--- Log opened Sat Mar 02 00:00:00 2013
--- Day changed Sat Mar 02 2013
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00:03 <@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
00:15 < nmz787> hi
00:15 < nmz787> what's that?
00:16 <@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
00:17 < nmz787> maybe it's just personal habit?
00:18 < 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
00:19 <@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 -_-
00:20 <@kanzure> s/environment/project structure
00:20 < nmz787> he seemed to rush his response to that terminal tranferase comment i made
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00:20 <@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
00:21 < 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
00:23 <@kanzure> you could just as easily teach courses online
00:24 <@kanzure> does ocw have videos on lab techniques?
00:24 <@kanzure> i don't remember
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01:01 < archels> http://www.hcilab.org/ah2013/program
01:02 < archels> Stuttgart, Germany, I could actually go there
01:02 < archels> € 230.00 for a student ticket though
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01:04 <@kanzure> superkuh: welcome back
01:04 < superkuh> Hello.
01:06 < archels> maybe ##hplusroadmap will sponsor me in exchange for liveblogging?
01:07 <@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.
01:09 < 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
01:12 < archels> that's a bit late for photoshopping my name onto one though
01:13 < 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
01:15 < 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
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02:43 < nmz787> i'd also splice human dna with american bison
02:44 < nmz787> whales and dolphins and maybe giant squid too
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05:40 < 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.
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10:05 <@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.
10:06 <@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."
10:07 <@kanzure> https://groups.google.com/d/msg/diybio/-/WGPjM3vH07QJ
10:11 < chris_99> cool, hadn't heard of sonoporation
10:12 <@kanzure> also look up sonoluminescence
10:13 <@kanzure> and sonostimulation
10:13 < chris_99> i bought transducers for sonoluminesence
10:13 <@kanzure> and shriek, a supervillain who mastered this art :p
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10:41 <@kanzure> so uh, a $25 transformation machine is pretty good. no calcium chloride bullshit, no buffers, no beads.
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10:46 < superkuh> What is "calcium chloride bullshit" in this context?
10:46 < superkuh> Also, awesome.
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10:47 <@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.
10:48 <@kanzure> s/preparation for transformation/preparation for competence/
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11:08 < nmz787> superkuh: CaCl2 is thought to reduce the negative charge on the DNA and allow it to condense on the surface of the cell
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11:13 < superkuh> Okay. Thanks. It might be of interest that divalent salts reduce the lipid bilayer elasticity.
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11:33 < ParahSailin_> its magic with probably many different mechanisms
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11:53 <@kanzure> i don't think it's magic, i just think it breaks often.
11:56 < 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
11:58 < 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
11:59 < nmz787> ParahSailin_: I seem to remember trying one or two distances apart, and a few different number of discharges
12:00 < ParahSailin_> acquire cash, buy timesavers
12:00 < nmz787> is that a high-voltage producing device?
12:01 < ParahSailin_> no, in general, time-saving expenditures are worth it
12:02 < nmz787> electroporation is generally a time-saver over heat-shock transformation
12:02 < ParahSailin_> crayons and aluminum foil not so much
12:03 < 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
12:04 < nmz787> i think the decay was probably the main difference
12:05 < 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
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12:05 < nmz787> but Al tape is available everywhere
12:05 < nmz787> using a cuvette wouldn't solve the discharge problem either
12:06 < chris_99> i was looking at a simple schematic for an electroporator and the parts came out at $500!
12:07 < 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
12:08 < 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?
12:09 < nmz787> gimp takes way too long to startup
12:09 < chris_99> not that large heh ParahSailin
12:10 < chris_99> ok got it, 25 µF, 5000 V $120.00 apparently
12:11 < chris_99> according to the BOM anyway
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12:12 < chris_99> which is why i'm trying to see if i can just get one 2nd hand
12:13 < ThomasEgi> you sure you need that much capacity?
12:14 < ThomasEgi> i mean... that's more than 300 joules of energy!!
12:15 < chris_99> one sec, ill link you to the schemati
12:15 < chris_99> c
12:16 < chris_99> google "HOMEMADE ELECTROPORATION APPARATUS" and it should be the first .doc
12:17 < 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 ;)
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12:23 < docl> nmz787: how's the kombucha coming?
12:24 < ThomasEgi> chris_99, long story short , delivering a constant current for a short duration ?
12:25 < chris_99> well it'd be an exponential decay wouldn't it over a short time
12:26 < 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?
12:27 < 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?
12:28 < 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
12:30 < chris_99> http://en.wikipedia.org/wiki/Cockcroft%E2%80%93Walton_generator was what i was thinking
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12:54 < nmz787> chris_99: that's also called, more simply, a http://en.wikipedia.org/wiki/Voltage_multiplier
12:55 < nmz787> they're pretty cheap, $5 in a 12V car ionizer circuits
12:58 < chris_99> i guess the main expense, is the capacitor that you charge after you've got up to the voltage you need
13:07 < 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
13:08 < chris_99> T=RC gives you the 'time constant' if i remember correctly
13:34 < ThomasEgi> chris_99, asking once more. what sort of voltage/current curve do you need?
13:35 < ThomasEgi> cause using a non-linear circuit might make it a lot cheaper
13:36 < chris_99> non-linear circuit?
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13:44 < 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
13:45 < nmz787> http://www.btxonline.com/ecm-2001-electroporation-system/
13:45 < nmz787> the quote was from http://www.btxonline.com/pages/FAQ.html#d
13:46 < 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
13:47 < 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
13:48 < nmz787> they don't say the capacitance values ThomasEgi, only Voltage and pulse duration
13:49 < chris_99> theres cap values in the link i posted before
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13:52 < 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
13:54 < nmz787> apparently I've talked about these details before: https://groups.google.com/forum/?fromgroups=#!topic/diybio/74CGVTQP3VY
13:59 < 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
14:00 < nmz787> http://www.radiolab.org/2012/nov/19/you-are-what-your-grandpa-eats/
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14:09 < 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
14:10 < chris_99> and you use a cuvette with a specific distance between electrodes
14:13 < ThomasEgi> are the electrodes isolated?
14:13 < chris_99> from the capacitor and resistor?
14:14 < chris_99> if so, it doesn't look like it
14:15 < 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
14:18 < 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
14:19 < ThomasEgi> any numbers on typical resistances for those?
14:20 < 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
14:21 < ThomasEgi> other than heating the water up.
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14:21 < chris_99> mm, yeah
14:21 < ThomasEgi> they are alternating too fast for anything to move other than jittering around
14:23 < 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?
14:24 < 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
14:25 < 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)
14:26 < nmz787> it's used for molecular crowding
14:26 < nmz787> basically they're really big long molecules that whip around in soluiton
14:27 < 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
14:28 < 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
14:29 < 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
14:30 < 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
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14:30 < chris_99> the problem is ThomasEgi is it looks like the cap you charge is expensive
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14:31 < ThomasEgi> chris_99, it's ways too big.
14:32 < 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
14:33 < 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
14:34 < 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
14:35 < 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
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14:36 < 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
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14:37 < 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
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14:39 < 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.
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14:45 < 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
14:47 < 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
14:48 < 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
14:55 < ThomasEgi> not sure why those commercial devices have so overrated capacitors. unlike those liquids suddenly start getting very conductive at a certain point
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15:13 <@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.
15:21 <@fenn> seems like the capacitor size is related to the cuvette volume
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15:23 < delinquentme> cheap microfluidics http://www.the-scientist.com/?articles.view/articleNo/34442/title/Sticky-Lithography/
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15:24 < ThomasEgi> another idea would be to use a big inductor, and use that as a one-shot-step-up converter
15:26 <@fenn> like a gasoline engine ignition system
15:26 <@fenn> you still generally need a beefy capacitor to charge the inductor (for flyback effect)
15:27 < ParahSailin_> how big is a tv capacitor
15:27 < ParahSailin_> from like the old xray kind
15:28 <@fenn> i dont remember finding any physically large capacitors in crt's i've taken apart
15:29 < ParahSailin_> its part of the tube
15:29 <@fenn> part of the tube?
15:29 <@fenn> what's the function of it
15:33 < ParahSailin_> making electrons go fasta
15:36 <@fenn> the acceleration grid's not a very good capacitor because there's no dielectric
15:39 < ThomasEgi> fenn, actually. a constant current would do just fine to "charge" the inductor
15:39 < ThomasEgi> and then cut the current off.
15:41 <@fenn> point taken
15:41 <@fenn> what's the 200V electrolytic capacitor in TV's for? is it just a wall mains power supply?
15:42 < ThomasEgi> there are so many uses of electrolytic caps in tv's
15:43 < 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
15:44 < ThomasEgi> would cost like 15bucks in total or so.
15:44 < ThomasEgi> if you get them brand new
15:45 <@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
15:46 <@fenn> with inductor you're only switching at low voltage
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15:49 < ThomasEgi> not sure what'd be so bad about switching high voltage tho
15:50 <@fenn> how would you do it?
15:50 < ThomasEgi> magnetic reed switch
15:50 < ThomasEgi> they make up to 10kV
15:54 < ThomasEgi> thyristors would be another option
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16:11 < nmz787> ThomasEgi: how did you go from 6kV 15nF and 30K kOhm to 450 uSec?
16:12 < ThomasEgi> simple rc-element. time constant is R*C which is 15nF*30kOhm
16:13 < ThomasEgi> giving me 450uS flat, and after each 450uS there'll be 63% less Voltage remaining.
16:13 < nmz787> T is in seconds?
16:14 < 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
16:15 < 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)
16:16 < 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
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16:19 < 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
16:20 < ThomasEgi> the question would be, does the liquid behave like a ohmian resistor. or has it some pretty nasty nonlinear properties
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16:21 < 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
16:23 < nmz787> 100pF to 3000pF would yield T 3 to 90
16:23 < nmz787> do they make kV pF caps?
16:24 < 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
16:29 < ThomasEgi> you probably wan't to have some spare-capacity left. to not get affected by stray capacities too much
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16:31 < 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
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16:51 < abetusk> evening all
16:52 < abetusk> has anyone had any success or experience with making graphene at a hobbyist level?
16:53 <@kanzure> tape + graphite
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16:59 < abetusk> and then a silicon plate and a microscope to find the appropriate sheets...
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18:31 < docl> abetusk: there is also supposed to be a method involving a DVD player.
18:32 < abetusk> yeah, it's making the rounds.  I was hoping to see someone who's done something comparable at the DIY level
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20:08 <@kanzure> stormyra: hello
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20:45 < 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
20:46 < 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.
20:47 < docl> It's pretty hardy. I've cultured it from kombucha beverage from the store.
20:49 <@fenn> once it gets moldy it usually stays moldy
20:52 < 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.
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21:18 <@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
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21:25 < 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?
21:26 < 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
21:27 <@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
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21:27 <@kanzure> paperbot :(
21:27 < yashgaroth> picked up 24 kilos of Tris this week, among other things
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21:28 < 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
21:29 <@kanzure> it's not exactly hard to make something better than what biocurious/genspace has heh
21:30 < 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
21:31 < yashgaroth> also jcline wants to make seaweed that produces vitamin B12, because vegans apparently
21:34 <@kanzure> well, what does the pathway look like?
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21:35 < 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
21:36 < 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
21:37 < 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
21:38 <@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
21:39 <@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
21:40 < 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
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21:40 < nmz787> with the right DC motor you can get insane precision on a rotating stage
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21:41 < nmz787> especiallyjust using back EMF sensing which is like 1 IC
21:41 < nmz787> to keep the current stable
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21:43 <@kanzure> nmz787: it loads http://issuu.com/bbiinternational/docs/jan.feb.13_bdm
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21:43 <@kanzure> pasky_: welcome back
21:43 <@kanzure> oh hm
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21:52 <@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.
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21:57 < nmz787> kanzure: get that Michael guy on it
21:58 < nmz787> turner i think
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22:03 < yashgaroth> kanzure: I'll talk to them, but holy shit that is pretty blatant
22:05 <@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..
22:10 < 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
22:11 <@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..
22:12 < 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
22:13 <@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
22:14 < yashgaroth> those two are fine, but the word 'biohacking' means almost as little as 'hacker' does these days, perhaps fittingly, but still aggravating
22:15 <@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
22:18 < 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
22:21 < nmz787> oO it says lepht is 'her'
22:25 < nmz787> tell lepht that it misrepresents them
22:26 < nmz787> yashgaroth: you lived in portland for some time right?
22:26 < yashgaroth> nope, seattle
22:27 < nmz787> yashgaroth: what should I do/see if I go back there again?
22:28 < yashgaroth> ummmmm well the underground tour is pretty good, also marijuana I guess
22:29 < 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
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22:36 < 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.
22:37 < abetusk> have you talked to her before?
22:37 <@kanzure> yes
22:39 <@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.)"
22:40 <@kanzure> hah
22:43 <@kanzure> still waiting to see what his response is going to be to my "computers everywhere" ideology.
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--- Log closed Sun Mar 03 00:00:16 2013