--- Log opened Mon Apr 09 00:00:27 2012
00:17 < diginet> how does one get PCR'd DNA into a plasmid vector, do you simply design the primers to correspond to splice sites of the primer?
00:18 < yashgaroth> basically, yes
00:19 < diginet> ah okay, that's less obnoxious than I thought
00:19 < diginet> do you have any suggestions on which vector to use for pichia?
00:20 < diginet> (I've decided to try pichia first, as according to a few papers, it seems it should be viable for my purposes)
00:21 < yashgaroth> nope, never worked with pichia
00:21 < diginet> ah okay
00:21 < diginet> I'm excited, I'm pretty sure I might be able to pull this off :)
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06:49 < kanzure> beep boop
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06:55 < ThomasEgi> kanzure,  blibblib.. plingding
06:56 < kanzure> ah yes that is completely comprehensible
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07:09 < archels> http://quincybioscience.com/files/MadisonMemoryStudy.pdf
07:17 < ThomasEgi> kanzure, whisteling and beeping is quite a good interface to machines. a lot better than natural language
07:17 < kanzure> archels: hi
07:18 < katsmeow-afk> it's slow but unambiguously error free?
07:20 < archels> hello kanzure
07:20 < kanzure> archels: what have you been up to?
07:20 < ThomasEgi> katsmeow-afk, not error free. but a lot less interpretation and processing is needed to make some sense from the input
07:21  * katsmeow-afk nods
07:21 < archels> kanzure: nothing mindboggling, some electronics hobby work on making a "digital poster" for showcasing my research.
07:21 < kanzure> haha.. "Well, my poster is about how I spent all this time making this poster.."
07:22 < archels> :) lots of fun building it, though
07:23 < archels> last time I looked at my actual research was 3 days ago, when I found that my problem was so stiff that none of the solvers built into the package I'm using can handle it.
07:27 < kanzure> hmm "People who receive organ donations from "living" donors are more likely to survive than those who receive organs from "deceased" donors."
07:27 < kanzure> maybe dead organs aren't useful
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07:28 < archels> meh, how long are we even going to be messing with donor organs still? A few decades at most, surely.
07:28 < katsmeow-afk> "the donor died of kidney failure, so did the recipient of the kidney, can anyone find the connection?"
07:34 < katsmeow-afk> i was/am desperately trying to not use chlorine in a potable water system, but seems it's a good idea even after 0.5 micron filters and carbon filters,, else i haveto do reverse osmosis or distillation
07:34  * katsmeow-afk sighs
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07:40 < kanzure> F7: yo
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08:03 < audy> Has anyone attempted to purify their own active T. aquaticus DNA polymerase holoenzyme?
08:03 < kanzure> holoenzyme?
08:04 < nmz787> holoenzye is enzyme with multiple subunits
08:04 < nmz787> intact
08:05 < kanzure> so.. does that just mean multiple purifications from lysate?
08:05 < nmz787> didnt kno pol was holoenzyme, is that just T. aq/?
08:07 < nmz787> oloenzyme
08:07 < nmz787> [hol′ō·en′zīm]
08:07 < nmz787> Etymology: Gk, holos + en, in, zymos, ferment
08:07 < nmz787> a complete enzyme-cofactor complex that gives rise to full catalytic activity.
08:08 < audy> they all are
08:10 < audy> oh neat you can precipitate it from cell lyase
08:11 < audy> using polyethylenimine which creates balls of condensed, positively charge DNA.
08:11 < audy> that's way easier than HPLC
08:12 < audy> Step 1 - Go camping in Yellowstone. Bring a centrifugre
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08:21 < Utopiah> http://www.technologyreview.com/blog/arxiv/27689/
08:38 < archels> Shannon an _unsung_ hero? What rock does this blogger live on?
08:49 < delinquentme> who KentuckyFC @ arxivblog.com ?
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09:01 < kanzure> roksprok_: hi
09:02 < roksprok_> hello kanzure
09:02 < roksprok_> how are things going?
09:02 < kanzure> pretty good
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09:47 < delinquentme> kanzure, how does one monitize reproducibility
09:53 < roksprok_> doesn't that take care of itself if you do useful stuff?
09:54 < kanzure> roksprok_: nope.. a lot of biology is "try 20 times, it works once, let's roll with it"
09:54 < roksprok_> like if your stuff is reproducable and useful you can start a company or license it or people will cite you a lot
09:54 < kanzure> you can license it even if it is barely reproducible, haha
09:54 < roksprok_> that's frusturating
09:55 < roksprok_> i guess its nice for people whose stuff isn't reproducable
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09:59 < nmz787> that techreview article really doesn't say anything useful at all
10:00 < delinquentme> kanz TLDRed it
10:01 < Mariu> I agree with kanzure on the biology thing :p
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10:22 < nmz787> the whole DNA info theory thing about shotgun sequencing kidnof gets blow out of the water if nanopore seq turns out to work as well as it sounds like it should
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10:39 < kanzure> fenn: ping
10:49 < F7> Just reading through datasheets over here, I just got caught up on the log in this channel
10:51 < F7> delinquentme: did you ask the resolution on an analog distance sensor earlier? hahahahaha
10:52 < F7> Resolution is one pixel, the distance resolution is defined by your ADC
10:52 < F7> and to a degree, the physical properties of the object you're pointing at
10:53 < F7> It's a little light and a detector
10:53 < F7> you tell distance by the amount reflected back
10:53 < F7> It's not meant to do anything accurate, or beyond like a foot
10:54 < F7> What did you want it for?
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11:09 < delinquentme> F7, yeah I was looking for that information
11:09 < delinquentme> i need accuracy thats the thing
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11:21 < delinquentme> F7, what do you know about sensors
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11:30 < F7> I know many things about sensors
11:30 < F7> What kind of accuracy do you need?
11:30 < F7> consider quadrature if it's linear or rotational encoding
11:31 < F7> Old dot matrix printers are built like tanks, for example. they're heavy enough that backlash isn't such a problem, and the linear axes are generally good to a twentieth of a mm.
11:31 < F7> And those are ooooold printers
11:35 < F7> A quadrature encoder gets 4 times the accuracy of the CPI of the encoder strip it is designed for
11:36 < nmz787> delinquentme: what are you doing that needs distance sensing?
11:36 < delinquentme> pumps
11:36 < F7> that's odd
11:36 < delinquentme> ultrasound are ehh
11:36 < F7> syringe pump?
11:36 < delinquentme> lasers could be expensive ( havnt looked into it )
11:36 < delinquentme> yeahh and the LH
11:37 < F7> why does it have to be contactless?
11:37 < delinquentme> magnetic sensors are fairy accurate but they've got interaction issues
11:37 < delinquentme> it doesnt
11:37 < F7> oh
11:37 < F7> how accurate does it need to be?
11:37 < nmz787> pump i was working on a while ago was for sterile solutions
11:38 < nmz787> was calculating the delta V of a hanging droplet
11:38 < nmz787> that was in a closed drip tube
11:38 < nmz787> getting nanoliter precision with wideVGA camera
11:40 < F7> I don't know why you're thinking along the lines of these esoteric sensing solutions
11:40 < F7> If you can do contact, you can do cheap, easy, accurate stuff
11:41 < F7> I don't know if it's just your unfamiliarity, delinquentme, or if I'm missing some kind of big limiting factor inherent to your setup
11:42 < ThomasEgi> F7, pumping nanoliters means.. moving veryveryveryvery little, mechanical setups simply have a hard time keeping up with that
11:43 < F7> I'm assuming the syringe pump is being driven with rotational to linear means?
11:43 < F7> like, some kind of mechanical advantage?
11:43 < F7> The same mechanical advantage can be used to advantage of the sensor
11:43 < ThomasEgi> that wont take mechanical problems into account. backlash, slip, etc.
11:44 < F7> I am unsure of the exact setup, so I cannot be sure whether or not that would be advantageous
11:45 < F7> the syringe could just be very overbuilt, or it could be dependent on some slip-shod springy plastic parts.
11:46 < F7> Okay, some info about linear encoders
11:47 < F7> 500 CPI strips are about four bucks per inch
11:47 < F7> the encoder that goes with it is like 30 bucks
11:47 < ThomasEgi> .. compare to a camera chip.
11:47 < F7> both can be scrapped from cheap printers
11:47 < nmz787> ThomasEgi: yeah it was r&d for a blood infusion pump
11:48 < F7> that nets 1/2000th of an inch
11:48 < nmz787> they have a really wide dynamic range
11:48 < F7> What is this camera volumetric stuff y'all are talking about?
11:48 < ThomasEgi> F7, a scanner chip can has 4800dpi
11:49 < nmz787> F7, basically just pointing a camera at a hanging droplet in a closed tube, watching as it grows, calculating delta V from frame to frame (filtering the noise was where I basically left the project)
11:50 < delinquentme> everyone loves scraping shit from printers for some reason
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11:50 < delinquentme> i guess its bc they're only making 1 off robotics?
11:50 < nmz787> we were basically finding the edge of the droplet and rotating each row of pixels to get volume
11:50 < ThomasEgi> delinquentme, until the day where you want to print something and notice... crap. my printer is all butched
11:50 < delinquentme> ^
11:51 < delinquentme> but yes F7 i know little about sensors
11:51 < nmz787> each row was diameter, since pi*r^2 = area, the row gave us area and since we knew the height we got slices of volumes
11:52 < delinquentme> F7, where would I get this sensor for the 500 CPI strips
11:52 < nmz787> then added the slices together to get drop vol
11:52 < nmz787> then looked at the differential of those
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11:52 < delinquentme> nmz787, am I wrong in thinking that all you need is a single side view of a droplet?
11:52 < nmz787> nope
11:52 < delinquentme> as the droplet will be uniform size
11:53 < nmz787> well
11:53 < nmz787> when the drop detaches, it actually jumps around
11:53 < nmz787> so there was talk about adding a second view
11:53 < delinquentme> so you just need the 'footprint' to determine the vol
11:53 < delinquentme> oh sure
11:53 < nmz787> or using structured light
11:54 < nmz787> when the drop detaches, it actuallt sends a ringing/oscillation of pressure up the orifice and into the feed tuube
11:54 < kanzure> stereographic drop images? heh
11:54 < nmz787> but yeah like I said, i left the project when we were finally getting somewhere with the theoretical stuff and moving into cleaning up the real signals
11:54 < F7> www.usdigital.com has quadrature encoders
11:55 < F7> I've never bought one ever, they're easy to scrap
11:55 < F7> A cheap laser mouse will have about a 2000 dpi sensor, and run at over 10K FPS
11:56 < F7> something like that would be amazing for sensing
11:56 < F7> the 'gamer' mice are probably much better
12:00 < ThomasEgi> F7, yeah but they have rather low resolution and for most  models, there is no way to access the actual image data
12:00 < ThomasEgi> just the final motion vector of the overall image.
12:00 < diginet> so, bio-rad has cuvettes for $15, but Invitrogen has them for $150, am I missing something, or there just insane mark-up going on there?
12:02 < diginet> oh wait, nevermind, bio-rad is selling a pack of 5, rather than 50
12:02 < nmz787> kanzure: http://eclecti.cc/hardware/blinded-by-the-light-diy-retinal-projection
12:04 < F7> ThomasEgi, let me check you on that. I'm pretty sure most of those sensors send info to a separate microcontroller to extract the vector.
12:07 < ThomasEgi> these days, sensors, motion extraction and usb controllers usualy are on one-chip
12:10 < kanzure> nmz787: what's the resolution
12:14 < kanzure> neat the guy also did lytro's file format.. http://eclecti.cc/computervision/reverse-engineering-the-lytro-lfp-file-format
12:18 < kanzure> oh neat. he's friends with randallagordon (who used to hang out here?)
12:18 < F7> I'm looking through datasheets, and most low resolution ones I can find go offboard
12:18 < F7> I haven't found any sheets for 'gamer' mice yet
12:19 < nmz787> kanzure: for the retina projector? the image was only 1.5mm, so if he was using the whole DLP chip, i'd say pretty good
12:19 < F7> it actually looks pretty straightforward to piece the high speed video together with a micro
12:19 < nmz787> i dont think it really quite works though
12:20 < nmz787> the eye is supposed to be the focus, and the image rests on your retina
12:20 < nmz787> so to get a seemingly big image, the incoming light needs to have a pretty wide angle
12:22 < kanzure> i would love to have per-cone addressable input to my eye :(
12:23 < kanzure> er.. cone-addressable
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12:41 < F7> I'd love to have one for other people's eyes
12:42 < F7> with long distance retinal lasers, one could be the master of illusion
12:42 < jrayhawk> I have a G500 that I'm not sure I care about
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12:51 < nmz787> kanzure: maybe we're pitching the DNA synthesizer in the wrong way
12:52 < nmz787> kanzure: maybe we should pitch it as an aide to solve developing world drug synthesis and production, or something
12:52 < kanzure> it's an aide to scratch my butt
12:52 < kanzure> oh, well.
12:53 < nmz787> http://newyork.craigslist.org/mnh/sci/2921681357.html
12:53 < nmz787> i could get that internship, then pitch ourselves
12:53 < nmz787> get you to come 'demo' something
12:53 < kanzure> haha
12:54 < kanzure> yeah there's a lot of vectors once we have a prototype
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13:40 < diginet> what is the general protocol for preparing a lysate from a tissue sample?
13:41 < ParahSailin__> bead beater and lysis buffer
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13:44 < nmz787> if you want to torture yourself you can get our LN2 and a mortar and pestle.... it can be tough though
13:45 < diginet> what is the lysis buffer composed of?
13:46 < ParahSailin__> depends on your sample
13:46 < ParahSailin__> you google it
13:46 < diginet> could I use laundry detergent, or would that not provide good enough quality?
13:47 < kanzure> it would probably be more specific?
13:48 < ParahSailin__> normally theres tris involved
13:48 < diginet> ah
13:49 < diginet> now, another thing I was thinking about: let's say I manage to transfect the genes into a cell, and I am able to culture a sizable quantity of them in some sort of tank, is there anyway to extract the protein (provided it is excreted of course) without disrupting the rest of the mixture?
13:50 < ParahSailin__> since i know what you are doing, you would go on mobio and their dna extraction kits come with bead beaters and all the buffers you need
13:50 < diginet> okay thanks
13:51 < ParahSailin__> you did not really provide enough context for a naive observer to answer your question
13:52 < diginet> I'm sorry
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13:52 < ParahSailin__> mobio gives free samples of *na extraction kits
13:53 < diginet> oh, wow
13:54 < diginet> thanks
13:54 < ParahSailin__> might need to use an institutional mailbox, which i still have
13:54 < diginet> thank you so much, again
13:56 < diginet> but yeah, if I were the CEO of some corporation, which was trying to produce a recombitant protein on an industrial scale, how would I go about it?  I could culture the transgenic cells, and then desctructively extract the protein, but that seems a waste.  Is there anyway to efficiently get it out of the tank with minimal disturbance to the culture?
13:57 < ParahSailin__> that spidroin has a golgi secretion tag on it
13:57 < kanzure> hairy root cultures
13:57 < ParahSailin__> it will be in the supernatant
13:57 < kanzure> in some biofuel operations they do secreting oils and then you harvest the oils from the pond scum (or something)
13:57 < F7> Just press it like it were olives?
13:58 < nmz787> i know some transgenics use secretion tags, so the golgi apparatus exports the proteins in vesicles which fuse to the cell membrane, releasing their contents into the extracellular medium (broth)
13:58 < kanzure> what's wrong with regularly sacrificing a part of your culture?
13:58 < nmz787> wasteful
13:58 < diginet> I know, it should excrete it, but is it trivial to extract the protein from the broth efficienctly?
13:58 < nmz787> more overhead
13:59 < nmz787> its a lot easier to extract from broth than intracellular
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13:59 < nmz787> you centrifuge the cells out first, and then purify for whatever you need
13:59 < diginet> is the centrifugation destructive?
14:00 < nmz787> to?
14:00 < diginet> the cells?
14:00 < nmz787> generally not
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14:04 < diginet> Is there any sort of available membrane which could act like a sieve for the cells and just let the broth through? One of the benefits of Pichia, so I've read, is that it doesn't secrete very much protein naturally
14:05 < ParahSailin__> centrifuge
14:12 < nmz787> nanopore membranes
14:12 -!- archels [~foo@sascha.esrac.ele.tue.nl] has joined ##hplusroadmap
14:12 < nmz787> http://www.simpore.com/products.html
14:12 < ParahSailin__> if you are doing pichia and you dont have a centrifuge, they will settle pretty quickly on their own
14:13 < ParahSailin__> like 1 cm/hr
14:26 < nmz787> looks like cofactorbio.com and seqify.com are offline
14:26 < nmz787> testing or dead?
14:27 < kanzure> haven't heard from mac in a while
14:27 < kanzure> last i heard he and josh were doing something
14:27 < nmz787> i thought seqify was it
14:27 < kanzure> but then josh is going out to china with $50k openpcr money or something
14:28 < nmz787> to make cheaper PCR machines?
14:28 < kanzure> haha no i doubt it
14:28 < kanzure> fulfilling the backlog of orders
14:28 < nmz787> backlog?
14:29 < nmz787> weird
14:29 < kanzure> yeh apparently they have a few ordes for openpcr boxes that they haven't satisfied
14:29 < nmz787> seems like it should be production by now
14:29 < nmz787> like, churn them out easily
14:29 < nmz787> are they taking new orders still?
14:31 < kanzure> yes
14:31 < diginet> one nice benefit is that the spidroin proteins are very heavy
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14:34 < fenn> guh so much email
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14:41 < fenn> that table looks familiar.. http://fennetic.net/irc/IMG_4615.JPG
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15:00 < kanzure> wut did they grab it off ebay
15:00 < kanzure> damn
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15:26 < fenn> ah nice http://eclecti.cc/hardware/blinded-by-the-light-diy-retinal-projection
15:27 < fenn> the newport table came from "centurian surplus" for i don't know how much
15:28 < kanzure> nmz787 posted a very similar link the other day
15:28 < kanzure> to such a table.
15:28 < fenn> apparently this place has tons of equipment sitting around
15:28 < fenn> yeah i know
15:35 < kanzure> " know of people who have done silencing work on themselves, and one chap who has self inoculated. There are others who have created autoimmune responses against targets."
15:36 < kanzure> "RNA interference was last autumn, Self inoculation was over a year back, and the autoimmune induction was jan this year, although I suspect that it has been going on for a few years."
15:36 < kanzure> "As for who, they are all bodybuilders bar one who is a pro in combat sports."
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15:50 < kanzure> nmz787: fenn is around
15:50 < kanzure> how long will a channel cut take on the cutter? like 1min/mm?
15:50 < kanzure> uh
15:50 < kanzure> 1mm/min
15:51 < fenn> that's ridiculously slow
15:52 < kanzure> well. it's worth knowing.
15:52 < kanzure> i think the total channel length will probably add up to multiple millimeters so.. it's important to know how long it would take
15:52 < nmz787> I think fenn said 1000rpm / 60 s/min * (635microns/turn)
15:53 < kanzure> yes but it also depends on the material/laser
15:53 < nmz787> Pdms comes off fast
15:53 < nmz787> But that would be our upper limit
15:53 < nmz787> I need to look at black acrylic with a spectrometer
15:54 < kanzure> nmz787: do you have access to a micron laser on campus
15:54 < nmz787> We might be able to use a NIR diode laser, which would be smaller and a little less complex optics/gantry-wise
15:54 < nmz787> Nope
15:55 < nmz787> No one makes these things
15:57 < nmz787> Someone converse with me... I'm bored in a liberal arts class
15:57 < fenn> nmz787: do you think mcmaster part 6350K137 is a good lead screw?
15:58 < nmz787> The one you originally chose?
15:58 < fenn> 3/8-40 acme
15:59 < nmz787> Yeah, looked like the best
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16:03 < kanzure> Kev_ant: hello
16:03 < nmz787> hi keg
16:04 < nmz787> Kev
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16:06 < nmz787> Kanzure... Remeber we roughly calculated 20000 drops would take at least 50cm
16:07 < kanzure> yep
16:07 < kanzure> so ideally it would take <30min of cutting
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16:07 < nmz787> So thats significantly more than your few mm comment earlier
16:08 < kanzure> ah true
16:09 < nmz787> At 1000rpm that's 16.66 turns per sec, which is about 10.5mm per sec
16:09 < nmz787> Or 1cm per sec
16:09 < nmz787> So I think less than 5 or 10 mins per layer for.cutting
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16:11 < kanzure> yo juul
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16:11 < nmz787> If we have 3 layers, 15 mins, plus time to prep those layers (spin coat, bake)... Say 10 min per layer (we'll do these in bulk in advance)
16:11 < juul> hey kanzure
16:11 < kanzure> nmz787: yeah i imagine we'd have a stock of uncuts
16:11 < fenn> nmz787: am i missing something? 50cm*50micron = 0.25 cm^2
16:12 < nmz787> and I figure 30 mins to bond 2 layers, at least in beginning
16:12 < fenn> if so, why do we need such a big stage?
16:12 < kanzure> no this was just a storage area
16:12 < nmz787> Fenn you need space between the channels
16:12 < fenn> yeah, 50 microns ought to be enough, no?
16:12 < fenn> anyway it increases linearly with spacing between channels
16:13 < fenn> to a first order approximation
16:14 < nmz787> I calf 3.55 cm per side for the 20000 drop column/pipe
16:14 < nmz787> Calc
16:14 < fenn> let's go over those calculations
16:14 < kanzure> the calculation was something like 20 micron diameter per drop * 50,000 drops
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16:14 < kanzure> and at least 20 microns in between each channel (like if it's zigzagging or something, no "infinitely thin" walls)
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16:15 < fenn> and spacing between drops?
16:15 -!- nmz787 [~androirc@nateevo.student.rit.edu] has quit [Read error: Connection reset by peer]
16:16 < fenn> how wide is the channel?
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16:17 < fenn> i'm assuming the area required is roughly the same whether it's a zigzag or a straight line with a given width
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16:18 < kanzure> let's say 5 or 10 microns in between drops?
16:18 < kanzure> channel is as wide as the drop
16:18 < nmz787> 20 Micron drop * 25000 drops = 50000 microns long
16:18 < fenn> and spacing between drops is what?
16:18 < nmz787> 20 Micron wide channel, plus 2.5 Micron wall on each side
16:18 < kanzure> yeah that's 50mm not 50cm
16:19 < nmz787> So 25 micron width per channel
16:19 < kanzure> 2.5 micron wall will probably break, but it's worth exploring
16:19 < fenn> no it's 50 cm
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16:19 < kanzure> how is 50,000 microns = 50 cm?
16:19 < fenn> 50cm * 25 micron = 0.125 cm^2
16:21 < kanzure> oh woops
16:21 < nmz787> Huh
16:22 < nmz787> 20 microns
16:22 < fenn> people mess up the square conversions all the time
16:22 < nmz787> 20 microns/drop * 25000 drops is not a sq
16:23 < fenn> 10000 microns per cm => (10000)^2 microns^2 per cm^2
16:23 < fenn> ok back up a second, what's the volume of the drop?
16:24 < nmz787> Doesn't matter
16:24 < kanzure> it's some weird oblique blob.. not quite a sphere
16:24 < fenn> rough estimate
16:25 < fenn> enough DNA for maybe 100 PCR reactions right?
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16:25 < kanzure> what are we talking about now?
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16:25 < kanzure> in the library scheme we would have beads in each drop
16:25 < fenn> how big each droplet is
16:26 < kanzure> and the dna is attached to the beads
16:26 < fenn> ok how big are the beads?
16:26 < kanzure> so there's probably a few million strands attached to each bead, and however many beads we want for whatever size we buy
16:26 < n_bentha> small
16:26 < kanzure> we can buy all sorts of beads
16:26 < kanzure> 1 micron beads, 100 micron beads..  0.1 micron beads..
16:26 < fenn> paralyzed by choice! :)
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16:26 < kanzure> we will probably just test a bunch of things
16:27 < kanzure> "load droplet with beads" is a big test
16:27 < kanzure> anyway, let's say 1 to 5 picoliters
16:28 < n_bentha> so all this spiffy lab voodoo. where will it be done?
16:28 < n_bentha> in a biosafety hood?
16:28 < fenn> ok 1pl is about 8 micron radius
16:28 < fenn> who cares about biosafety
16:29 < fenn> this is DNA
16:29 < kanzure> this isn't even DNA yet
16:29 < nmz787> So to get a square of snaking channel, (25x)*(50000/x)=1250000
16:29 < yashgaroth> safety for the dna, not for the user
16:29 < nmz787> That's not including the turns on the ends to connect each row, actually
16:30 < n_bentha> u just don't want contamination of dust, bacteria, etc
16:30 < fenn> the system's sealed, it's not open to the air
16:30 < n_bentha> oh ok. cool
16:30 < kanzure> bacteria! i'd love bacteria to get into the drops. dam.
16:30 < kanzure> *dam
16:30 < kanzure> moIDKfaa *damn
16:31 < fenn> nmz787: if you think about it, the turns add to the path length
16:31 < fenn> imagine a spiral instead of a zigzag
16:31 < kanzure> where does the spiral exit ?
16:31 < fenn> nowhere
16:32 < fenn> why would it need to exit?
16:32 < fenn> okay, two spirals
16:32 < kanzure> oh you could do a double spiral, right..
16:32 < kanzure> heh
16:32 < fenn> we'll have to have 2 zigzags
16:32 < nmz787> Exit through the top layer?
16:32 < fenn> it just needs a volume in the center to collect working fluid
16:32 < kanzure> 2x spiral means once it gets to the "center" it starts going "out"
16:33 < fenn> anyway the point is that the formula for area is the same whether it's a long line or a zigzag
16:33 < fenn> kanzure: oh, like a bifilar coil
16:34 < kanzure> double spiral: http://www.prodigyquilter.com/ProductImages/double%20spiral.gif
16:34 < kanzure> has an entrance and exit
16:34 < fenn> right
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16:35 < fenn> so i guess we can forget about building a motion stage
16:35 < kanzure> why
16:36 < kanzure> piezo+mirror?
16:36 < n_bentha> lol
16:36 < fenn> because it only needs to be 5mm on a side, so we can just use one of the readily available 50mm microscopy positioning stages
16:37 < kanzure> no we might want features longer than 5mm :(
16:37 < kanzure> in fact i'm sure of it
16:37 < fenn> longer than 50mm?
16:38 < kanzure> centimeters!
16:38 < fenn> gosh
16:38 < nmz787> That's only for drop storage
16:38 < nmz787> For 25k drops
16:38 < nmz787> We could do a million drops
16:39 < nmz787> In late stages tho
16:39 < kanzure> that will be our 1028 bit version :)
16:39 < nmz787> But we definitely need some longer straight tubes for silica columns and or agarose
16:40 < nmz787> We shouldnt under build
16:40 < fenn> even for a million drops, drop storage is only 30mm on a side
16:41 < kanzure> the chip isn't 30mm x 30mm
16:41 < kanzure> it's 5cm x 5cm or something, at least
16:42 < kanzure> you have all sorts of features including world interconnects
16:42 < nmz787> Plus we need room to fit valving pistons or whatever on top, so they need mm between each
16:42 < kanzure> which you don't want crammed into a 30mm^2 area
16:42 < nmz787> Rift
16:42 < nmz787> Right
16:42 < n_bentha> shit will evaporate!
16:43 < kanzure> n_bentha: in oil
16:43 < nmz787> Plus I think the cutter resolution  specs are good
16:43 < n_bentha> oh
16:43 < kanzure> fenn: http://www.nature.com/nature/journal/v442/n7101/images/nature05058-f1.2.jpg
16:43 < nmz787> Also on chip perstaltic pumps could happen, more space required
16:44 < fenn> kanzure: a dime is 18mm diameter, so that chip's not more than 30mm on a side
16:44 < nmz787> That's also a really simple chip
16:44 < kanzure> i should probably know what this chip does before i keep citing it
16:44 < nmz787> With basically no onboard stuff but pipes
16:45 < kanzure> ah this was whitesides' chip.. from http://www.nature.com/nature/journal/v442/n7101/full/nature05058.html#B65
16:46 < kanzure> oh hell no
16:46 < kanzure> http://lesswrong.com/lw/b98/minicamps_on_rationality_and_awesomeness_may_1113/
16:46 < kanzure> fff “I do not say this lightly... but if you're looking for superpowers, this is the place to start.”
16:46 < fenn> SUPERPOWERS
16:46 < kanzure> rationality superpowers? god damn it
16:47 < nmz787> http://m.sciencemag.org/content/309/5731/137/F1.expansion.html
16:47 < nmz787> Ttyl8r, driving
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16:50 < fenn> i wonder why the channel width varies so much
16:51 < kanzure> between labs?
16:52 < fenn> well, that too, but if you look at the image, the red channels seem to shrink and grow as they cross other channels
16:52 < fenn> this image http://m.sciencemag.org/content/309/5731/137/F1.large.jpg
16:52 < kanzure> pressure valves.. where they cross, you're trying to increase the amount of pressure to drive down the membrane to cover the other channel
16:53 < kanzure> oh also it looks like they might be trying to control pressure or concentration?
16:53 < kanzure> like look under the word "loop" in green on the bottom left
16:53 < fenn> F7: the EZ430 is really chunky.. i'm not sure i want to wear it all the time
16:54 < fenn> under "loop", is that a valve?
16:55 < fenn> the one above "pump" looks like it's valving something
16:55 < kanzure> the one under loop is idk
17:05 < fenn> F7: for example it's hard to reach into my pocket with it on
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18:03 < kanzure> fenn: did you get the parts all picked uot
18:03 < kanzure> out
18:06 < bkero> kanzure: ping
18:07 < bkero> Anything I should see while in Copenhagen?
18:07 < kanzure> juul: superping
18:07 < kanzure> whatever juul recommends
18:07 < kanzure> copenhagen suborbitals. go steal his submarine.
18:08 < kanzure> bioligigaragen
18:08 < bkero> fwah?
18:08 < juul> bkero, Kristiania and Labitat
18:08 < kanzure> Mogens Hvidtfeldt <mogens@hvidtfeldt.dk>
18:08 < kanzure> Lasse Nørfeldt <lasse@norfeldt.dk>
18:08 < juul> yeah and if you can get a tour of copenhagen suborbitals but i don't really have contacts for that
18:08 < kanzure> Tobias H. Michaelsen
18:08 < kanzure> Martin Malthe Borch
18:08 < juul> yeah and biologigaragen is in Labitat
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18:08 < kanzure> oh
18:08 < kanzure> right then! labitat.
18:09 < kanzure> bkero: yeah you should definitely check out his submarine
18:09 < juul> then there's Illutron which is an old tiny ferry-type boat
18:09 < juul> also hacker/maker types
18:09 < bkero> Who?'s submarine?
18:09 < juul> there's actually three submarines
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18:09 < kanzure> http://forums.somethingawful.com/showthread.php?threadid=3005279&userid=0&perpage=40&pagenumber=2
18:09 < kanzure> http://forums.somethingawful.com/showthread.php?threadid=3271649&userid=0&perpage=40&pagenumber=1
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18:10 < juul> https://en.wikipedia.org/wiki/UC3_Nautilus
18:10 < bkero> kanzure: that's super badass
18:11 < bkero> kanzure: Who's Morgens, Lasse, Tobias, and Martin?
18:12 < kanzure> i'm not really sure how i know them. i just talk with them about biohacking and they are in copenhagen.
18:12 < bkero> haha cool
18:12 < bkero> Members of the diybio list?
18:12 < kanzure> no not to my knowledge
18:12 < juul> http://biologigaragen.org/
18:13 < bkero> found that
18:14 < bkero> juul, kanzure: don't know anybody at copenhagen suborbitals though?
18:14 < kanzure> lemme check
18:15 < juul> no, unfortunately not, but you should go talk to the illutron people as there is overlap in people and the space/tools they use
18:15 < kanzure> aha
18:15 < kanzure> this guy uc3nautilus@hotmail.com
18:16 < kanzure> that's peter madsen's email
18:16 < bkero> cool
18:16  * bkero is going to be in copenhagen for a mercurial code sprint next month and is staying an extra week for touring
18:17 < kanzure> mergecurial
18:17 < juul> for regular touristy stuff you could go visit vesterbro + noerrebrogade (equivalent to the mission district in SF). I recommend that you rent a bike, as Copenhagen is an excellent bike city.
18:17 < juul> cool
18:17 < juul> tivoli is fun, but touristy
18:18 < juul> take a bike ride / walk along the lakes
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18:19 < bkero> yea
18:19 < bkero> I'm looking on airbnb now for where to stay for the extra week
18:19 < juul> labitat has meeting nights on tuesdays starting at around 7 pm and you can probably find someone to act as your guide
18:19  * bkero will try to do that
18:19 < juul> there's also couchsurfing :)
18:19 < bkero> yea
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18:20 < bkero> I need something reliable since I won't really be taking any time off of work.
18:20 < bkero> (I telecommute)
18:20 < juul> ah
18:20 < bkero> Or I could just take the week off, I have built up PTO
18:20 < kanzure> haha i would hope mozilla lets you telecommute. geeze.
18:21 < bkero> they might be relocating me to london
18:21  * bkero takes off for dinner
18:22 < bkero> Thanks for the info and if you're ever in Portland or the Bay Area let me know and I'll make sure you have a good time )
18:22 < bkero> :)
18:22 < kanzure> he is in the bay area haha
18:22 < bkero> juul: I'm Ben Kero by the way, don't think we've been introduced.  I'm a hacker interested in ##hplusroadmap topics and general open sourcery.
18:22 < bkero> I'm a sysadmin at Mozilla
18:23 < bkero> juul: let's meet up next time I'm in the bay then, it'll only be a few months
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18:37 < juul> bkero, cool, yeah let's
18:37 < juul> I'm Marc Juul
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19:19 < kanzure> hi klafka
19:19 < klafka> sup
19:20 < kanzure> SF startup shuffle.. always a fun ride
19:20 < klafka> ?
19:20 < klafka> what's that
19:21 < kanzure> hustle and bustle
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20:23 < kanzure> nmz787: hi
20:23 < nmz787> hey
20:23 < nmz787> whats new
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21:12 < kanzure> yashgaroth: do you know the person who is doing diy RNAi?
21:12 < yashgaroth> nope?
21:12 < kanzure> me either.
21:13 < yashgaroth> you mean that stuff you quoted earlier? where was it from
21:13 < kanzure> i don't even remember
21:13 < nmz787> you just had it in a text file?
21:13 < nmz787> untagged?
21:13 < kanzure> no it was from some dark part of the interwebs
21:13 < nmz787> ahh
21:14 < nmz787> so the price of the cutter isnt too bad
21:14 < nmz787> i still need to figure out the optics
21:14 < kanzure> yes please :P
21:14 < nmz787> i dont have a frickin spectrometer to measure the damn acrylic
21:15 < kanzure> what happened to your spectrophotometer
21:15 < nmz787> i guess i can just power this NIR laser on at some acrylic and see if it burns
21:15 < nmz787> etches
21:15 < nmz787> i need to design the optics
21:15 < nmz787> :P
21:15 < kanzure> heh i sense a theme
21:15 < nmz787> yeaaahhh
21:16 < nmz787> time has been an issue
21:16 < nmz787> cant talk now actually
21:16 < nmz787> ttyl
21:16 < kanzure> seeya
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21:17 < yashgaroth> I can't imagine what target they'd pick for inducing autoimmunity, if they're sticking with the bodybuilding theme
21:18 < yashgaroth> even inducing one to soluble myostatin would be rather dangerous
21:18 < kanzure> might be bullshit
21:18 < yashgaroth> nah, I'm sure someone's been doing it, at least the RNAi stuff
21:19 < kanzure> RNAi at least doesn't cause AIDS
21:19 < kanzure> or wait.. what's the self-rejection disease called
21:19 < yashgaroth> there's many...lupus?
21:19 < kanzure> it's not lupus
21:19 -!- lichen [~lichen@c-76-105-164-184.hsd1.or.comcast.net] has quit [Ping timeout: 244 seconds]
21:19 < yashgaroth> never
21:20 < yashgaroth> wait were you referencing House or were you actually thinking of another one
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21:20 < kanzure> yashgaroth: another one
21:20 < kanzure> what is house?
21:20 < yashgaroth> tv show with hugh laurie where he diagnoses diseases
21:21 < yashgaroth> a semi-catchline of it is "it's never lupus"
21:21 < kanzure> oh, you mean house the show
21:21 < kanzure> right. yes.
21:21 < kanzure> anyway, no, i think there's another autoimmune disease
21:21 < yashgaroth> well, diabetes, MS, uh
21:22 < yashgaroth> eczema
21:22 < yashgaroth> and a hundred super-rare ones
21:23 < yashgaroth> oh psoriasis
21:26 < klafka> there are tons
21:27 < yashgaroth> but inducing one would be rather insane
21:28 < klafka> yes
21:29 < klafka>  that sounds like a really terrible idea
21:33 < diginet> inducing autoimmune disorders? wat?
21:35 < yashgaroth> indeed
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21:38 < diginet> heh, if you want to be disturbed, read pro-anorexia forums. yes, they exist.
21:40 < kanzure> surely that is not the most disturbing thing you can find on the internet
21:40 < kanzure> you're not even trying
21:41 < joshcryer> Don't Google Mexican chainsaw beheading.
21:42 < kanzure> still not trying hard enough
21:42 < joshcryer> I'm not sure I would want to see anything more disturbing than that.
21:45 < diginet> the most disturbing thin on the internet is the weird parts of reddit
21:46 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has quit [Read error: Connection reset by peer]
21:46 < diginet> like "PicsOfDeadChildren"
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21:46 < yashgaroth> how I envy you
21:47 < klafka> lol
21:47 < diginet> I don't look at that stuff
21:52 < kanzure> yashgaroth: hah
21:52 < kanzure> diginet: yeah, that's unfortunately not the worst of the internet
21:53 < klafka> not nearly
21:54 < klafka> my friend works for youtube spamops
21:54 < klafka> he definitely sees the worst of the internet
21:55 < juul> my friend runs a Tor exit node
21:55 < juul> also pretty bad
21:56 < diginet> kanzure, I'm sure the guy who runs that I'm sure has something else up his sleeve
21:56 < diginet> tor/freenet are pretty disgusting, about the only thing they are really uses for is CP, which is about the most vile thing I can think of
21:57 < juul> diginet, wut? no that is definitely not true
21:57 < juul> run an exit node and see for yourself
21:57 < diginet> what else is it used for?
21:58 < kanzure> holy carp
21:58 < kanzure> yeah, tons of legitimate activity
21:58 < diginet> every directyory I see on there is riddled with CP
21:58 < diginet> or just porn
21:59 < joshcryer> Wait, what is the worst of the internet?
21:59 < diginet> I mean, there's porn, people claiming to be hitmen, Randroids, that's about all I see, but who knows
21:59 < kanzure> joshcryer: 1000x worse than the dnepropetrovsk maniacs
22:00 < kanzure> diginet: whatever you do don't type in anything you see from us in the past 20min or the next 20min
22:00 < kanzure> diginet: you have been unscathed by the internet and you should cherish this
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22:01 < ParahSailin__> heh Randroids arent even close to the worst
22:01 < joshcryer> No actually I agree that Randroids do ruin the internet.
22:01 < diginet> kanzure, thanks L)
22:01 < diginet> :)
22:02 < diginet> I love all the Randroids on reddit, it's funny how all the chauvinists/eugenicists/racists/etc on there are probably losers in real life, who wouldn't live up to their own standards
22:03  * ParahSailin__ moderates /r/Objectivism
22:03  * diginet quickly tries to avoid massive argument
22:04 < kanzure> also, can we stop talking about reddit
22:04 < kanzure> let's ban reddit
22:04 < diginet> sorry I brought it up
22:04 < joshcryer> Reddit will make you rich dude. Get on the front page, profit!
22:04 < klafka> so guys did you see reddit last night?
22:05 < diginet> no
22:09 < joshcryer> From an H+ perspective, probably the neo-Luddites are the worst.
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22:11 < fenn> mmm dead children
22:12 < kanzure> fenn: optics?
22:12 < fenn> afraid i'm too stupid to function today
22:12 < fenn> think i caught some sort of flu
22:13 < diginet> I hate radiation fear-mongers
22:13 < fenn> i definitely don't want an RS485 stepper controller
22:14 < kanzure> diginet: you surround yourself with the oddest people. maybe if you stop visiting reddit your circle of friends will improve. like.. for instance, not radiation fearmongerers
22:14 < diginet> oh, I hate reddit
22:14 < diginet> I don't go there
22:14 < kanzure> fenn: why do you say that
22:14 < fenn> also, i work hard to keep the price down so that people who want to reproduce our results are able to do so without massive engineering
22:15 < fenn> a $225 stepper motor driver is just dumb
22:15 < diginet> I don't really have "friends" per se, anyhow though
22:15 < kanzure> ah didn't know the price
22:15 < kanzure> diginet: i'll be your friend.
22:15 < diginet> awwww :)
22:15 < fenn> anyway, i'd rathe run EMC, and serial comms is not compatible
22:15 < kanzure> you can even facebook me. http://facebook.com/kanzure
22:15 < kanzure> fenn: sure. i'd prefer emc too.
22:15 < diginet> I'm kind of a loner IRL
22:15 < fenn> diginet: aside from diamonds, what is there you _do_ like?
22:16 < fenn> oh, and spiders
22:16 < kanzure> diamonds and spiders
22:16 < kanzure> because he's spiderman
22:16 < diginet> spider diamonds?
22:16 < diginet> Umm
22:16 < diginet> let me think
22:16 < diginet> I like physics, dead languages, Roman and Byzantine history
22:16 < fenn> maybe a role model
22:17 < ParahSailin__> diginet, i want to go to tx-rx but i wanna bring someone along in case its weird
22:17 < diginet> kanzure: requested
22:18 < diginet> ParahSailin__, if you don't mind me asking: how old are you?
22:18 < kanzure> hmm my guess is at least 23
22:18 < diginet> I'm 18, but I look about 15-16
22:18 < joshcryer> I'm 35 and look about 20.
22:18 < ParahSailin__> im 26
22:18 < kanzure> i'm eternally 12
22:19 < joshcryer> I got carded for lottery tickets recently.
22:19 < diginet> I'm immature and mature at the same time, I've always enjoyed the company of older people rather than my peers, but yet at the same time I like doing "childish" things, and am somewhat (well very) naive
22:19 < diginet> ParahSailin__, how much does it cost?
22:20 < ParahSailin__> dunno, i think ill go to the next open house, but not this week because im out of town then
22:20 < kanzure> ParahSailin__: you should go with F7
22:20 < kanzure> F71: ping
22:21 < kanzure> diginet: attendance is free
22:21 < diginet> ah okay
22:21 < joshcryer> What is tx-rx?
22:21 < kanzure> membership probably costs
22:21 < kanzure> joshcryer: some hackerspace
22:21 < diginet> well kanzure if you accept my friend request you'll get to enjoy all my acerbic status updates
22:21 < diginet> I do love that word
22:22 < kanzure> diginet: dude you have rage comics and "literally hitler" everywhere. you're from reddit.
22:22 < joshcryer> Oh Houston.
22:22 < klafka> LOL
22:23 < diginet> Rage comics?
22:23 < diginet> wat
22:23 < diginet> no
22:23 < yashgaroth> hiterally litler
22:23 < klafka> kanzure is eternally 12
22:23 < diginet> also my last name isn't Palaiologos, it's Keith. The Palaiologos comes from the last dynasty of the Byzantine Empire
22:23 < diginet> the "literally hitler" was sarcasm
22:23 < klafka> i feel like an adult because i'm going to buy furniture from ikea soon
22:23  * joshcryer contemplates friending kanzure
22:23 < klafka> :(
22:24 < joshcryer> Are you a frequent updater kanzure?
22:24 < diginet> kanzure, did you know my scumbag byzantine memes?
22:24 < diginet> I feel like such a loser
22:24 < klafka> i bet he posts a lot to linkedin
22:24 < klafka> just chatting all the time there
22:24 < kanzure> joshcryer: i update like once a year
22:25 < joshcryer> OK, that's good.
22:25 < kanzure> i have more friends on google+ :(
22:25 < joshcryer> I now have 24 friends.
22:25 < diginet> GOOGLE+ IS LITERALLY SATAN
22:25 < kanzure> https://plus.google.com/102967708777429109844/posts
22:25 < diginet> no, but seriously I hate Google with a fiery passion
22:25 < klafka> why?
22:26 < diginet> because, they're monopolist bastards
22:26 < klafka> how are they monopolist?
22:26 < joshcryer> Wait who is Eudoxia and how do we both know them kanzure?
22:26 < diginet> DON'T QUESTION ME
22:26 < diginet> I'm weird, I hate communism, but I also hate most big businesses
22:26 < klafka> why do you hate communism?
22:26 < yashgaroth> eudoxia is the resident uruguayan
22:26 < klafka> or big businesses?
22:26 < diginet> well, I'm weird in general, that is merely one facet of my hatred
22:26 < kanzure> klafka: don't poke the troll
22:27 < diginet> I'm not trolling :(
22:27 < diginet> sorry
22:27 < klafka> so you just irrationally dislike these things?
22:27 < klafka> or do you have reasons
22:27 < diginet> I go off on tangents
22:27 < kanzure> you hate like all of us
22:27 < joshcryer> yashgaroth, ahh yes I recall now.
22:27 < diginet> no, you guys are awesome
22:27 < diginet> I have rational and irrational reasons
22:27 < klafka> illuminative
22:27 < diginet> I more hate relativism/cultural marxism than communism itself
22:28 < diginet> but I think I already articulated that before
22:28 < diginet> but I do have TONS of irrational hatreds
22:28 < diginet> like flip flops
22:28 < diginet> I LOATHE THOSE VILE EXCUSES OF "SHOES"
22:28 < diginet> sorry
22:29 < diginet> you don't understand how much I hate flip flops, or open shoes in general
22:29 < joshcryer> So you hate toes?
22:29 < diginet> I also hate alcohol
22:29 < diginet> I hate visible feet
22:29 < kanzure> ParahSailin__: http://diyhpl.us/~bryan/images/aubrey.jpg
22:29 < klafka> so do you have any fetishes?
22:29 < klafka> what are your kinks?
22:29 < klafka> do you like to tie people up?
22:29 < yashgaroth> man you're gonna hate college, no flip flops or alcohol
22:29 < diginet> I'm asexual, so I don't have any I guess
22:29 < ParahSailin__> lol
22:29 < diginet> oh, I already do
22:30 < diginet> colleges are full of douchebags, ugh
22:30 < klafka> i didn't drink or wear flip flops all through college
22:30 < klafka> it was pretty awesome
22:30 < diginet> actually, colleges have basically everything I hate about the world in one nice little tidy package
22:30 < klafka> learning?
22:31 < kanzure> libraries?
22:31 < klafka> academia?
22:31 < kanzure> women?
22:31 < klafka> frogs?
22:31 < diginet> Okay I like those
22:31 < klafka> you don't like women
22:31 < klafka> you've already said that
22:31 < diginet> I like women
22:31 < joshcryer> They have feet.
22:31 < diginet> I just don't like their feet
22:31 < diginet> but women are all right
22:31 < diginet> some of my favourite people are women
22:31 -!- mode/##hplusroadmap [+o kanzure] by ChanServ
22:31 < joshcryer> There are women without feet, true.
22:31 -!- joshcryer was kicked from ##hplusroadmap by kanzure [klafka diginet]
22:31 <@kanzure> fdklsadasfkaslda
22:31 <@kanzure> what
22:31 < klafka> LOL
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22:32 < klafka> FINE
22:32 <@kanzure> that went terribly
22:32 < diginet> :(
22:32 < diginet> were you meaning to kick me?
22:32 <@kanzure> joshcryer: i am sorry bro
22:32 < yashgaroth> what's going onnnn
22:32 < joshcryer> I'm just glad to be first on the list.
22:32 < klafka> i'm going to watch st:tng and fall asleep :P
22:32 < diginet> does everyone hate me now?
22:32 < klafka> since i have to get up at 630 tomorrow
22:32 < klafka> no
22:32 < klafka> i'm pretty apathetif
22:32 < diginet> night night klafka
22:32 <@kanzure> diginet: nobody hates you
22:32 < klafka> apathetic
22:32 < diginet> ah okay
22:32 <@kanzure> but the signal to noise is all out of whack
22:33 < diginet> I'm sorry, my meds wear off about this hour
22:33 < joshcryer> I was barely contributing. But I was still the first to be listed in fail kick alias. :P
22:33 < fenn> eat dark green leafy vegetables
22:33 < klafka> i need to eat more of those
22:34 < diginet> is it just me or are colleges STD infected cesspools or exposed feet, drunkenness, and date-rape?
22:34 < katsmeow-afk> Adrafinil is being made again, if that helps
22:34 < diginet> *of
22:35 -!- mode/##hplusroadmap [+o fenn] by ChanServ
22:35 -!- mode/##hplusroadmap [-o kanzure] by ChanServ
22:35 < kanzure> fenn's problem now
22:36 < diginet> because when I toured at Rice (no offense ParahSailin__) my guide person just seemed to brag about how they get drunk at parties and sleep around
22:36 < diginet> two things absolutely no appeal to me
22:36 < diginet> *with
22:38 < diginet> alright back to business: does anyone here know anything about continuous bioreactors?
22:39 < yashgaroth> yes
22:41 < diginet> what can you tell me about them? would it be hard for me to build one?
22:41 < yashgaroth> lots; yes
22:42 < diginet> should I just give up on that and go for batch?
22:42 < yashgaroth> yes, flasks are much easier unless you've got money to burn
22:43 < diginet> I wonder what kind of yields I could get with batch
22:44 < yashgaroth> absolute peak yields are 1-20 grams per liter, depending on cell type and how much effort you put into optimizing expression
22:44 < diginet> do you think DIY growth medium would be feasible?
22:45 < yashgaroth> for bacteria and yeast, sure
22:45 < yashgaroth> cells from multicellular organisms need blood factors
22:45 < diginet> I'm trying to use Pichia
22:46 < diginet> what are good sources for the nutrients I would need?
22:47 < yashgaroth> vegemite
22:47 < diginet> seriously?
22:47 < yashgaroth> yeast extract and salt, mixed with water
22:48 < yashgaroth> but you can get the various ingredients in bulk and mix them yourself for fairly cheap
22:48 < diginet> can one even buy that in the states?
22:48 < diginet> haha
22:48 < yashgaroth> it's sold as marmite
22:49 < diginet> this may sound stupid: would plant fertilizer work?
22:49 < ParahSailin__> seriously i will borrow extra lb from my lab so that you dont have to do that
22:49 < yashgaroth> no not plant fertilizer
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22:49 < diginet> ParahSailin__, wow, thanks for being so nice to me :)
22:49 < yashgaroth> but seriously it's pretty cheap for unicellulars, don't worry about that
22:49 < diginet> I didn't think so
22:50 < diginet> well, I'm going to need a fair amount of the spidroins to make any sizeable quantity of silk
22:51 < ParahSailin__> diginet, check pm
22:51 -!- capiscuas [~capiscuas@ppp-58-8-178-253.revip2.asianet.co.th] has joined ##hplusroadmap
22:56 < ParahSailin__> night
23:00 < diginet> ah okay, night
23:02 < diginet> oh, I also adore classical music
23:03 < diginet> yashgaroth: one thing I'm potentially concerned about is the difficulty of purifying the protein
23:03 -!- ctobin [~cory.tobi@DHCP-52-143.caltech.edu] has quit []
23:04 < yashgaroth> depends whether it'll start forming fibers in the media or during the purification
23:05 < yashgaroth> I dunno what conditions cause them to start polymerizing, but especially when purifying they'll be at high concentrations and close to each other
23:05 < yashgaroth> might be better off trying to dissolve one of those huge communal spiderwebs and weaving them into something else
23:06 < diginet> I'm not concerned with that as much, you have to induce polymerization by lowering the pH
23:06 < diginet> and extruding it
23:07 < diginet> (the act of squeezing causes fibers to form
23:07 < diginet> =)
23:07 < diginet> I'm just wondering how hard protein purification is in general
23:07 < yashgaroth> it can be easy
23:08 < yashgaroth> ...ish
23:09 < diginet> uh oh
23:13 < yashgaroth> I'm sure you can find a suitable method
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23:16 < ParahSailin__> F71, you are in houston?
23:25 -!- F71 [~Adium@50.15.211.25] has quit [Ping timeout: 264 seconds]
23:26 < ParahSailin__> You're just jealous.  This dropped a huge stage full of funding/legitimacy on both syn bio and this community. ... You're typing, for free, on Al Gore's Internet, which used to be called ARPANET, with the first D missing ...
23:26 < ParahSailin__> rage
23:27 < yashgaroth> ?
23:27 < ParahSailin__> some thread on diybio list
23:28 < diginet> could malt extract be used for a nutrient source for my yeast?
23:28 -!- capiscuas [~capiscuas@ppp-58-8-178-253.revip2.asianet.co.th] has quit [Quit: Leaving]
23:29 < yashgaroth> oh jcline
23:29 -!- F71 [~Adium@50.15.211.25] has joined ##hplusroadmap
23:30 < yashgaroth> you'd need to hydrolyse the malt extract but sure why not
23:30 < diginet> well it's really cheap, and pre-groud
23:30 < diginet> so I thought it might be a good option
23:33 -!- cory_tobin [cory.tobin@71-92-71-97.static.mtpk.ca.charter.com] has joined ##hplusroadmap
23:36 < diginet> as much as I hate alcohol, all of the DIY beer brewing information is really useful for my purposes
23:39 -!- skorket [~skorket@cpe-24-58-232-122.twcny.res.rr.com] has joined ##hplusroadmap
23:39 < skorket> hey folks
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--- Log closed Tue Apr 10 00:00:29 2012