| --- Day changed Thu Apr 30 2009 | ||
| fenn | low cost pcr only $95 for the book?? | 00:08 |
|---|---|---|
| fenn | what planet are these people from | 00:08 |
| fenn | that last arrow in your diagram should be labeled "and then a miracle happens..." | 01:20 |
| kanzure- | not if you have a small database of quickie equations | 01:29 |
| kanzure- | campbell did his thesis with 300 components in that format | 01:29 |
| kanzure- | er, sorry, I mean the format that represented that bottom mechanical thingy portion of the diagram | 01:30 |
| fenn | i'm skimming a-design, it actually looks pretty good | 01:30 |
| kanzure- | gasp | 01:30 |
| kanzure- | yeah, I found the FP stuff odd (page 43 or 63, I don't know which is which) | 01:30 |
| genehacker | link? | 01:30 |
| kanzure- | it was basically the same thing as what I was calling "control point" | 01:30 |
| kanzure- | http://heybryan.org/books/Manufacturing/campbell/thesis.pdf | 01:31 |
| fenn | http://www.andrew.cmu.edu/org/IDIG/The A-Design approach to managing automated design synthesis.pdf | 01:31 |
| kanzure- | oh. I linked you to the thesis :p | 01:31 |
| fenn | not sure i want to read 63 pages right now | 01:31 |
| fenn | 404 | 01:31 |
| kanzure- | that's only because it hates you | 01:31 |
| fenn | fair enough | 01:32 |
| kanzure- | http://heybryan.org/books/Manufacturing/campbell/campbell-dissertation.pdf | 01:32 |
| kanzure- | I would not recommend reading it | 01:32 |
| kanzure- | most of it was just lots of fluff/padding | 01:32 |
| fenn | what's the difference between a thesis and a dissertation anyway? | 01:32 |
| kanzure- | ooh, I've never seen that | 01:34 |
| kanzure- | "Is the design as presented above good? [Y/N]" | 01:34 |
| kanzure- | so instead of straight up using physical quantities, he and some previous students have been using bondgraph voodoo magic | 01:35 |
| kanzure- | http://heybryan.org/books/papers/campbell-bondgraphs.png | 01:35 |
| kanzure- | http://heybryan.org/books/papers/design-utility-search.png | 01:35 |
| fenn | that last diagram makes no sense unless you're reading the paper | 01:38 |
| fenn | so if he put all this work into a-design how come you're all using graphsynth which totally sucks and does nothing useful? | 01:40 |
| kanzure- | I'm not sure .. but I've already had to "re-come-up-with-stuff" that turns out looking like a-design (particularly the representation portions) | 01:41 |
| kanzure- | so I emailed him after reading his thesis (or the parts of it that were useful) | 01:43 |
| kanzure- | and he responded with this paper as clarification re: the representation stuff | 01:43 |
| kanzure- | http://heybryan.org/books/papers/New%20advances%20in%20the%20functional%20modeling%20of%20electro-mechanical%20components.pdf | 01:43 |
| genehacker | hey kanzure you don't think you could make an automated design program that designs 3d cartesian positioning systems? | 01:54 |
| genehacker | IE automatically design a better reprap cartesian robot | 01:54 |
| kanzure- | what is involved in a cartesian positioner | 01:54 |
| kanzure- | and why not use emc? | 01:54 |
| genehacker | the ability to move in 3 dimensions | 01:55 |
| kanzure- | hrm | 01:55 |
| genehacker | I want to find a way to replace all that threaded rod with plastic | 01:55 |
| kanzure- | so I'm not very familiar with different types of positioners | 01:55 |
| kanzure- | I know there are some piezos, but that's not really a design issue | 01:55 |
| genehacker | really? | 01:55 |
| kanzure- | that's more of an issue of getting a hunk of piezo crystal | 01:56 |
| genehacker | not even SCARA? | 01:56 |
| kanzure- | wha? | 01:56 |
| kanzure- | what's that? | 01:56 |
| genehacker | http://en.wikipedia.org/wiki/SCARA | 01:56 |
| genehacker | it's what we have to figure out how to drive in ME 218 | 01:56 |
| kanzure- | what's 218? | 01:57 |
| genehacker | a class | 01:57 |
| kanzure- | which one | 01:57 |
| genehacker | engineering computation methods | 01:57 |
| kanzure- | neat | 01:57 |
| genehacker | ME205 levelled up | 01:57 |
| kanzure- | so, what do you mean by referencing SCARA | 01:57 |
| genehacker | you don't drive a really robot | 01:57 |
| kanzure- | do you mean you have a SCARA robot and you have to write software for it? | 01:57 |
| kanzure- | or do you mean you get to design linkages, or what? | 01:57 |
| genehacker | it's a non-cartesian positioning system | 01:57 |
| kanzure- | wikipedia says it can access the xy plane | 01:58 |
| genehacker | you write a program that takes a point and outputs angles on the arm | 01:58 |
| kanzure- | how is that non-cartesian | 01:58 |
| fenn | what was that FEA shape optimization program | 01:58 |
| kanzure- | fenn: freefem++ | 01:58 |
| fenn | was that it? looks like just a generic FEA engine | 01:59 |
| genehacker | non-cartesian as in the coordinate system it makes isn't cartesian | 01:59 |
| genehacker | think polar vs. cartesian | 01:59 |
| kanzure- | fenn: yes. it was another paper that did the optimization magic. | 01:59 |
| kanzure- | search for "structural optimization with freefem++" | 01:59 |
| kanzure- | paper: http://heybryan.org/books/papers/Structural%20optimization%20with%20FreeFem++.pdf | 01:59 |
| fenn | ah here we go http://www.cmap.polytechnique.fr/~allaire/freefem_en.html | 01:59 |
| kanzure- | but it was a web page that they had | 01:59 |
| genehacker | the vector you input to the robot is the angles of the arm | 02:00 |
| kanzure- | so, I still don't understand | 02:00 |
| fenn | so anyway, genehacker throw your constraints into that and it should barf out some optimized plastic shapes | 02:00 |
| fenn | at least that's my kanzure-level understanding of it :P | 02:00 |
| kanzure- | do you get to choose different actuators? | 02:00 |
| kanzure- | if so, which actuators are fair game? | 02:00 |
| genehacker | no, but if you want | 02:00 |
| kanzure- | do you get to use weird linkages? | 02:00 |
| kanzure- | huh? | 02:01 |
| kanzure- | so yes or no? | 02:01 |
| genehacker | if you want to | 02:01 |
| kanzure- | fenn: err. what? | 02:01 |
| genehacker | I was just thinking of optimizing the current desing | 02:01 |
| kanzure- | fenn: constraints for cartesian movement? | 02:01 |
| genehacker | you have 3 orthogonal axes of movement | 02:01 |
| fenn | btw genehacker emc runs SCARA kinematics just fine | 02:01 |
| genehacker | EMC? | 02:01 |
| * kanzure- sighs | 02:01 | |
| fenn | ffs you dont know about emc? | 02:01 |
| genehacker | I did at one point | 02:02 |
| fenn | linuxcnc.org | 02:02 |
| genehacker | but in my current sleep deprived state | 02:02 |
| genehacker | WHOA | 02:02 |
| genehacker | wait a second | 02:02 |
| genehacker | wait one second | 02:02 |
| * fenn waits | 02:02 | |
| genehacker | did you just say runs SCARA kinematics? | 02:02 |
| genehacker | as in figures out how to move a machine tool? | 02:02 |
| kanzure- | hahahah | 02:03 |
| kanzure- | on the news, there was a mother talking about the flu | 02:03 |
| kanzure- | and how she is protecting her child | 02:03 |
| kanzure- | and she said at the end, | 02:03 |
| genehacker | to machine stuff | 02:03 |
| fenn | http://wiki.linuxcnc.org/cgi-bin/emcinfo.pl?videos | 02:03 |
| genehacker | by not vaccinating | 02:03 |
| kanzure- | "so just do what you're supposed to do, keep them clean and keep them in doors if they're sick" | 02:03 |
| kanzure- | "and hopefully they'll find a vaccine soon" | 02:03 |
| kanzure- | not that we, you know, don't already have one :p | 02:03 |
| genehacker | unfortunately there isn't going to be one soon | 02:04 |
| genehacker | however... | 02:04 |
| kanzure- | er, wait | 02:04 |
| genehacker | if we get this gene synth working... | 02:04 |
| kanzure- | I've screwed up | 02:04 |
| genehacker | fenn can it do polar robots | 02:04 |
| fenn | yes | 02:04 |
| kanzure- | isn't that just a form of coordinate transformation though? | 02:04 |
| kanzure- | am I missing something substantial? | 02:05 |
| fenn | it's "just" a coordinate transformation | 02:05 |
| kanzure- | right | 02:05 |
| genehacker | can it move the head at constant velocity> | 02:05 |
| kanzure- | doesn't that depend on your controller | 02:05 |
| genehacker | if it does | 02:06 |
| fenn | there's all kinds of other crap you have to keep separate in the cognitive model though, which trips up a lot of people (programmers) | 02:06 |
| kanzure- | when doing coordinate transformations? | 02:06 |
| kanzure- | hrm. | 02:06 |
| genehacker | is it compatible with legos? | 02:06 |
| fenn | what do you mean constant velocity? | 02:06 |
| genehacker | hmmmm... | 02:06 |
| genehacker | move in straight line at 3 units/s | 02:06 |
| fenn | there's variable blending of corners to keep the speed up, if that's what you mean | 02:06 |
| fenn | sure, that's the most basic thing | 02:07 |
| genehacker | I want to move the arm of a scara robot in a straight line at constant speed | 02:07 |
| genehacker | actually I want to use a polar robot to make straight lines of goop | 02:08 |
| fenn | aw poo now i can't find the screencast of the scara simulation | 02:08 |
| fenn | i never did figure out how to do a screencast of opengl stuff | 02:08 |
| fenn | or i'd just record it myself | 02:09 |
| kanzure- | the mesa 3d people should know | 02:09 |
| kanzure- | (software layer opengl) | 02:09 |
| genehacker | looks like it might work for me fenn | 02:09 |
| fenn | i was using software rendering | 02:09 |
| genehacker | so you know I made a polar 3d printer | 02:09 |
| fenn | so you say | 02:09 |
| kanzure- | you're all liars! | 02:10 |
| genehacker | I never got around to writing software to drive it | 02:10 |
| fenn | yes, i cut down your cherry tree | 02:10 |
| fenn | i cannot tell a lie | 02:10 |
| genehacker | http://www.statesman.com/ | 02:11 |
| kanzure- | what about it? | 02:11 |
| genehacker | swine flu | 02:12 |
| genehacker | well I'm going to bed | 02:12 |
| genehacker | enjoy this: | 02:12 |
| genehacker | http://www.mrdv.org/experiences.html | 02:14 |
| genehacker | automatic assembly of sand molds and stuff | 02:15 |
| genehacker | http://www.honeybeerobotics.com/eva-compatible.html | 02:15 |
| genehacker | special truss joints made for robots to assemble | 02:16 |
| genehacker | can't figure out how they work | 02:16 |
| genehacker | fenn that simulation show the arm moving at constant velocity! | 02:18 |
| fenn | heh "Egypt slaughtered all its pigs" | 02:18 |
| genehacker | $100 genome | 02:19 |
| genehacker | http://www.technologyreview.com/biomedicine/22112/ | 02:19 |
| genehacker | well I'm AFK | 02:19 |
| * kanzure- is still looking for his sap | 02:24 | |
| kanzure- | or some way to make roots weep. | 02:25 |
| kanzure- | "The ability to secrete a vast array of compounds into the rhizosphere is one of the most remarkable metabolic features of plant roots, with nearly 5% to 21% of all photosynthetically fixed carbon being transferred to the rhizosphere through root exudates (Marschner, 1995)." | 02:28 |
| fenn | wow | 02:29 |
| kanzure- | it would be so amazingly awesome if we can just get roots to cry out our recombinant proteins | 02:29 |
| kanzure- | put those things into a mist/vapor bioreactor | 02:29 |
| kanzure- | hang them on some metal mesh | 02:30 |
| kanzure- | probably something like a plastic bag + fan + water bottle + growth media of undetermined substrate | 02:30 |
| kanzure- | er, plastic bag would have a hole at the top so that the greeneries could be facing the sun or something | 02:30 |
| kanzure- | or a lighting system. | 02:30 |
| kanzure- | # Marschner H (1995) Mineral Nutrition of Higher Plants, Ed 2. Academic Press, London | 02:32 |
| kanzure- | well that's not encouraging | 02:32 |
| kanzure- | "Structural analysis of secreted root slime from maize" | 02:35 |
| kanzure- | interesting. plant cells "separate" from the root cap to go out to test the soil for various pathogenic-incompatibilities before a root "decides" to grow in one direction in some species. | 02:38 |
| kanzure- | heh "mucilage" | 02:38 |
| fenn | scout cells? | 02:43 |
| kanzure- | yes | 02:47 |
| kanzure- | I wish *I* had scout cells for dealing with potentially moving into new places or with new people .. | 02:48 |
| kanzure- | leave a few neurons behind or something? | 02:48 |
| kanzure- | eric might find a use for something like that | 02:49 |
| kanzure- | hrm. there's not much of an evolutionary advantage to secrete any particular protein | 02:50 |
| kanzure- | there seems to be advantages to secreting that slime of organic compounds | 02:50 |
| kanzure- | I would think that protein excretion could at least be used to break down hard soil, right? | 02:51 |
| kanzure- | "Regulation of synthesis and transport of secreted proteins in cereal aleurone | 02:51 |
| fenn | a lot of secreted "slime" (glycoprotein) is used for communication with bacteria and moisture retention | 02:56 |
| kanzure- | this is the best I can find | 02:56 |
| kanzure- | http://heybryan.org/books/papers/Production%20of%20recombinant%20proteins%20in%20plant%20root%20exudates.pdf | 02:56 |
| kanzure- | production of recombinant proteins in plant root exudates | 02:56 |
| fenn | why plants btw? is yeast or bacteria not good enough? | 02:57 |
| kanzure- | I like the concept of dripping | 02:57 |
| kanzure- | and want to avoid buffers, purification steps, centrifugation | 02:57 |
| kanzure- | god, I suck for wanting to avoid centrifugation | 02:57 |
| fenn | you know you can code for protein secretion from cells | 02:58 |
| fenn | er, bacteria and yeast | 02:58 |
| fenn | well, bacteria at least | 02:58 |
| kanzure- | right | 02:58 |
| kanzure- | I've seen a few papers about that | 02:58 |
| kanzure- | but it secretes it into the growth medium | 02:58 |
| kanzure- | and that isn't necessarily human digestable | 02:58 |
| fenn | yeah it's full of cells :\ | 02:58 |
| kanzure- | not that I'm necessarily interested in the human digestion of the products | 02:58 |
| kanzure- | but it would be a very nice perk | 02:58 |
| fenn | fertilizer doesnt sound too appetizing either | 02:59 |
| kanzure- | for plants? | 02:59 |
| kanzure- | that's why you use a mist/vapor reactor | 02:59 |
| fenn | plant fertilizer for human digestion | 02:59 |
| fenn | mist is unnecessary complication | 02:59 |
| kanzure- | why? | 03:00 |
| fenn | you can grow plants in a pot of water if needed | 03:00 |
| kanzure- | but then you have the roots in the water | 03:00 |
| fenn | sfw | 03:00 |
| kanzure- | fertilizer? | 03:00 |
| fenn | if you catch mist droplets it'll be full of water and fertilizer too | 03:00 |
| kanzure- | I think we can mechanically constrain that cleverly | 03:00 |
| fenn | how? | 03:01 |
| fenn | you can't have one droplet full of protein and another droplet full of fertilizer, not without some kind of purification | 03:01 |
| kanzure- | make the mist travel more in one direction and have a collection unit thingy | 03:01 |
| fenn | bah whatever | 03:01 |
| * fenn stomps off to do some errand | 03:01 | |
| kanzure- | well, I'll consider putting it in water | 03:02 |
| kanzure- | but not if the fertilizer is some nasty cow shit | 03:02 |
| kanzure- | "In modern tobacco farming, Nicotiana seeds are scattered onto the surface of the soil, as their germination is activated by light." (that last paper uses tobacco plants) | 03:31 |
| kanzure- | looks ok to seed them in manure but then wash them thoroughly when transplanting them to a liquid medium or something (once the roots start growing significantly) | 03:31 |
| kanzure- | is it illegal to grow tobacco, and should I care? | 03:32 |
| ybit | finally the interwebs are working again | 03:38 |
| ybit | who's solved the flu epidemic yet | 03:40 |
| ybit | any i never got a response (unless it was while i was offline all day), where did this nice cell membrane svg come from | 03:43 |
| kanzure- | ybit: solved, sort of | 03:43 |
| kanzure- | not really though | 03:43 |
| kanzure- | did you see the oseltamivir synthesis steps I posted to diybio? | 03:44 |
| kanzure- | the genome has been partly sequenced and links were posted to diybio | 03:44 |
| kanzure- | in other news, I've been reading up on recombinant protein expression in plant roots. | 03:44 |
| ybit | from latex right? | 03:45 |
| ybit | of a dandelion or something like that | 03:45 |
| kanzure- | well, the latex stuff is if you want to crunch up a dandelion stem and leafs | 03:45 |
| kanzure- | and then you have to centrifuge it | 03:45 |
| kanzure- | but, roots just secrete shit all the time | 03:45 |
| ybit | http://imgbin.org/images/473.jpg :: picture of the newly planted garden | 03:46 |
| ybit | taken this sunday | 03:46 |
| ybit | http://imgbin.org/images/474.jpg | 03:46 |
| ybit | http://imgbin.org/images/474.jpg | 03:46 |
| ybit | eh | 03:47 |
| kanzure- | your garden? | 03:47 |
| ybit | http://imgbin.org/images/475.jpg | 03:47 |
| ybit | yup | 03:47 |
| kanzure- | not to be mean, but the quality of those photos is terrible | 03:47 |
| ybit | i am mapping it out as well | 03:47 |
| ybit | not mean at all | 03:47 |
| ybit | it's from my crappy cell | 03:47 |
| ybit | that's my initial take on it with inkscape: http://imgbin.org/images/472.png | 03:48 |
| ybit | need to find some better mapping tools and need to have the soil tested as well | 03:48 |
| ybit | there's also a creek there, forgot to put it on there | 03:49 |
| ybit | so what did drew endy have to say? :P | 03:51 |
| kanzure- | nothing much | 03:52 |
| kanzure- | he just pointed out some big problems with the article | 03:53 |
| kanzure- | for instance, the author said that you could get free biobricks from the biobrick foundation | 03:53 |
| kanzure- | or that diybio-boston would send you plasmids | 03:53 |
| ybit | meh, got to hate that | 03:53 |
| kanzure- | so he was concerned about the lies | 03:53 |
| kanzure- | and in particular also concerned with the "anti-scientist" mentality being portrayed | 03:53 |
| ybit | ..when journalists botch an article | 03:54 |
| ybit | here's an example, though not as interesting as diybio: www.florala.net/news/2009/01/29/Life/Quidditch.Tournament-3602923.shtml | 03:54 |
| * ybit wonders why he didn't go for the journalist | 03:55 | |
| kanzure- | oh yay, http://www.google.com/search?q=grow+your+own+tabacco&ie=utf-8&oe=utf-8&aq=t&rls=com.ubuntu:en-US:unofficial&client=firefox-a | 03:55 |
| kanzure- | apparently people already do it | 03:55 |
| kanzure- | hrm. and people already do hydroponic tobacco. | 03:56 |
| kanzure- | http://forums.gardenweb.com/forums/load/hydro/msg0819555231905.html | 03:56 |
| kanzure- | http://www.hydroponicsonline.com/faq/growing+tobacco.html | 03:58 |
| ybit | not yet... "[22:43] <kanzure-> did you see the oseltamivir synthesis steps I posted to diybio?" | 03:59 |
| kanzure- | http://www.howtogrowtobacco.com/forum/viewtopic.php?f=14&t=226 | 03:59 |
| kanzure- | 5 to 10 gallon bubbler? blah. | 03:59 |
| kanzure- | how is it that they were using just a flask in the paper? | 03:59 |
| ybit | sweet. i'm looking forward to doing a lot of what's mentioned on the mailing lists soon, money is starting to accumulate so that i may | 04:02 |
| kanzure- | this is looking increasingly more reasonable | 04:04 |
| kanzure- | did you see the agrobacterium harvesting stuff? | 04:04 |
| kanzure- | you can hunt around a forest for it | 04:04 |
| kanzure- | freeze-thaw method of transformation | 04:04 |
| kanzure- | then streak it over the leafs of your favorite plant | 04:04 |
| ybit | i saw it, haven't read it yet | 04:04 |
| ybit | have you guys seen the studies showing that older bilingual minds are sharper than monolingual ones? | 04:08 |
| ybit | i wonder how similar a bilingual mind is with a monolingual computer scientist or mathematician | 04:11 |
| kanzure- | maybe supermemo.com has something | 04:15 |
| ybit | i forgot about supermemo | 04:15 |
| ybit | never tried it either | 04:19 |
| ybit | there are some interesting faqs though | 04:19 |
| kanzure- | hrm. generation of induced pluripotent stem cells via recombinant proteins. | 04:27 |
| kanzure- | http://heybryan.org/books/papers/Generation%20of%20induced%20pluripotent%20stem%20cells%20using%20recombinant%20proteins%20-%20purely%20protein%20pluripotency.pdf | 04:27 |
| kanzure- | and then the recent one I just linked to- re: recombinant protein expression in tobacco roots, .. might be interesting. | 04:28 |
| kanzure- | those proteins reprogram somatic cells. which is interesting. | 04:28 |
| kanzure- | taq polymerase. | 04:30 |
| kanzure- | hey cis-action | 04:57 |
| fenn | so, once you get a transformed tobacco plant, can you keep it alive indefinitely? | 10:10 |
| fenn | or could you breed it and make seeds? | 10:10 |
| fenn | kanzure-: did you ever read the paper about transforming with pollen? they used tobacco specifically | 10:18 |
| fenn | by Wantana Tangpremsri | 10:26 |
| * fenn kicks filebin.* | 10:27 | |
| fenn | ftp://166.111.30.161/pub/3.ÉúÎïÎÄÏ×/Methods in Molecular Biology/Agrobacterium Protocols I.pdf | 12:40 |
| fenn | ftp://166.111.30.161/pub/3.ÉúÎïÎÄÏ×/Methods in Molecular Biology/Agrobacterium Protocols II.pdf | 12:40 |
| fenn | 500 pages with pictures is a bit more than i expected in a 5MB file | 12:52 |
| wrldpc | Colossus: http://video.google.com/videoplay?docid=-7412690463406323384 | 13:49 |
| wrldpc | The film is being played today at the Brattle Square theatre in Cambridge as part of the Cambridge Sci Festival. | 13:49 |
| wrldpc | http://www.openfarmtech.org | 13:51 |
| kanzure- | fenn: no, what pollen paper? | 13:58 |
| kanzure- | wrldpc: we talk about openfarmtech.org in here all the time :p | 13:58 |
| wrldpc | sorry | 13:58 |
| kanzure- | wrldpc: why? | 14:03 |
| kanzure- | oh, you gave me an author name. thank you. | 14:13 |
| kanzure- | hrm. pollen as a vector. | 14:13 |
| kanzure- | http://www.fao.org/agris/search/display.do?f=./1998/v2410/TH1998000390.xml;TH1998000390 | 14:13 |
| fenn | "Genetic transformation in Nicotiana tabacum using pollen as a vector", specifically | 14:16 |
| fenn | but it looks like the same protocol | 14:16 |
| kanzure- | don't have access. | 14:19 |
| fenn | if you can find a place for me to upload .pdf's that isnt broken, i'll upload it | 14:19 |
| wrldpc | filedropper.com | 14:19 |
| fenn | web 2.0: making simple things complicated! | 14:21 |
| kanzure | fenn: you already have a user account on adl.serveftp.org | 14:21 |
| fenn | ah so i do | 14:22 |
| kanzure | no idea what the password is | 14:22 |
| fenn | good :) | 14:23 |
| kanzure | are you able to log in? | 14:23 |
| fenn | yes | 14:23 |
| kanzure | please put it in public_html just for the sake of it | 14:24 |
| kanzure | or, er, nevermind | 14:24 |
| kanzure | http://adl.serveftp.org/papers/pollen_transformation.pdf | 14:25 |
| fenn | yay | 14:25 |
| faceface | I am not sure if this is the right place to post this but I do not know | 14:27 |
| faceface | who else to ask. I am currently applying to college and want to study | 14:27 |
| faceface | bioinformatics. I have a few questions which my college advisors cannot | 14:27 |
| kanzure- | "any DNA introduced into the pollen tube tip this way would have to .." | 14:27 |
| kanzure- | RAPE | 14:27 |
| faceface | wrong channel | 14:27 |
| faceface | its not me its some other dude | 14:27 |
| kanzure- | yeah I saw the email | 14:27 |
| faceface | kanzure-: meant to paste in #bioinf | 14:27 |
| faceface | kanzure-: I am a director of bioinf.org now | 14:27 |
| kanzure- | do you mean bioinformatics.org ? | 14:28 |
| faceface | yup | 14:28 |
| kanzure- | hm | 14:28 |
| faceface | I don't know what it means | 14:28 |
| faceface | but they voted me in | 14:28 |
| kanzure- | well, make sure you take good care of /pogo/ | 14:28 |
| faceface | Page not found | 14:28 |
| faceface | The Pogo - Posam Project! | 14:29 |
| kanzure | http://www.bioinformatics.org/pogo/ | 14:29 |
| kanzure | seems to work for me. | 14:29 |
| faceface | I read pongo | 14:29 |
| faceface | but I see it now | 14:29 |
| faceface | what can I do to help? | 14:30 |
| kanzure- | just don't let it vanish | 14:31 |
| kanzure- | fenn: so, this looks easier than hunting for agrobacterium | 14:31 |
| splicer | (I wonder if it's control system is named after the old punk rock dance) | 14:34 |
| splicer | (( http://en.wikipedia.org/wiki/Pogo_(dance) )) | 14:35 |
| kanzure | neat, koyaanisqatsi is on google video now | 14:51 |
| kanzure | http://video.google.com/videoplay?docid=5539613947839465921&hl=en | 14:51 |
| faceface | awesome! | 14:52 |
| faceface | I love that | 14:52 |
| splicer | speaking of google video... did you see the show about bacteriophages? apparently the georgians have used bacteriophages and since the 40:ies... and use them as often as traditional antibiotics still. | 15:02 |
| splicer | http://video.google.com/videoplay?docid=8887931967515748990 | 15:02 |
| splicer | seems to be a possible solution to the resistant bacteria problem | 15:02 |
| kanzure | http://singularityhub.com/2009/04/29/who-is-diybioorg/ | 15:11 |
| splicer | I love the quote "Once you go around the internet a certain number of times, you begin to run into the same people, ..." | 15:21 |
| kanzure | are you being sarcastic? | 15:29 |
| splicer | no | 15:31 |
| splicer | it's something that's true... just never heard it put like that before | 15:31 |
| splicer | (Powaqqatsi and Naqoyqatsi are on google video too) | 15:32 |
| kanzure | http://prezi.com/51683/view/#47 annoying bodyhacking presentation | 15:34 |
| kanzure | (for austin) | 15:34 |
| kanzure | splicer: I like "Anima Mundi". | 15:34 |
| splicer | looks nice | 15:37 |
| splicer | (anima mundi) | 15:37 |
| kanzure- | I forgot how terrible most AMVs are. people don't even know how to synch up clips to music any more. | 15:56 |
| kanzure- | and rarely anybody edits out mouth movement .. amateurs. | 15:56 |
| kanzure- | splicer: I like 10:40~ in the video in particular. | 15:57 |
| xp_prg | zinc fingers look cool! | 17:07 |
| xp_prg | can zinc fingers be used in a xenopus egg? | 17:08 |
| kanzure | what is a pro domain? | 17:14 |
| genehacker | kanzure I think you are forgetting the true purpose of AMVs | 17:21 |
| genehacker | the true purpose of an AMV is to liberate music by using fair use | 17:22 |
| -!- duzt|sleep is now known as duzt | 17:57 | |
| kanzure | cis-action: hey. | 17:58 |
| cis-action | hi. | 17:59 |
| kanzure | any idea what a prodomain is? | 17:59 |
| genehacker | http://technology.timesonline.co.uk/tol/news/tech_and_web/the_web/article6169488.ece | 18:21 |
| genehacker | we need mesh nets | 18:21 |
| kanzure | so.. | 18:23 |
| kanzure | there's a protein we can express in tobacco | 18:23 |
| kanzure | that inhibits myostatin | 18:23 |
| genehacker | hehehehehe | 18:24 |
| genehacker | hope they aren't right about internet brownouts | 18:29 |
| genehacker | hmmm.... | 18:32 |
| genehacker | we need wifi blimps | 18:32 |
| genehacker | how would we do long range communication though? | 18:35 |
| kanzure | satellites | 18:35 |
| kanzure | lasers | 18:35 |
| kanzure | pidgeons | 18:35 |
| genehacker | what about rain? | 18:36 |
| genehacker | that stops lasers | 18:36 |
| genehacker | though I've heard of military submarines talking to satellites WHILE UNDERWATER | 18:36 |
| genehacker | perhaps just build so many wifi blimps that the FCC doesn't bother asking for liscenses | 18:37 |
| kanzure | residues 42 through 115 of myostatin can be expressed to inhibit myostatin. | 18:37 |
| kanzure | 42 through 115. just remember that and you're good to go. | 18:38 |
| genehacker | huh? | 18:38 |
| kanzure | don't know if this has to be intraveneous or if oral administration of this propeptide will cause myostatin inhibition. hrm. | 18:38 |
| genehacker | mystatin inhibits myostatin? | 18:38 |
| kanzure | a region of myostatin :) | 18:38 |
| genehacker | interesting | 18:39 |
| genehacker | makes sense | 18:39 |
| genehacker | why are you trying to inhibit myostatin again? | 18:40 |
| genehacker | I know what the result is | 18:41 |
| kanzure | becaues it is easier to observe myostatin inhibition than it is to figure out whether or not gene expression modulation in the brain is taking place | 18:42 |
| kanzure | think of it as a precursor experiment | 18:42 |
| genehacker | is this what you want to make with those weird recombination plant roots | 18:42 |
| kanzure | maybe, it's certainly an option | 18:42 |
| genehacker | you aren't going to... | 18:42 |
| kanzure | although taq polymerase is also a candidate option | 18:42 |
| genehacker | well let's make a DNA synth first | 18:43 |
| genehacker | so | 18:43 |
| genehacker | we need an anoxic chamber | 18:43 |
| kanzure | why | 18:43 |
| genehacker | don't you have to do DNA synthesis in an oxygen free environment? | 18:43 |
| kanzure | what type of DNA synthesis? | 18:43 |
| kanzure | because remember, DNA synthesis was originally done by pipetting shit in a lab | 18:44 |
| genehacker | hmmm... | 18:44 |
| genehacker | then why does posam do it in an anoxic chamber | 18:44 |
| kanzure | Syringe method for stepwise chemical synthesis of oligonucleotides | 18:44 |
| kanzure | http://heybryan.org/books/Biology/Syringe%20method%20for%20stepwise%20chemical%20synthesis%20of%20oligonucleotides.pdf | 18:44 |
| genehacker | yeah | 18:44 |
| kanzure | posam is a different technique- an inkjet oligonucleotide arrayer thingy | 18:44 |
| genehacker | I'll think I'll read some papers again | 18:44 |
| kanzure | be sure to take notes. | 18:44 |
| genehacker | why's it done in an anoxic chamber? | 18:44 |
| genehacker | or I might hold off on this until after finals | 18:45 |
| kanzure | drying | 18:46 |
| kanzure | and control of relative humidity | 18:46 |
| genehacker | oh that makes sense | 18:47 |
| genehacker | this makes things easier for us ;0 | 18:47 |
| genehacker | so, we need to find if LCD screens pass UV | 18:48 |
| genehacker | so one of the limits to how small we can make the spot on the slide is the wavelength of light | 18:50 |
| genehacker | otherwise we need to figure out how to get some DMD chips | 18:52 |
| genehacker | NOT THE ONES FROM GOLDMINE | 18:52 |
| genehacker | http://www.invertercentral.com/qrySpecSheet.asp?page=srlp&model=L3P09X-25G01&Country= | 18:57 |
| genehacker | this one looks like it should work | 18:57 |
| genehacker | according to this paper | 18:57 |
| genehacker | http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THG-4S0PK6W-1&_user=108429&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059713&_version=1&_urlVersion=0&_userid=108429&md5=31060c0c6a75500c1e9022af03525872 | 18:57 |
| kanzure- | GASP-1 http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=9737&log$=databasead&logdbfrom=protein | 19:00 |
| kanzure- | (GASP-1 inhibits myostatin) | 19:00 |
| kanzure- | aha, here we go | 19:02 |
| kanzure- | http://www.ncbi.nlm.nih.gov/nuccore/150378450?report=fasta | 19:02 |
| genehacker | ummm | 19:03 |
| genehacker | that paper used a VERY tiny LCD screen | 19:03 |
| genehacker | a very high res LCD screen | 19:03 |
| genehacker | Screen size18.5 mm × l3.9 mm | 19:03 |
| genehacker | Pixel size18 μm × 18 μm | 19:03 |
| genehacker | Number of pixels1028 × 772 | 19:03 |
| genehacker | NA>54% | 19:03 |
| genehacker | MicrolensBuilt-in | 19:04 |
| kanzure | rats. GASP-1 is 5985 bp. | 19:09 |
| kanzure | guess we'll have to build a DNA synthesizer. | 19:09 |
| genehacker | http://www.surplusshed.com/pages/item/l3590.html | 19:09 |
| genehacker | blast | 19:09 |
| genehacker | not available! | 19:09 |
| kanzure | or | 19:09 |
| kanzure | just the primers | 19:10 |
| genehacker | pretty cheap | 19:10 |
| kanzure | so that we could copy it out of the human genome | 19:10 |
| genehacker | It is expected that this technique can be applied to the fabrication of μTAS chips such as the flow channel with tapered shapes. 3D MEMS devices may also be fabricated without requiring a repetitive exposure procedure. In addition, this technique is expected to be applied to synthesis technology in DNA chip production because this technique can be applied for controlling the lighting area... | 19:12 |
| genehacker | ...and exposure distribution in order to control various photochemical reactions. | 19:12 |
| genehacker | heh | 19:12 |
| genehacker | indeed | 19:12 |
| genehacker | if we could only get that 13 by 18 mm LCD | 19:12 |
| kanzure | have you read the papers that I have? | 19:13 |
| kanzure | http://heybryan.org/books/papers/Generation%20of%20laser-induced%20cavitation%20bubbles%20with%20a%20digital%20hologram%20-%20LCD%20-%20spatial%20light%20modulator.pdf | 19:13 |
| kanzure | http://heybryan.org/books/papers/Versatile%20stepper%20based%20maskless%20microlithography%20using%20a%20liquid%20crystal%20display%20(LCD)%20for%20direct%20write%20of%20binary%20and%20multilevel%20microstructures%20-%202007%20-%20awesome.pdf | 19:13 |
| kanzure | http://heybryan.org/books/papers/Photolithography%20system%20with%20liquid%20crystal%20display%20as%20active%20gray-tone%20mask%20for%203D%20structuring%20of%20photoresist.pdf | 19:13 |
| genehacker | http://cgi.ebay.com/Infocus-X2-Projector-BURNT-BULB-industrial-home-theater_W0QQitemZ170324893314QQcmdZViewItemQQptZLH_DefaultDomain_0?hash=item170324893314&_trksid=p3286.c0.m14&_trkparms=66%3A2|65%3A1|39%3A1|240%3A1318|301%3A0|293%3A1|294%3A50 | 19:19 |
| genehacker | I think we have a winner | 19:19 |
| genehacker | btw look up grayscale lithography | 19:19 |
| genehacker | it's crazy | 19:19 |
| genehacker | you can make wedges | 19:20 |
| genehacker | http://cgi.ebay.com/Optoma-EP735-DLP-Projector-BROKEN-GOOD-FOR-PARTS_W0QQitemZ230339429134QQcmdZViewItemQQptZLH_DefaultDomain_2?hash=item230339429134&_trksid=p3286.c0.m14&_trkparms=66%3A2|65%3A1|39%3A1|240%3A1318|301%3A1|293%3A1|294%3A50 | 19:25 |
| genehacker | heheheheh | 19:25 |
| genehacker | maybe we should try goodwill? | 19:25 |
| genehacker | heard they have flat panel tvs real cheap | 19:25 |
| kanzure | so, I'm moving in next to a harbor freight | 19:26 |
| kanzure | and will have spending/project monies | 19:26 |
| kanzure | is this dangerous? | 19:26 |
| genehacker | yes | 19:35 |
| genehacker | don't they sell cheap chinese mills? | 19:35 |
| genehacker | yeah | 19:36 |
| genehacker | they do | 19:36 |
| kanzure- | how big? | 19:40 |
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