| --- Log opened Sat Mar 02 00:00:00 2013 | ||
| --- Day changed Sat Mar 02 2013 | ||
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| @kanzure | On Sat, Mar 2, 2013 at 12:07 AM, Patrik D'haeseleer <patrikd@gmail.com> wrote: | 00:03 |
|---|---|---|
| @kanzure | > Speaking of day-to-day email chatter - mind if we move this discussion over | 00:03 |
| @kanzure | > to the Memberships email list to hash out the details? That's one of the | 00:03 |
| @kanzure | > reasons I set it up for. | 00:03 |
| @kanzure | "members only" on something that isn't particularly important to keep private? | 00:03 |
| @kanzure | strikes me as the wrong way to go about doing things | 00:03 |
| nmz787 | hi | 00:15 |
| nmz787 | what's that? | 00:15 |
| @kanzure | i wonder if it would be economical for biocurious to rent equipment and hire a staffer to do runs on the equipment. | 00:16 |
| @kanzure | that's just a quote from a biocurious email that was sent out, seemed a little strange to me. | 00:16 |
| @kanzure | for whatever reason the biocurious people like to separate things off into tiny subgroups that nobody has access to | 00:16 |
| nmz787 | maybe it's just personal habit? | 00:17 |
| nmz787 | gmail doesn't do filtering to their liking, i dunno | 00:18 |
| @kanzure | or an evil plot to <insert something sinister> | 00:18 |
| @kanzure | also it was funny the other day when jonathan sent out some ideas about the bioprinter | 00:18 |
| @kanzure | and patrik sent back "WHERE IS YOUR VERSION OF THE MACHINE? HUH?" | 00:19 |
| @kanzure | well patrik, you guys only published some drawings to instructables, so basically nowhere because you have specifically chosen an environment not ameniable to outside contributions -_- | 00:19 |
| @kanzure | s/environment/project structure | 00:20 |
| nmz787 | he seemed to rush his response to that terminal tranferase comment i made | 00:20 |
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| @kanzure | maybe he is having to pick up some slack at biocurious that he's not talking about | 00:20 |
| nmz787 | maybe he's uber busy and stressed or something | 00:20 |
| @kanzure | yeah | 00:20 |
| nmz787 | yeah | 00:21 |
| nmz787 | that could be it | 00:21 |
| nmz787 | or filling a management position he didn't intend to | 00:21 |
| nmz787 | if we would've moved to siliValley I think I woulda tried taking up a pretty active role there | 00:21 |
| nmz787 | I could teach all kinds of courses | 00:21 |
| @kanzure | you could just as easily teach courses online | 00:23 |
| @kanzure | does ocw have videos on lab techniques? | 00:24 |
| @kanzure | i don't remember | 00:24 |
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| archels | http://www.hcilab.org/ah2013/program | 01:01 |
| archels | Stuttgart, Germany, I could actually go there | 01:02 |
| archels | € 230.00 for a student ticket though | 01:02 |
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| @kanzure | superkuh: welcome back | 01:04 |
| superkuh | Hello. | 01:04 |
| archels | maybe ##hplusroadmap will sponsor me in exchange for liveblogging? | 01:06 |
| @kanzure | just show up. what are they going to do, kick you out? | 01:07 |
| @kanzure | just say you're one of the speakers (make sure you pick a name in advance), they won't know. | 01:07 |
| archels | that might work if I can get my hands on their name badge templates | 01:09 |
| @kanzure | conferences usually distribute badges at the door | 01:09 |
| archels | that's a bit late for photoshopping my name onto one though | 01:12 |
| archels | oh, I bet a telepresence robot wouldn't get kicked out, even if it wasn't wearing a badge | 01:13 |
| @kanzure | no you don't photoshop your name on it, you tell them your name is one of the speakers', then they give you that name tag | 01:13 |
| @kanzure | then you walk in, and take off the name tag | 01:13 |
| padz | then people will ask where your name tag is | 01:15 |
| @kanzure | padz: have you ever been to a conference? | 01:15 |
| padz | if you have to ask, you already know the answer | 01:15 |
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| nmz787 | i'd also splice human dna with american bison | 02:43 |
| nmz787 | whales and dolphins and maybe giant squid too | 02:44 |
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| streety | I've never been to a conference where the other attendees would ask about a missing name badge but frequently there are staff checking badges at the entrance to the various rooms. | 05:40 |
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| @kanzure | "But I believe a microbubble agent is required as explained in http://en.wikipedia.org/wiki/Sonoporation (I'm rather happy of writing that wikipedia entry 'cause it's one of the few I've written that remained factual/undoctored..)" | 10:05 |
| @kanzure | go jonathan. | 10:05 |
| @kanzure | "Success! Here's a picture of pGLO E.coli colonies under UV light, transformed using the $25 35W 42kHz ultrasonic cleaner I bought to clean the bioprinter cartridges." | 10:06 |
| @kanzure | https://groups.google.com/d/msg/diybio/-/WGPjM3vH07QJ | 10:07 |
| chris_99 | cool, hadn't heard of sonoporation | 10:11 |
| @kanzure | also look up sonoluminescence | 10:12 |
| @kanzure | and sonostimulation | 10:13 |
| chris_99 | i bought transducers for sonoluminesence | 10:13 |
| @kanzure | and shriek, a supervillain who mastered this art :p | 10:13 |
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| @kanzure | so uh, a $25 transformation machine is pretty good. no calcium chloride bullshit, no buffers, no beads. | 10:41 |
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| superkuh | What is "calcium chloride bullshit" in this context? | 10:46 |
| superkuh | Also, awesome. | 10:46 |
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| @kanzure | many transformations require calcium chloride as a step in the preparation for transformation, and i am just expressing general distaste for multiple steps because of how often this means that more things can go wrong, compared to the simplicity of not having to do that. | 10:47 |
| @kanzure | s/preparation for transformation/preparation for competence/ | 10:48 |
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| nmz787 | superkuh: CaCl2 is thought to reduce the negative charge on the DNA and allow it to condense on the surface of the cell | 11:08 |
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| superkuh | Okay. Thanks. It might be of interest that divalent salts reduce the lipid bilayer elasticity. | 11:13 |
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| ParahSailin_ | its magic with probably many different mechanisms | 11:33 |
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| @kanzure | i don't think it's magic, i just think it breaks often. | 11:53 |
| ParahSailin_ | if you want high transformation efficiency, commercial competent cells are great, otherwise you can pretty much do anything with e coli and dna soup and get colonies | 11:56 |
| nmz787 | ParahSailin_: I tried electroporating with two strips of aluminum-adhesive-backed foil on glass microscope slides with crayon drawn between the electrodes... pipetting a line of e coli + plasmid in the middle | 11:58 |
| nmz787 | ParahSailin_: no colonies using a piezo sparker attached | 11:58 |
| nmz787 | ParahSailin_: I seem to remember trying one or two distances apart, and a few different number of discharges | 11:59 |
| ParahSailin_ | acquire cash, buy timesavers | 12:00 |
| nmz787 | is that a high-voltage producing device? | 12:00 |
| ParahSailin_ | no, in general, time-saving expenditures are worth it | 12:01 |
| nmz787 | electroporation is generally a time-saver over heat-shock transformation | 12:02 |
| ParahSailin_ | crayons and aluminum foil not so much | 12:02 |
| nmz787 | it should be | 12:03 |
| nmz787 | the electrodes in the disposable cuvettes look aluminum | 12:03 |
| nmz787 | it was actually a wax pencile, lab-grade | 12:03 |
| nmz787 | i think the decay was probably the main difference | 12:04 |
| ParahSailin_ | you can get a free sample of a cuvette from a place and then clean it every use if you're super poor | 12:05 |
| nmz787 | and maybe the piezo was too rippled compared to a cap discharging | 12:05 |
| nmz787 | i have cuvettes | 12:05 |
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| nmz787 | but Al tape is available everywhere | 12:05 |
| nmz787 | using a cuvette wouldn't solve the discharge problem either | 12:05 |
| chris_99 | i was looking at a simple schematic for an electroporator and the parts came out at $500! | 12:06 |
| nmz787 | I think that's at most 10X too high | 12:07 |
| nmz787 | especially if you just want ecoli | 12:07 |
| chris_99 | high voltage caps are expensive | 12:07 |
| chris_99 | for large farads | 12:08 |
| nmz787 | disposable cameras have them pretty cheap | 12:08 |
| nmz787 | do you need large farads? | 12:08 |
| chris_99 | relatively speaking yes | 12:08 |
| chris_99 | i'll try and find the schematic | 12:08 |
| ParahSailin_ | would a tv capacitor work? | 12:08 |
| nmz787 | gimp takes way too long to startup | 12:09 |
| chris_99 | not that large heh ParahSailin | 12:09 |
| chris_99 | ok got it, 25 µF, 5000 V $120.00 apparently | 12:10 |
| chris_99 | according to the BOM anyway | 12:11 |
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| chris_99 | which is why i'm trying to see if i can just get one 2nd hand | 12:12 |
| ThomasEgi | you sure you need that much capacity? | 12:13 |
| ThomasEgi | i mean... that's more than 300 joules of energy!! | 12:14 |
| chris_99 | one sec, ill link you to the schemati | 12:15 |
| chris_99 | c | 12:15 |
| chris_99 | google "HOMEMADE ELECTROPORATION APPARATUS" and it should be the first .doc | 12:16 |
| ThomasEgi | if you discharge 300 joules into 1 gram of water.. you'd have it boiling instantly. | 12:17 |
| chris_99 | maybe you're forgetting the resistor ;) | 12:17 |
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| docl | nmz787: how's the kombucha coming? | 12:23 |
| ThomasEgi | chris_99, long story short , delivering a constant current for a short duration ? | 12:24 |
| chris_99 | well it'd be an exponential decay wouldn't it over a short time | 12:25 |
| ThomasEgi | yeah in that circuit. but if you only need a constant current at a couple of hundrets volts. it can be done easier | 12:26 |
| chris_99 | i needs to be KV | 12:26 |
| ThomasEgi | how many kV? | 12:26 |
| ThomasEgi | 1, 2 , 5 ? | 12:27 |
| chris_99 | around 2 i think | 12:27 |
| chris_99 | i was thinking the cock-watcroft thingymajig could maybe be used | 12:27 |
| chris_99 | (spelt that wrong probably) | 12:27 |
| ThomasEgi | how much current for what discharge duration is required? | 12:27 |
| chris_99 | it tells you the exact voltages for e. coli etc. in there i think | 12:28 |
| ThomasEgi | bbl. shopping. | 12:28 |
| ThomasEgi | ~20min or so | 12:28 |
| chris_99 | http://en.wikipedia.org/wiki/Cockcroft%E2%80%93Walton_generator was what i was thinking | 12:30 |
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| nmz787 | chris_99: that's also called, more simply, a http://en.wikipedia.org/wiki/Voltage_multiplier | 12:54 |
| nmz787 | they're pretty cheap, $5 in a 12V car ionizer circuits | 12:55 |
| chris_99 | i guess the main expense, is the capacitor that you charge after you've got up to the voltage you need | 12:58 |
| nmz787 | i know the more fancy sets, for people working with finicky or non-ecoli organisms, you can switch the capacitors out to change the time constant (decay time I think) | 13:07 |
| nmz787 | I don't really understand why it's called a time constant | 13:07 |
| chris_99 | T=RC gives you the 'time constant' if i remember correctly | 13:08 |
| ThomasEgi | chris_99, asking once more. what sort of voltage/current curve do you need? | 13:34 |
| ThomasEgi | cause using a non-linear circuit might make it a lot cheaper | 13:35 |
| chris_99 | non-linear circuit? | 13:36 |
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| nmz787 | "Can I transform bacteria or yeast with a square waveform? | 13:44 |
| nmz787 | Yes. While the square waveform is not optimal for bacterial or yeast transformation, it can still | 13:44 |
| nmz787 | transform the cells. That being said, the transformation efficiencies will be lower using the square | 13:44 |
| nmz787 | waveform than with the exponential decay waveform." | 13:44 |
| chris_99 | interesting | 13:44 |
| nmz787 | http://www.btxonline.com/ecm-2001-electroporation-system/ | 13:45 |
| nmz787 | the quote was from http://www.btxonline.com/pages/FAQ.html#d | 13:45 |
| nmz787 | "What is the difference between the square waveform and the exponential decay waveform?" | 13:46 |
| nmz787 | An exponential decay wave is a waveform that is delivered then exponentially decays. This waveform | 13:46 |
| nmz787 | is ideal when transforming bacteria and yeast. With the majority of the current being delivered | 13:46 |
| nmz787 | immediately, the tough cell wall becomes permeable to allow the molecule of interest to enter. | 13:46 |
| nmz787 | The square wave form differs from the exponential decay in the way it is delivered. The square | 13:46 |
| nmz787 | wave pulse actually looks like a square. The benefit to this waveform is that it is better accepted | 13:46 |
| nmz787 | by more delicate cells, such as mammalian cells. The square wave allows a period of homeostasis | 13:46 |
| nmz787 | to be reached in the cells before the wave is removed. As a result, there is a lower mortality rate | 13:46 |
| nmz787 | in cells while maintaining transfection efficiencies. While both waveforms are capable of electroporating | 13:46 |
| nmz787 | bacterial, yeast and mammalian cells, each waveform has its benefits. Exponential decay waves will | 13:46 |
| nmz787 | result in a higher rate of cell mortality in mammalian cells and square waves will result in lower | 13:46 |
| nmz787 | transformation efficiencies in bacteria and yeast. | 13:47 |
| nmz787 | 13:47 | |
| nmz787 | eek | 13:47 |
| chris_99 | i'm gonna email more companies on alibaba see what the cheapest machines go for | 13:47 |
| nmz787 | they don't say the capacitance values ThomasEgi, only Voltage and pulse duration | 13:48 |
| chris_99 | theres cap values in the link i posted before | 13:49 |
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| nmz787 | chris_99: ThomasEgi http://pages.towson.edu/jsaunder/Saunders%20Publications/46.Pulse%20Generators%20for%20Electrofusion%20and%20Electroporation.pdf | 13:52 |
| nmz787 | lists a bunch of tech details for many commercial units | 13:52 |
| nmz787 | apparently I've talked about these details before: https://groups.google.com/forum/?fromgroups=#!topic/diybio/74CGVTQP3VY | 13:54 |
| nmz787 | "We conclude that sex-specific, male-line transgenerational responses exist in humans and hypothesise that these transmissions are mediated by the sex chromosomes, X and Y. Such responses add an entirely new dimension to the study of geneenvironment interactions in development and health." | 13:59 |
| nmz787 | paperbot: http://www.nature.com/ejhg/journal/v14/n2/abs/5201538a.html | 13:59 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Sex-specific%2C%20male-line%20transgenerational%20responses%20in%20humans.pdf | 13:59 |
| nmz787 | http://www.radiolab.org/2012/nov/19/you-are-what-your-grandpa-eats/ | 14:00 |
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| ThomasEgi | chris_99, is there any current going? or is it just a elecrtic field applied with isolated electrodes? | 14:09 |
| chris_99 | you charge the capacitor and then discharge via a resistor | 14:09 |
| chris_99 | that's all i know really | 14:09 |
| chris_99 | and you use a cuvette with a specific distance between electrodes | 14:10 |
| ThomasEgi | are the electrodes isolated? | 14:13 |
| chris_99 | from the capacitor and resistor? | 14:13 |
| chris_99 | if so, it doesn't look like it | 14:14 |
| ThomasEgi | the electrodes of the cuvette | 14:15 |
| chris_99 | they're just connected to the output from the capacitor and resitor directly i thought | 14:15 |
| ThomasEgi | yeah but the question is, are they directly exposed to the content of the cuvette | 14:18 |
| nmz787 | ThomasEgi: current is going | 14:18 |
| nmz787 | ThomasEgi: there is a risk of sparking if the media has too much salt | 14:18 |
| nmz787 | i.e. resistance is too low | 14:18 |
| ThomasEgi | any numbers on typical resistances for those? | 14:19 |
| nmz787 | i recorded some once | 14:20 |
| nmz787 | looking for the paper notebooks now | 14:20 |
| chris_99 | dumb question, could a microwave 'pierce' the cell walls | 14:20 |
| ThomasEgi | they'll just go through with no real effect | 14:20 |
| ThomasEgi | other than heating the water up. | 14:21 |
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| chris_99 | mm, yeah | 14:21 |
| ThomasEgi | they are alternating too fast for anything to move other than jittering around | 14:21 |
| nmz787 | 80 uL dH20 0.714 MOhm | 14:23 |
| nmz787 | LB broth ~34 KOHm | 14:23 |
| chris_99 | this sonoporation thing seems like the idea solution then for cost effectiveness? | 14:23 |
| nmz787 | LB+2 Day overnight culture + DL39 growth (i dunno if that's a plasmid) ~34 K Ohm | 14:24 |
| nmz787 | chris_99: maybe, it would need optimized a lot more to be really cool | 14:24 |
| nmz787 | as it stands, I think MgS04 and PEG is probably cheaper | 14:24 |
| nmz787 | sonoporation is less steps though | 14:25 |
| chris_99 | what method is that sorry? | 14:25 |
| chris_99 | and what's PEG | 14:25 |
| nmz787 | poly ethylene glycol | 14:25 |
| nmz787 | (all one molecule) | 14:25 |
| nmz787 | it's used for molecular crowding | 14:26 |
| nmz787 | basically they're really big long molecules that whip around in soluiton | 14:26 |
| nmz787 | ThomasEgi: another few readings ashould 45-62 K Ohm | 14:27 |
| chris_99 | https://github.com/cathalgarvey/biohacking-protocols/blob/master/E.coli%20Transformation%20With%20PEG%2BMgSO4.md | 14:27 |
| chris_99 | just found that | 14:27 |
| chris_99 | looks cool | 14:27 |
| ThomasEgi | nmz787, and the pulse is like 25μs long? | 14:28 |
| chris_99 | could i use that method with yeast nmz787? | 14:28 |
| nmz787 | ThomasEgi: seems like 1-99 us is common range | 14:28 |
| ParahSailin_ | how do i embed tricky stuff in a pdf to dial home when someone i send my resume to opens it | 14:28 |
| chris_99 | haha | 14:28 |
| nmz787 | chris_99: I'm not sure, you'd need to check google scholar | 14:28 |
| chris_99 | yeah i'll have a look | 14:28 |
| nmz787 | chris_99: for yeast i've heard electroporation or protoplast generation then heat shock | 14:29 |
| nmz787 | they might call them something besides protoplasts | 14:29 |
| nmz787 | but it involves some kind of lithium usually | 14:29 |
| ThomasEgi | nmz787, in that case. properly done. a CW generator, or a simply flyback and a couple of smaller/cheaper caps should do, with a thyristor or igbt for triggering | 14:30 |
| chris_99 | yeah, you can get that from batteries | 14:30 |
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| chris_99 | the problem is ThomasEgi is it looks like the cap you charge is expensive | 14:30 |
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| ThomasEgi | chris_99, it's ways too big. | 14:31 |
| nmz787 | ThomasEgi: I'd love a skeleton BOM and schematic if you ever have free time | 14:32 |
| ThomasEgi | if the resistance really ranges in the 2digit kOhm range. with 20 to 100μs pulse duration. you can get with a capacitor that's only a 1000th of the size | 14:32 |
| nmz787 | you should be able to easily tune the resistance with media/buffer/dH20 | 14:33 |
| nmz787 | chris_99: the lithium is probably pretty specific, not sure it would be easy to generate a protocol from battery juice | 14:33 |
| nmz787 | battery innards* | 14:34 |
| chris_99 | heh, yeah, people also use it for crystal meth apparently too, so it must react somewhat i imagine | 14:34 |
| chris_99 | maybe if i soaked it in acid to clean it | 14:35 |
| nmz787 | recently i heard meth mouth (teeth/jaw/bone/soft-tissue loss, etc) isn't caused by meth smoking itself | 14:35 |
| ThomasEgi | if you go with a CW generator , given you can run it at like 100kHz, you can get away with even less capacitance. my guess would be 2digit nF range. which sells for just a few bucks even with like 6kV rating | 14:35 |
| nmz787 | rather it's the impurities | 14:35 |
| nmz787 | so good chems def matter even in meth world | 14:35 |
| chris_99 | haha interesting | 14:35 |
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| nmz787 | i think that's the same reason krocodil is so bad for russians | 14:36 |
| nmz787 | http://en.wikipedia.org/wiki/Desomorphine#.22Krokodil.22 | 14:36 |
| chris_99 | time for bed, toodles | 14:36 |
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| nmz787 | "Since the home-made mix is routinely injected immediately with little or no further purification, "krokodil" has become notorious for producing severe tissue damage, phlebitis and gangrene, sometimes requiring limb amputation in long-term users" | 14:37 |
| nmz787 | -100 for Hplus | 14:37 |
| nmz787 | :( | 14:37 |
| nmz787 | or DIY | 14:37 |
| nmz787 | both kindof | 14:37 |
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| ThomasEgi | nmz787, building a CW generator for starters won't hurt you can always use it to charge a capacitor bank. in wrost case, you can wire them in series to increase the max voltage, it reduces capacity but you can work with cheaper parts. | 14:39 |
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| ThomasEgi | nmz787, like you can get foil caps. you can get 2kV caps. 47nF , 3 in series. resulting in 6kV total at bout 15nF. with a 30kOhm cuvette that'd give you a discharge decay time of 450μS (discharge by 63%) | 14:45 |
| ThomasEgi | with those 3 caps costing no more than 5 bucks in total | 14:45 |
| ThomasEgi | if that shouldnt be enough, you can parallel cap rows. if it is too much , you can parallel a resistor in parallel to the cuvette | 14:47 |
| ThomasEgi | a couple of regular resistors in series (to deal with the high voltage) should be enough. there should be no need for expensive 10W caps | 14:48 |
| ThomasEgi | not sure why those commercial devices have so overrated capacitors. unlike those liquids suddenly start getting very conductive at a certain point | 14:55 |
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| @kanzure | ParahSailin_: depends on the version of pdf, but more or less you just open the file and add a new pdfstream object with no encoding (just ascii text) stating your javascript. i think it might have to be "bound" somewhere but i'm not sure. | 15:13 |
| @fenn | seems like the capacitor size is related to the cuvette volume | 15:21 |
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| delinquentme | cheap microfluidics http://www.the-scientist.com/?articles.view/articleNo/34442/title/Sticky-Lithography/ | 15:23 |
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| ThomasEgi | another idea would be to use a big inductor, and use that as a one-shot-step-up converter | 15:24 |
| @fenn | like a gasoline engine ignition system | 15:26 |
| @fenn | you still generally need a beefy capacitor to charge the inductor (for flyback effect) | 15:26 |
| ParahSailin_ | how big is a tv capacitor | 15:27 |
| ParahSailin_ | from like the old xray kind | 15:27 |
| @fenn | i dont remember finding any physically large capacitors in crt's i've taken apart | 15:28 |
| ParahSailin_ | its part of the tube | 15:29 |
| @fenn | part of the tube? | 15:29 |
| @fenn | what's the function of it | 15:29 |
| ParahSailin_ | making electrons go fasta | 15:33 |
| @fenn | the acceleration grid's not a very good capacitor because there's no dielectric | 15:36 |
| ThomasEgi | fenn, actually. a constant current would do just fine to "charge" the inductor | 15:39 |
| ThomasEgi | and then cut the current off. | 15:39 |
| @fenn | point taken | 15:41 |
| @fenn | what's the 200V electrolytic capacitor in TV's for? is it just a wall mains power supply? | 15:41 |
| ThomasEgi | there are so many uses of electrolytic caps in tv's | 15:42 |
| ThomasEgi | you could get a bunch of regular electrolytic caps tho. some are rated up to 450V | 15:43 |
| ThomasEgi | with 5 in series you can still get pretty decent max voltages. while maintaining 2-digit μF ratings | 15:43 |
| ThomasEgi | would cost like 15bucks in total or so. | 15:44 |
| ThomasEgi | if you get them brand new | 15:44 |
| @fenn | you still need to switch the ~2kV output though, better to use an inductor so you dont need a thyratron or something silly like that | 15:45 |
| @fenn | with inductor you're only switching at low voltage | 15:46 |
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| ThomasEgi | not sure what'd be so bad about switching high voltage tho | 15:49 |
| @fenn | how would you do it? | 15:50 |
| ThomasEgi | magnetic reed switch | 15:50 |
| ThomasEgi | they make up to 10kV | 15:50 |
| ThomasEgi | thyristors would be another option | 15:54 |
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| nmz787 | ThomasEgi: how did you go from 6kV 15nF and 30K kOhm to 450 uSec? | 16:11 |
| ThomasEgi | simple rc-element. time constant is R*C which is 15nF*30kOhm | 16:12 |
| ThomasEgi | giving me 450uS flat, and after each 450uS there'll be 63% less Voltage remaining. | 16:13 |
| nmz787 | T is in seconds? | 16:13 |
| ThomasEgi | of course. what else do you messure time in? | 16:14 |
| ThomasEgi | i meanj check the units. it's ohm*farrad. or V/A*As/V | 16:14 |
| nmz787 | cool | 16:14 |
| nmz787 | that's easy math | 16:14 |
| nmz787 | why 63% charge? | 16:15 |
| ThomasEgi | e function | 16:15 |
| nmz787 | 1 std dev is 68% | 16:15 |
| ThomasEgi | remaining voltage = startvoltage *e(-t/tau) | 16:15 |
| ThomasEgi | and tau = R*C | 16:16 |
| nmz787 | -t? | 16:16 |
| nmz787 | ahh time | 16:16 |
| nmz787 | cool | 16:16 |
| ThomasEgi | but | 16:16 |
| nmz787 | isn't e a constant? | 16:16 |
| ThomasEgi | this only works under the assumption that the cuvette is linear | 16:16 |
| ThomasEgi | what a? | 16:16 |
| ThomasEgi | oh yeah | 16:16 |
| ThomasEgi | e is e :D | 16:16 |
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| ThomasEgi | which is pretty much where the 63% decay comes in. as e^-1 is bout -.36 (what's remaining) | 16:19 |
| nmz787 | so at 450uSec wouldn't the right hand side = .36 | 16:19 |
| nmz787 | not .63 | 16:19 |
| ThomasEgi | well it loses 63% of the voltage | 16:19 |
| ThomasEgi | so about 36% are left | 16:19 |
| nmz787 | ahh | 16:19 |
| nmz787 | hmm | 16:19 |
| ThomasEgi | the question would be, does the liquid behave like a ohmian resistor. or has it some pretty nasty nonlinear properties | 16:20 |
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| nmz787 | hmm | 16:21 |
| @fenn | it's more like a capacitor with series resistance, if you're looking at it from a high frequency perspective | 16:21 |
| nmz787 | well seems you'd need less nF | 16:21 |
| nmz787 | since the time constant in literature is like 1-99 | 16:21 |
| nmz787 | 100pF to 3000pF would yield T 3 to 90 | 16:23 |
| nmz787 | do they make kV pF caps? | 16:23 |
| superkuh | Yes. It is easy to do so yourself as well. | 16:24 |
| ThomasEgi | most kV caps range between a couple of pF and single digit nF | 16:24 |
| ThomasEgi | you probably wan't to have some spare-capacity left. to not get affected by stray capacities too much | 16:29 |
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| ThomasEgi | you may want to look for foil caps. they often go up to 1600 or even 2000V. with 2 or 3 in series you can get where you need to go. (of course putting them in series cuts down the capacity accordingly) | 16:31 |
| ThomasEgi | they sell for 30 cent each or so | 16:31 |
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| abetusk | evening all | 16:51 |
| abetusk | has anyone had any success or experience with making graphene at a hobbyist level? | 16:52 |
| @kanzure | tape + graphite | 16:53 |
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| abetusk | and then a silicon plate and a microscope to find the appropriate sheets... | 16:59 |
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| docl | abetusk: there is also supposed to be a method involving a DVD player. | 18:31 |
| abetusk | yeah, it's making the rounds. I was hoping to see someone who's done something comparable at the DIY level | 18:32 |
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| @kanzure | stormyra: hello | 20:08 |
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| nmz787 | docl: I haven't checked the kombucha since adding it to fresh media | 20:45 |
| nmz787 | docl: but it's sitting covered on top of my fridge... so we'll see how it goes | 20:45 |
| nmz787 | docl: worst case, if it's contaminated at all, I'll just keep subculturing until the contamination goes away... assuming kombucha can outcompete most other stuff | 20:46 |
| docl | Probably forming a thin layer by now. | 20:46 |
| docl | It's pretty hardy. I've cultured it from kombucha beverage from the store. | 20:47 |
| @fenn | once it gets moldy it usually stays moldy | 20:49 |
| docl | Hmm. I think I've killed mold and saved the kombucha by pouring vinegar on it. It's been a while so I could be misremembering. | 20:52 |
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| @kanzure | yashgaroth: report? | 21:18 |
| yashgaroth | ? | 21:18 |
| @kanzure | didn't feel like saying sup this time | 21:18 |
| yashgaroth | oh yeah give me a few minutes | 21:18 |
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| yashgaroth | mmkay so I'm switching jobs, today was the last day at my old place, start at the new one on the 11th | 21:25 |
| yashgaroth | which gives me a full week of faffing about | 21:25 |
| @kanzure | new one is the startup? | 21:25 |
| yashgaroth | nope, some other company that does medical test devices using antibodies - I will be making the antibodies | 21:26 |
| @kanzure | isn't this the job of a robot | 21:26 |
| yashgaroth | 20% payrise, 2nd shift | 21:26 |
| @kanzure | 2nd shift antibodies heh | 21:26 |
| yashgaroth | nah there's still a lot of manual crap to do, moving hoses and whatnot I don't know they pay me so whatevs | 21:26 |
| @kanzure | "3rd shift antibodies" would be a neat company name | 21:27 |
| yashgaroth | also the place I'm leaving has supplied me with all the materials I need | 21:27 |
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| @kanzure | paperbot :( | 21:27 |
| yashgaroth | picked up 24 kilos of Tris this week, among other things | 21:27 |
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| yashgaroth | re the carlsbad lab, we have vinyl flooring down in the 'cell culture lab', and while we have another volunteer to help with the website, I offered your help | 21:28 |
| @kanzure | alright | 21:28 |
| yashgaroth | so feel free to djanguby the site and let us know | 21:28 |
| @kanzure | it's not exactly hard to make something better than what biocurious/genspace has heh | 21:29 |
| yashgaroth | biocurious especially | 21:30 |
| @kanzure | geocities version of biocurious | 21:30 |
| @kanzure | :blink: PLASMIDS :blink: | 21:30 |
| yashgaroth | what's the term for traumatizing nostalgia | 21:30 |
| yashgaroth | also jcline wants to make seaweed that produces vitamin B12, because vegans apparently | 21:31 |
| @kanzure | well, what does the pathway look like? | 21:34 |
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| yashgaroth | I dunno there's some enzymes and shit, but there's probably a good reason it's only made in prokaryotes, like how nitrogen fixation is prok-only | 21:35 |
| nmz787 | kanzure: i like the sound of that | 21:35 |
| nmz787 | this chat room doesn't interpret :BLINK: | 21:35 |
| nmz787 | lame | 21:35 |
| nmz787 | what kind of chat room is this | 21:35 |
| yashgaroth | I discussed the more realistic microplate+liquid handler dna synthesizer plan with him as well, he is interested | 21:35 |
| nmz787 | is seaweed prok? | 21:36 |
| @kanzure | by interested you mean "willing to do work" ? | 21:36 |
| yashgaroth | one hopes/assumes | 21:36 |
| yashgaroth | seaweed is euk I thought | 21:36 |
| yashgaroth | he expressed concerns about robots handling sub-microliter volumes, and also evaporation, which was useful | 21:37 |
| @kanzure | geneart apparently only uses tecan machines to do their dna synthesis | 21:37 |
| @kanzure | or possibly their own custom liquid-moving machines. | 21:38 |
| @kanzure | but the point is, nothing fancy. | 21:38 |
| yashgaroth | they seem to be the standard, debugging your own DIY version would be a big hassle | 21:38 |
| nmz787 | kanzure: what is this ? http://issuu.com/bbiinternational/docs/jan.feb.13_bdm?mode=window | 21:38 |
| @kanzure | jonathan has already done that for us | 21:38 |
| @kanzure | http://cpansearch.perl.org/src/JCLINE/Robotics-0.23/lib/Robotics/Tecan/Genesis.pm | 21:39 |
| yashgaroth | well he's reverse-engineering a tecan, I mean building your own robot out of capacitors and servos and all that EE shit | 21:39 |
| @kanzure | nmz787: flash | 21:39 |
| nmz787 | ahh | 21:39 |
| @kanzure | yashgaroth: servos aren't that hard, compared to the power engineering stuff EEs put up with | 21:39 |
| nmz787 | yes it's crashing on me | 21:40 |
| yashgaroth | well I hope to have jcline to deal with all those words | 21:40 |
| nmz787 | jcline mentioned polar systems too | 21:40 |
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| nmz787 | with the right DC motor you can get insane precision on a rotating stage | 21:40 |
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| nmz787 | especiallyjust using back EMF sensing which is like 1 IC | 21:41 |
| nmz787 | to keep the current stable | 21:41 |
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| @kanzure | nmz787: it loads http://issuu.com/bbiinternational/docs/jan.feb.13_bdm | 21:43 |
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| @kanzure | pasky_: welcome back | 21:43 |
| @kanzure | oh hm | 21:43 |
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| @kanzure | haha what "“Grinders” adhere to an anarchist strain of biopunk that emphasizes non-hierarchical science and DIY" | 21:52 |
| @kanzure | because biopunks aren't anarchist? what a load of crap.. | 21:52 |
| @kanzure | i see that grindhouse has spammed http://en.wikipedia.org/wiki/Biohacking | 21:52 |
| @kanzure | they even have an explicit link to their site | 21:52 |
| @kanzure | and they link to a faq with 3 questions -_- | 21:52 |
| @kanzure | these guys are the worst and don't believe in the existing community. | 21:52 |
| @kanzure | citing their own website as a source is just poor form, too. | 21:52 |
| @kanzure | i don't even know how to fix this. | 21:52 |
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| nmz787 | kanzure: get that Michael guy on it | 21:57 |
| nmz787 | turner i think | 21:58 |
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| yashgaroth | kanzure: I'll talk to them, but holy shit that is pretty blatant | 22:03 |
| @kanzure | but not only is it blatant.. it's also wrong on so many levels (factually (their distinction between diybio/biohacking/biopunk is meaningless)), by wikipediamanship (advertising yourself is a no-no), citation policy (third party sources of merit, like some scholarly articles are okay), etc.. | 22:05 |
| yashgaroth | who the hell is Hzh..."grinder" mentioned 13 times on the page...who the fuck is dave asprey...this is worse than I thought | 22:10 |
| @kanzure | dave asprey spammed the page a long long time ago, i went in and cleaned things up a bit with citations and legible sentences but.. | 22:11 |
| yashgaroth | what's the protocol for having a wikipedia article just razed to the fucking ground, because that might be the best option at this point | 22:12 |
| @kanzure | there's been an on-going issue with the articles on biohacking, diybio and biopunk | 22:12 |
| @kanzure | i've argued that they need to be merged | 22:13 |
| @kanzure | but the biopunk article has a history on wikipedia of being an article about biopunk (in science fiction) | 22:13 |
| @kanzure | http://en.wikipedia.org/wiki/Talk:DIYbio | 22:13 |
| @kanzure | http://en.wikipedia.org/wiki/Talk:Biopunk | 22:13 |
| yashgaroth | those two are fine, but the word 'biohacking' means almost as little as 'hacker' does these days, perhaps fittingly, but still aggravating | 22:14 |
| @kanzure | i went to the trouble of making a huge list of wikipedia-usable citations | 22:15 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/citations.txt | 22:15 |
| @kanzure | but nobody has bothered to write an actual article based on this | 22:15 |
| yashgaroth | can't we just raze everything, that seems easier | 22:18 |
| @kanzure | well, an article still needs to be written at some point i think | 22:18 |
| @kanzure | otherwise this will keep happening | 22:18 |
| @kanzure | ideally we would have some neutral third party person who would want to write a good article | 22:18 |
| yashgaroth | ha | 22:18 |
| nmz787 | oO it says lepht is 'her' | 22:21 |
| nmz787 | tell lepht that it misrepresents them | 22:25 |
| nmz787 | yashgaroth: you lived in portland for some time right? | 22:26 |
| yashgaroth | nope, seattle | 22:26 |
| nmz787 | yashgaroth: what should I do/see if I go back there again? | 22:27 |
| yashgaroth | ummmmm well the underground tour is pretty good, also marijuana I guess | 22:28 |
| nmz787 | I found a joint on the ground in a dispensary baggy the last time I was there, it was like a week after the new law passed | 22:29 |
| yashgaroth | yeah I've found weed on the sidewalk there, that's seattle for you | 22:29 |
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| abetusk | https://www.youtube.com/watch?v=p_JpPMIriAI | 22:36 |
| @kanzure | .title | 22:36 |
| yoleaux | Cybernetics for the Masses - 27C3 - YouTube | 22:36 |
| @kanzure | ugh | 22:36 |
| @kanzure | no thanks, we've already had enough lepht for one lifetime. | 22:36 |
| abetusk | have you talked to her before? | 22:37 |
| @kanzure | yes | 22:37 |
| @kanzure | "If the design needs a chip-to-chip communication method more than 10 cm it should use a differential voltage physical layer (ethernet Ok). Otherwise the motors will induce glitches. This and other reasons is why industrial/automotive/lab equipment typically uses CAN bus (which is basically a fancy multi-device UART). It is better with a multi-component system in prototyping phase to have probe points in between each module which provide ... | 22:39 |
| @kanzure | ... easy-to-read debug output - this includes points for bus sniffing which spit out readable data, as opposed to hard-to-decypher data (ethernet not Ok). If boards are going to be linked together in series then the communication method should best be daisy chainable (ethernet not Ok, CAN Ok). " | 22:39 |
| @kanzure | "128 kB because? The motor control algorithms take a whopping 4 kB and need plenty of room to grow I guess! (Focus on simplicity of parts, not $ cost of memory.) Limits of hardware is not the problem, getting good developers usually is. With poor developers it's best to make their project area small and well defined. (Tiny memory, tiny algorithms, and small isolated components that have all outputs well tested under all input conditions.)" | 22:39 |
| @kanzure | hah | 22:40 |
| @kanzure | still waiting to see what his response is going to be to my "computers everywhere" ideology. | 22:43 |
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