortolan_ | no, over-expressed | 22:45 |
| kanzure | i think some universities just run a lab for doing transgenic mice for whoever needs them on campus | 22:46 |
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| Mokbortolan_ | "knock-in" | 22:46 |
| kanzure | http://www.nih.gov/science/models/mouse/deltagenlexicon/list.html | 22:47 |
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| yashgaroth | I'm assuming brain-specific expression? | 22:47 |
| Mokbortolan_ | yes | 22:47 |
| 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 | 22:48 |
| 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 | 22:49 |
| Mokbortolan_ | if you're going to buy a pet rat, why not the smartest rat? | 22:50 |
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| 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 | 22:50 |
| 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 | 22:51 |
| 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 | 22:52 |
| 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. | 22:53 |
| yashgaroth | Mok - did you have a specific paper with this nr2b research? | 22:54 |
| 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 | 22:55 |
| 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 | 22:56 |
| yashgaroth | kanzure: did they test those mice for enhanced mental function or do they just have big brains | 22:58 |
| 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 :) | 22:59 |
| yashgaroth | but no I don't think they went on to live healthy lives | 23:00 |
| 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 | 23:02 |
| 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 | 23:03 |
| kanzure | Structure of the cerebral cortex of the humpback whale, Megaptera novaeangliae (Cetacea, Mysticeti, Balaenopteridae).pdf | 23:05 |
| rdb | *yawn* morning all | 23:05 |
| kanzure | sleep is for the weak | 23:06 |
| kanzure | there will be no more of this, sleep, thing. | 23:06 |
| rdb | mk | 23:07 |
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| kanzure | http://www.piccolo.cc/ well, the autonomously-draw-random-forests is a nice feature i guess | 23:20 |
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| kanzure | but why not just use the drawstring-whiteboard-drawing-bots instead | 23:21 |
| yashgaroth | that's the cutest robot I've seen since that one that spews ketchup | 23:22 |
| kanzure | what was it called.. huxbee? | 23:22 |
| rdb | it doesn't look too sturdy to me | 23:23 |
| yashgaroth | automato :D | 23:23 |
| kanzure | you know.. this thing http://www.youtube.com/watch?v=FmCWx30g7Ks | 23:24 |
| kanzure | geeze it needs to use another string for stabilization i think | 23:25 |
| kanzure | maybe not http://www.youtube.com/watch?v=i5rxxGuWUo8 | 23:26 |
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| yashgaroth | time for sleep | 23:37 |
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| --- Log closed Fri Feb 17 00:00:14 2012 | ||
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