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| nsh | kanzure | 09:31 |
|---|---|---|
| nsh | what's new? | 09:31 |
| kanzure- | Hi nsh. | 10:01 |
| kanzure- | I got your emails- Ed and I have talked before. | 10:01 |
| kanzure- | 10:01 | |
| kanzure- | http://edboyden.org/ | 10:01 |
| nsh | suspected as much | 10:17 |
| nsh | btw, have you watched a japanese anime called Paprika? | 10:17 |
| nsh | (film) | 10:17 |
| kanzure- | No, I also haven't heard of it. | 10:18 |
| nsh | ah, i watched it last night. you might like it | 10:18 |
| 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 | 10:19 |
| * nsh wonders about non-invasive optogenetic technology possibilities | 10:21 | |
| kanzure- | didn't that require some sort of genetic augmentation? | 10:22 |
| 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 | 10:23 |
| 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 | 10:24 |
| 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. | 10:25 |
| 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 | 10:26 |
| 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. | 10:28 |
| 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 | 10:29 |
| 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)? | 10:30 |
| fenn | i wish filelight could show slices sorted by number of files instead of size | 10:31 |
| kanzure- | no | 10:31 |
| kanzure- | hrm. | 10:31 |
| 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 | 10:32 |
| 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 | 10:33 |
| 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 | 10:34 |
| fenn | btw kanzure you might want to use some materials from "software carpentry" | 10:35 |
| fenn | it's right up their alley | 10:35 |
| fenn | perhaps we could implement this for OM: http://bikeshed.com/ | 11:53 |
| fenn | more on this line of thought: http://www.codinghorror.com/blog/archives/000922.html | 11:57 |
| kanzure- | "the amount of noise generated by a change is inversely proportional to the complexity of the change" | 11:58 |
| 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" | 12:04 |
| kanzure- | http://mail.python.org/pipermail/python-list/2003-August/218440.html win32, solidworks, com | 12:25 |
| fenn | for a one-off "git r done" project, CAD'ing a gel box is silly | 12:26 |
| fenn | hehe i wonder if "markus wankus" is his real name | 12:27 |
| fenn | EJ just wanted to share a source of platinum wire, not be a project maintainer | 12:28 |
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| kanzure | fenn: I see. | 15:06 |
| 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? | 15:10 |
| kanzure | Anyone know about the shrinky-dink autoclaving? | 15:15 |
| fenn | they're just polystyrene so i assume it's fine | 15:21 |
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| 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. | 15:40 |
| fenn | you mean "bluntly obvious"? | 15:43 |
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| 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 | 15:58 |
| 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) | 15:59 |
| fenn | *zzzz* | 16:00 |
| fenn | where's my communications succinctness act | 16:00 |
| kanzure | in the trash can. | 16:02 |
| kanzure | also, why am I reading papers about microliter-volume fluid separations. this is stupid. | 16:04 |
| 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" | 16:05 |
| 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) | 16:07 |
| fenn | hmm i had it right the first time | 16:10 |
| fenn | "The Year They Hanged The Lawyers" | 16:10 |
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| kanzure | ah, http://heybryan.org/folders.html works now. | 17:51 |
| kanzure | nsh wants me to finish the story at the bottom | 17:53 |
| 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! | 17:58 |
| kanzure | oh yay, Jeswin John posted images | 17:59 |
| kanzure | woah, his droplets are huge | 18:00 |
| xp_prg | Kanzure where are the pics man? | 18:02 |
| 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! | 18:03 |
| 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 | 18:04 |
| kanzure | true somewhat | 18:05 |
| kanzure | there's no control over it | 18:05 |
| kanzure | this is basically just good for filtering I think | 18:05 |
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| 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?) | 18:05 |
| 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 | 18:06 |
| kanzure | like what? | 18:07 |
| kanzure | were there any words that you did not understand? | 18:07 |
| xp_prg | let me check it again | 18:07 |
| xp_prg | ok, so you put water in it and it stays away fromt he sharpie right? | 18:11 |
| 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 | 18:12 |
| 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 | 18:13 |
| 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 | 18:14 |
| 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 | 18:15 |
| kanzure | the first one does | 18:16 |
| kanzure | try the other ones. | 18:16 |
| 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: | 18:17 |
| xp_prg | * * * * | 18:18 |
| xp_prg | * * * * | 18:18 |
| xp_prg | etc... where the dots are sharpie dots? | 18:18 |
| kanzure | yes | 18:18 |
| xp_prg | ok then how does that help with electrophoresis? | 18:19 |
| kanzure | dna hits the dots. | 18:19 |
| 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? | 18:20 |
| 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. | 18:22 |
| 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 | 18:23 |
| 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 | 18:24 |
| 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 | 18:25 |
| 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? | 18:26 |
| xp_prg | also, do you apply a voltage to it somehow? | 18:27 |
| 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? | 18:28 |
| 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 | 18:29 |
| 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 | 18:30 |
| 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? | 18:31 |
| xp_prg | I am totally confused by why this is useful | 18:32 |
| kanzure | have you ever heard of the phrase "lab on a chip"? | 18:34 |
| xp_prg | yes | 18:34 |
| 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. | 18:35 |
| 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/ | 18:36 |
| xp_prg | so basically your making a way for the chemicals to flow right? | 18:38 |
| 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 | 18:39 |
| 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 | 18:40 |
| 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? | 18:41 |
| 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 | 18:42 |
| 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 | 18:43 |
| 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? | 18:44 |
| 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. | 18:45 | |
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| kanzure | ok. | 18:48 |
| xp_prg | kanzure can you answer my question please? | 18:48 |
| kanzure | what question? | 18:48 |
| xp_prg | how does the laser move the cells? | 18:49 |
| kanzure | photons. | 18:51 |
| kanzure | transfer of energy into kinetic energy | 18:51 |
| kanzure | (eh, sort of) | 18:51 |
| xp_prg | what about the sharpie fluid causes the water to stay away from it? | 18:52 |
| kanzure | have you ever drawn with sharpie on a whiteboard? | 18:53 |
| xp_prg | yes | 18:54 |
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| xp_prg | ok and? | 18:56 |
| kanzure | you can't erase it easily, can you? | 18:56 |
| 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? | 18:57 |
| kanzure | some chemicals are hydrophobic, some are hydrophillic | 18:58 |
| xp_prg | what is hydrophillic? | 18:58 |
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| 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 | 20:23 |
| fenn | mobile fab lab - bringing laser printers to everyone! | 20:48 |
| xp_prg | I don't see the posting | 20:56 |
| xp_prg | where is it? | 20:56 |
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| kanzure | fenn: you're welcome to make a better mobile contraption, perhaps a mobile fabratory, and you can bring super laser pointers to everyone | 21:47 |
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| kanzure | hm, for some reason I said 100 microns = 1 mm on diybio. that is wrong. | 22:36 |
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