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09:31 < nsh> kanzure
09:31 < nsh> what's new?
10:01 < kanzure-> Hi nsh.
10:01 < kanzure-> I got your emails- Ed and I have talked before.
10:01 < kanzure-> *email
10:01 < kanzure-> http://edboyden.org/
10:17 < nsh> suspected as much
10:17 < nsh> btw, have you watched a japanese anime called Paprika?
10:17 < nsh> (film)
10:18 < kanzure-> No, I also haven't heard of it.
10:18 < nsh> ah, i watched it last night. you might like it 
10:19 < kanzure-> I do find it intersting that in the wired article there's more information on how to build Boyden's/Superkuh's TMS setup than either of them have previously released
10:19 < kanzure-> just by virtue of the photograph of the damn fscking breadbard
10:19 < kanzure-> *breadboard
10:19 < nsh> hah!
10:19 < kanzure-> *interesting
10:21  * nsh wonders about non-invasive optogenetic technology possibilities
10:22 < kanzure-> didn't that require some sort of genetic augmentation?
10:23 < kanzure-> of course, with the microfluidics virus gradient reactor + my work with pinkarmy, that might be doable, but oncolytic viruses are supposed to only infect cancerous cells
10:23 < kanzure-> and adenoviruses kill some people, so :-(
10:23 < nsh> electroporation 
10:23 < nsh> might be an option
10:23 < nsh> if you could do that somehow noninvasively
10:23 < kanzure-> uhh
10:23 < kanzure-> yeah because the first thing in the morning that I plan to do
10:23 < kanzure-> is put my head into a giant fucking electroporator
10:24 < kanzure-> no thanks :)
10:24 < kanzure-> hehe
10:24 < nsh> hey, it's better than daytime tv
10:24 < nsh> :-)
10:24 < kanzure-> probably.
10:24 < nsh> btw, read your 2.2009 page on folder organisation
10:24 < kanzure-> oh?
10:24 < nsh> you should continue that story about the king and the 10 brightest men
10:24 < kanzure-> heh
10:25 < kanzure-> that was january btw
10:25 < nsh> ah, mybad
10:25 < kanzure-> a few days after dad died.
10:25 < kanzure-> had to keep myself busy.
10:25 < nsh> ah, hadn't heard. sorry
10:25 < nsh> what program did you use to make the image, btw?
10:25 < kanzure-> gd something. 
10:26 < kanzure-> gdisk viewer?
10:26 < kanzure-> on /shots/, there's an image that has the name of the program in the filename
10:26 < nsh> ah, will check
10:28 < kanzure-> hm
10:28 < kanzure-> I think my server is down
10:28 < kanzure-> this isn't good. my presentation is stored on the server.
10:29 < nsh> noticed that too
10:29 < nsh> program was Graphical Disk Map --http://www.makeuseof.com/tag/how-to-analyze-your-disk-usage-pattern-in-linux/
10:29 < kanzure-> yes
10:29 < fenn> i like filelight
10:30 < kanzure-> hrm, I can't remotely powercycle my box
10:30 < nsh> the concentric models are interesting
10:30 < kanzure-> since sshd is failing to respond too.
10:30 < nsh> i think you could expand them with some interactivity
10:30 < nsh> kanzure, damn; that's never good
10:30 < kanzure-> (I was copying a few hundred GB over the network)
10:30 < nsh> p(accidentally fill the disk)?
10:31 < fenn> i wish filelight could show slices sorted by number of files instead of size
10:31 < kanzure-> no
10:31 < kanzure-> hrm.
10:32 < nsh> Philesight seems to show number of files by lines
10:32 < nsh> http://www.makeuseof.com/wp-content/uploads/2009/02/philesight.jpg
10:32 < nsh> (from page linked above)
10:32 < nsh> although, maybe i'm misinterpreting that
10:33 < nsh> what would be nice would be if you could use an arbitrary fractal algorithm
10:33 < fenn> when you're comparing 2,000 lines vs 400,000 lines it gets a little iffy
10:33 < nsh> (anything that cuts a finite area into proportal segments)
10:33 < nsh> aye
10:33 < kanzure-> so how am I supposed to do an svn tutorial without access to my svn server.
10:33 < kanzure-> any ideas?
10:33 < kanzure-> I guess tortoisesvn allows local repositories
10:33 < fenn> set up an svn server
10:33 < kanzure-> guess I could set one up on this machine
10:33 < fenn> why do you need to do a svn tutorial?
10:33 < kanzure-> because adl has no source code management whatsoever
10:34 < fenn> then why teach them something lame
10:34 < kanzure-> and they will not understand git
10:34 < kanzure-> bbl
10:34 < fenn> they will piss and moan no matter what
10:35 < fenn> btw kanzure you might want to use some materials from "software carpentry"
10:35 < fenn> it's right up their alley
11:53 < fenn> perhaps we could implement this for OM: http://bikeshed.com/
11:57 < fenn> more on this line of thought: http://www.codinghorror.com/blog/archives/000922.html
11:58 < kanzure-> "the amount of noise generated by a change is inversely proportional to the complexity of the change"
12:04 < kanzure-> gah, that Ej post to diybio sucks
12:04 < kanzure-> "sorry, this is too simple for me to bother CADing up. and I don't know what CAD or .py is"
12:25 < kanzure-> http://mail.python.org/pipermail/python-list/2003-August/218440.html win32, solidworks, com
12:26 < fenn> for a one-off "git r done" project, CAD'ing a gel box is silly
12:27 < fenn> hehe i wonder if "markus wankus" is his real name
12:28 < fenn> EJ just wanted to share a source of platinum wire, not be a project maintainer
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15:06 < kanzure> fenn: I see.
15:10 < kanzure> On Wed, Mar 4, 2009 at 1:05 PM, Jonathan Cline <jncline@gmail.com> wrote:
15:10 < kanzure> > Is the sharpie idea for single use, or multi-use after cleaning?
15:10 < kanzure> > Do you think the shrinky dinks can be autoclaved or are they
15:10 < kanzure> > 1-use-then-throw-away?
15:15 < kanzure> Anyone know about the shrinky-dink autoclaving?
15:21 < fenn> they're just polystyrene so i assume it's fine
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15:40 < kanzure> " When a particle is flowing in a microchannel, the center position of the particle cannot be present in a certain distance from sidewalls, which is equal to the particle radius." <-- I like how blunt these papers are.
15:43 < fenn> you mean "bluntly obvious"?
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15:58 < kanzure> yes.
15:58 < kanzure> fenn: do not bother with the p2presearch list.
15:58 < kanzure> it's basically marc fawzi's stomping grounds 
15:58 < fenn> oh don't worry, i was just sophistrizing
15:59 < fenn> i think the point of that email was lost in the shuffle
15:59 < kanzure> http://frwebgate3.access.gpo.gov/cgi-bin/TEXTgate.cgi?WAISdocID=20316230645+0+1+0&WAISaction=retrieve 
15:59 < kanzure> http://frwebgate3.access.gpo.gov/cgi-bin/TEXTgate.cgi?WAISdocID=20316230645+0+1+0&WAISaction=retrieve Office of Biotechnology Activities; Recombinant DNA Research: 
15:59 < kanzure> Proposed Actions Under the NIH Guidelines for Research Involving 
15:59 < kanzure> Recombinant DNA Molecules (NIH Guidelines)
16:00 < fenn> *zzzz*
16:00 < fenn> where's my communications succinctness act
16:02 < kanzure> in the trash can.
16:04 < kanzure> also, why am I reading papers about microliter-volume fluid separations. this is stupid.
16:05 < fenn> it was in a robert heinlein book
16:05 < kanzure> at best you'd just make a giant array of microfluidic devices
16:05 < fenn> "the day they got rid of the lawyers"
16:07 < kanzure> but at 1 mL/hr, you'd need 100,000 sorters just for 1 cubic meter of water..
16:07 < kanzure> (to process it in an hour, I mean)
16:10 < fenn> hmm i had it right the first time
16:10 < fenn> "The Year They Hanged The Lawyers"
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17:51 < kanzure> ah, http://heybryan.org/folders.html works now.
17:53 < kanzure> nsh wants me to finish the story at the bottom
17:58 < kanzure> "I did it today. It was pretty fun and showed some basic concepts of microfluidics. Now you got me hooked on this stuff, Bryan. Maybe someone could hack an inkjet printer to print on slides. Sharpie lines are a bit thick. I see alot of potential especially for seperating proteins by their sizes or shape. Is this already done? I think this has great DIYbio potential."
17:58 < kanzure> yay
17:58 < kanzure> somebody somewhere did something about something!
17:59 < kanzure> oh yay, Jeswin John posted images
18:00 < kanzure> woah, his droplets are huge
18:02 < xp_prg> Kanzure where are the pics man?
18:03 < fenn> i like the paper "fused toner on polyester film" or whatever it's called
18:03 < kanzure> xp_prg: on the email
18:03 < kanzure> fenn: was that on my server?
18:03 < kanzure> was that the lamination paper?
18:03 < fenn> basically, laminate two laser printed transparencies together
18:03 < kanzure> yeah
18:03 < kanzure> and then the circuit is in the middle / in between?
18:03 < fenn> search for 'polyester' in that folder
18:03 < xp_prg> oh cool, didn't see them!
18:04 < xp_prg> what did it do?
18:04 < fenn> it doesn't do anything :\
18:04 < kanzure> there was also "Rapid prototyping of micropatterned substrates using conventional laser printers"
18:04 < fenn> that's the thing i dont get about this microfluidics stuff
18:04 < kanzure> hm?
18:04 < fenn> it's like etching circuit boards but you have no electronic components to populate it with
18:05 < kanzure> true somewhat
18:05 < kanzure> there's no control over it
18:05 < kanzure> this is basically just good for filtering I think
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18:05 < kanzure> or maybe directing microscale reactions
18:05 < kanzure> unless you're able to make the microheater array thingy
18:05 < kanzure> with 256 addressible resistors
18:05 < kanzure> (did you see that?)
18:06 < xp_prg> kanzure tell me what those pics are all about, what did he do?
18:06 < kanzure> did you read my email?
18:06 < kanzure> they are pictures of what I describe in my email
18:06 < xp_prg> well I didn't really understand the email either
18:07 < kanzure> like what?
18:07 < kanzure> were there any words that you did not understand?
18:07 < xp_prg> let me check it again
18:11 < xp_prg> ok, so you put water in it and it stays away fromt he sharpie right?
18:12 < kanzure> sort of- only droplets- unless you soak one of the glass panels in piranha for a while
18:12 < kanzure> or rain-x coat it instead of piranha
18:12 < xp_prg> but how is that useful, what is so great?
18:12 < kanzure> and then you can just "flood it" with water (don't *actually* flood it, but I mean you can run small volumes of water (non-droplet) thorugh it)
18:12 < kanzure> uhh
18:12 < kanzure> well, people have done PCR using these systems
18:12 < kanzure> and DNA sequencing
18:12 < kanzure> and DNA synthesis
18:13 < kanzure> and gel electrophoresis without gels
18:13 < xp_prg> ok I have done gel electrophoresis
18:13 < kanzure> and Jonathan Cline has been having me read some papers about doing this to make an electroporator
18:13 < xp_prg> can you help me to understand that using this method?
18:13 < kanzure> you make an array of dots
18:13 < kanzure> http://heybryan.org/books/papers/microfluidics/A%20Brownian%20dynamics-finite%20element%20method%20for%20simulating%20DNA%20electrophoresis%20in%20nonhomogeneous%20electric%20fields%20-%20complicated%20geometries.pdf
18:13 < kanzure> http://heybryan.org/books/papers/microfluidics/Conformational%20Preconditioning%20by%20Electrophoresis%20of%20DNA%20through%20a%20Finite%20Obstacle%20Array.pdf
18:13 < kanzure> http://heybryan.org/books/papers/microfluidics/Construction%20of%20refreshable%20microfluidic%20channels%20and%20electrophoresis%20along%20them.pdf
18:13 < kanzure> http://heybryan.org/books/papers/microfluidics/Field%20gradient%20electrophoresis.pdf
18:14 < kanzure> http://heybryan.org/books/papers/microfluidics/High%20resolution%20DNA%20separations%20using%20microchip%20electrophoresis.pdf
18:14 < kanzure> http://heybryan.org/books/papers/microfluidics/PCR%20-%20An%20inexpensive%20and%20portable%20microchip-based%20platform%20for%20integrated%20RT-PCR%20and%20capillary%20electrophoresis.pdf
18:14 < kanzure> fenn: this is a "must-read": http://heybryan.org/books/papers/microfluidics/Microthermal%20Devices%20for%20Fluidic%20Actuation%20by%20Modulation%20of%20Surface%20Tension%20-%20Basu%20-%20awesome.pdf
18:15 < xp_prg> an array of dots, all I know about right now is 2 panes of glass
18:15 < xp_prg> where are the dots etc... ?
18:15 < xp_prg> oh man that paper has lots of math in it
18:16 < kanzure> the first one does
18:16 < kanzure> try the other ones.
18:17 < kanzure> anything that you draw on one of the slides must be drawn on the other slide as well (a mirror image)
18:17 < kanzure> an array of dots: make dots. uh. in a grid.
18:17 < xp_prg> so like:
18:18 < xp_prg> * * * *
18:18 < xp_prg> * * * *
18:18 < xp_prg> etc... where the dots are sharpie dots?
18:18 < kanzure> yes
18:19 < xp_prg> ok then how does that help with electrophoresis?
18:19 < kanzure> dna hits the dots.
18:20 < xp_prg> ok, here is what I know, in gel electrophoresis you have a gel, you put the dna in one side of the gel, you then soak the gel in a buffer and then apply a voltage difference and the dna stretches out through the gel in a line
18:20 < xp_prg> when you say dna hits the dots I just don't understand how that makes sense, are we not stretching the dna out?
18:22 < kanzure> do you know why dna stretches out when running it through gels?
18:22 < xp_prg> yes because dna is electrically charged
18:22 < kanzure> why use the gel then.
18:22 < xp_prg> cuz it has to push through the gel and the gel traps it
18:22 < kanzure> but then you might as well just get rid of the gel.
18:23 < xp_prg> so how do the dots come into play as the dna spreads out?
18:23 < kanzure> think of it actually more like a cheese grater method
18:24 < kanzure> only the dna that straightens out will flow downwards more quickly
18:24 < kanzure> because the cross-section of a pinhead is smaller than the lateral length of dna
18:24 < kanzure> i.e. one nucleotide versus an entire friggin' genome
18:24 < kanzure> which will inevitably hit one of the dots.
18:24 < xp_prg> so once it hits the dots what happens?
18:24 < kanzure> look up the videos on the bionanomatrix website btw
18:25 < kanzure> (that's on the nanoscale though)
18:25 < xp_prg> kanzure please help me understand this, I know I can :>
18:25 < kanzure> well, depending on how fine the dots are, the dna will have to go in a certain direction, and so will somewhat straighten out
18:25 < kanzure> depending on the contact angle with the circular dot
18:25 < xp_prg> oh ok
18:26 < kanzure> but these have to be very tiny dots, otherwise the water will just bounce off of the dots and the dna will never touch it
18:26 < kanzure> erm
18:26 < kanzure> I don't know how to better explain that part
18:26 < kanzure> it might not work because of that issue
18:26 < kanzure> but read the other papers, they should help explain things.
18:26 < xp_prg> so as the dna expands it kind of follows the path the dots lay for it?
18:27 < xp_prg> also, do you apply a voltage to it somehow?
18:28 < kanzure> I don't remember. I'll have to read back over the papers.
18:28 < xp_prg> well can you explain what Jeswin did?
18:29 < kanzure> Jeswin just did what I wrote in my first email
18:29 < kanzure> http://groups.google.com/group/diybio/msg/1197606e3c3dc439
18:29 < kanzure> http://groups.google.com/group/diybio/attach/f5048fdc3c5e5866/IMG_0521.JPG?part=5&view=1
18:29 < kanzure> http://groups.google.com/group/diybio/attach/f5048fdc3c5e5866/IMG_0524.JPG?part=4&view=1
18:30 < kanzure> Look at the numbers in that email I first sent (#1, #2, #3, #4)
18:30 < fenn> you dont want the DNA to straighten out in electrophoresis
18:30 < xp_prg> yes the water stays away from the sharpie lines right?
18:30 < fenn> normally it bunches up into a blob, roughly spherical
18:30 < kanzure> oh crap
18:30 < kanzure> djlfkjadslfkjas
18:30 < xp_prg> fenn you don't?
18:30 < kanzure> fenn: forgive me!
18:30 < fenn> then the size of the blob is proportional to the length of the dna
18:31 < kanzure> erm. hrm.
18:31 < fenn> if it stretches out like a snake, then all DNA flows the same speed, more or less
18:31 < xp_prg> hmm... ok
18:31 < fenn> so that's why they have the multi-electrode gel boxes
18:31 < kanzure> I was confusing the DNA sequencing method, sorry
18:31 < fenn> to move it in a zigzag motion to keep it from stretching out
18:31  * kanzure must go clense his skin.
18:31 < fenn> no biggie
18:31 < xp_prg> kanzure the water stays away from the sharpies lines why is that useful?
18:32 < xp_prg> I am totally confused by why this is useful
18:34 < kanzure> have you ever heard of the phrase "lab on a chip"?
18:34 < xp_prg> yes
18:35 < xp_prg> so basically your saying you can direct fluids
18:35 < kanzure> this can potentially be used to implement a lab on a chip
18:35 < kanzure> that people can draw. with a sharpie. or print out with an inkjet printer.
18:36 < xp_prg> can you give me a small example of that, what would be a potential lab experiment you might do?
18:36 < kanzure> http://heybryan.org/books/papers/microfluidics/pcr/
18:36 < kanzure> http://heybryan.org/books/papers/microfluidics/synthesis/
18:38 < xp_prg> so basically your making a way for the chemicals to flow right?
18:39 < kanzure> and do separations.
18:39 < kanzure> (filtration)
18:39 < xp_prg> how would filtration work?
18:39 < xp_prg> making the space so small only certain things could get through it?
18:39 < kanzure> no
18:40 < kanzure> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2527745#R31
18:40 < kanzure> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2527745&rendertype=figure&id=F1
18:40 < kanzure> (that's the gravity version)
18:40 < xp_prg> well I don't want to read all that just now, can you just tell me some things?
18:40 < kanzure> why not look at the image I just linked to
18:40 < kanzure> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2527745&rendertype=figure&id=F1
18:41 < kanzure> what's so hard about that
18:41 < fenn> woah is that a microfluidic mass spectrometer?
18:41 < kanzure> I guess so :)
18:41 < kanzure> except recording is kind of not the same
18:41  * fenn bounces off the walls
18:41 < xp_prg> cuz I am at work and I could get in trouble for reading that is all :(
18:41 < kanzure> in mass spec you usually throw shit at a drum for recording, right?
18:42 < fenn> i remember something about atmospheric mass spectrometers glued to the backs of trained honeybees
18:42 < fenn> like 15 years ago
18:42 < kanzure> hah, seriously?
18:42 < kanzure> my legion of doom is growing more complete by the day!
18:42 < fenn> it was at a science conference my mom went to, i could never find anything about it on the web
18:43 < kanzure> I need to go through the papers and collect the images of these separators/filters
18:43 < kanzure> anything that says 'asymmetric', 'hydrodynamic', 'gravity', 'dean vortices', or 'bifurcation' in the paper name is going to have a neat design for these purposes
18:43 < kanzure> and usually some of the 'gradient' papers, but I'm not entirely sure if Whitesides' work is 1-to-1 relevant
18:44 < kanzure> (his work on gradient generators via resistor networks, I mean)
18:44 < kanzure> Yamada's papers are goldmines (see refs #32-38 in that pubmedcentral.gov link above)
18:44 < xp_prg> I watched the laser microfluidics video, how did the laser control what was happening just curious?
18:44 < kanzure> do you know what a laser is?
18:45 < xp_prg> electrons in a beam
18:45 < kanzure> sigh
18:45 < fenn> bzzt
18:45 < xp_prg> photons
18:45 < xp_prg> I meant
18:45 < fenn> i sense the force is wrong in this one
18:45  * kanzure will be back in a sec.
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18:48 < kanzure> ok.
18:48 < xp_prg> kanzure can you answer my question please?
18:48 < kanzure> what question?
18:49 < xp_prg> how does the laser move the cells?
18:51 < kanzure> photons.
18:51 < kanzure> transfer of energy into kinetic energy
18:51 < kanzure> (eh, sort of)
18:52 < xp_prg> what about the sharpie fluid causes the water to stay away from it?
18:53 < kanzure> have you ever drawn with sharpie on a whiteboard?
18:54 < xp_prg> yes
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18:56 < xp_prg> ok and?
18:56 < kanzure> you can't erase it easily, can you?
18:57 < xp_prg> nope
18:57 < kanzure> sharpie is hydrophobic. water avoids it.
18:57 < xp_prg> oh ok
18:57 < kanzure> so surface tension is generally caused by hydrogen bonds
18:57 < xp_prg> but are chemicals like that?
18:57 < xp_prg> does dna stay away from hydrophobic things?
18:58 < kanzure> some chemicals are hydrophobic, some are hydrophillic
18:58 < xp_prg> what is hydrophillic?
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20:23 < kanzure> hm, "
20:23 < kanzure> hm, "
20:23 < kanzure> Martin D. Leach, Ph.D. 
20:23 < kanzure> Executive Director Basic Research & Biomarker IT 
20:23 < kanzure> Merck & Co. Inc." just posted to diybio
20:48 < fenn> mobile fab lab - bringing laser printers to everyone!
20:56 < xp_prg> I don't see the posting
20:56 < xp_prg> where is it?
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21:47 < kanzure> fenn: you're welcome to make a better mobile contraption, perhaps a mobile fabratory, and you can bring super laser pointers to everyone
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22:36 < kanzure> hm, for some reason I said 100 microns = 1 mm on diybio. that is wrong.
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