| --- Day changed Tue May 12 2009 | ||
| genehacker | http://www.sciencedaily.com/releases/2009/05/090510200001.htm | 02:05 |
|---|---|---|
| fenn | how convenient | 02:20 |
| fenn | but is it more convenient than just engineering whatever you're after to be expressed in e. coli? | 02:20 |
| genehacker | ??? | 02:24 |
| genehacker | dunno | 02:24 |
| -!- genehacker_ is now known as genehacker | 02:36 | |
| faceface | kanzure-: about transfection - yup and yup - both great ideas. | 09:02 |
| kanzure- | faceface: which two were good ones | 15:50 |
| kanzure- | Functional cross-kingdom conservation of mammalian and moss (Physcomitrella patens) transcription, translation and secretion machineries | 15:50 |
| kanzure- | http://adl.serveftp.org/papers/Functional%20cross-kingdom%20conservation%20of%20mammalian%20and%20moss%20(Physcomitrella%20patens)%20transcription,%20translation%20and%20secretion%20machineries.pdf | 15:50 |
| kanzure- | huh. apparently /tmp needs to be chmod'd for global read/write. | 15:55 |
| kanzure- | fenn: feel like coming into the lab today? | 15:58 |
| kanzure- | "Devil's Theory of Innovation: Competition produces stasis. Only complacency drives change. .. animals' appearance alters and their behavior changes not in conditions of scarcity, but in landscapes of plentitude. This pattern makes for 'relaxed selection'." | 16:07 |
| genehacker | glad you saw that one | 16:23 |
| genehacker | also heybryan was down last time I checked | 16:24 |
| xp_prg | kanzure do you see the demonizing of do it yourself biologists? | 17:16 |
| kanzure- | xp_prg: I see morons. | 17:42 |
| kanzure- | genehacker: I don't have an internet connection at the apartment yet. | 17:42 |
| kanzure- | genehacker: are you on campus? | 17:42 |
| xp_prg | what is the best wiki to use kanzure? | 18:50 |
| kanzure- | hahah http://common-lisp.net/project/clpython/ | 19:22 |
| cis-action | kanzure-: http://www.vimeo.com/4614021 | 19:36 |
| kanzure- | what is it? | 19:37 |
| cis-action | it's a video and my notes about searching across large pdf collections | 19:38 |
| cis-action | I also am in the middle of testing out the olpc and the kindle as mobile readers for the pdf library. I have some pictures comparing them. | 19:38 |
| kanzure- | okay | 19:39 |
| kanzure- | on Wednesday I should be back to my normal self | 19:39 |
| cis-action | ... is it exam time or something? | 19:39 |
| kanzure- | yes | 19:39 |
| kanzure- | but I also do not have an internet connection back at the apartment | 19:39 |
| cis-action | oh. | 19:39 |
| kanzure- | just moved. | 19:39 |
| fenn | kanzure-: just got up. i actually was thinking about coming down to the lab today | 19:41 |
| genehacker | check out diybio | 19:42 |
| genehacker | http://groups.google.com/group/diybio/browse_thread/thread/7a108447506cd579?hl=en | 19:42 |
| genehacker | http://groups.google.com/group/diybio/browse_thread/thread/7a108447506cd579?hl=en | 19:43 |
| kanzure- | genehacker: what about it | 19:44 |
| genehacker | oh no, biohackers are gonna STEAL YOUR DNA AND USE IT TO GROW HORRIBLE DOOMSDAY VIRUSES THAT WILL CAUSE COMMUNISM IN AMERICA | 19:45 |
| genehacker | is pretty much what those articles said | 19:45 |
| genehacker | That's when the phone rang. A man saying he was doing research for the U.S. government called with a few polite, pointed questions: How did she build that lab? Did she know other people creating new life forms at home? | 19:45 |
| genehacker | hmmmm... | 19:45 |
| genehacker | makes me want to build that DNA synth from a projector even more | 19:46 |
| genehacker | they'd totally freak out | 19:46 |
| kanzure- | "don't poke the bear" | 19:48 |
| genehacker | if I got a call from the government, I'd totally troll them | 19:48 |
| genehacker | oh yeah, we need to figure out how to extract DNA from microarrays before we can have fun | 19:48 |
| kanzure- | what do you mean 'extract' | 19:49 |
| kanzure- | usually you just have a bead bound to a surface via streptavidin | 19:49 |
| kanzure- | and then you release the streptavidin bond via some enzyme or something | 19:49 |
| genehacker | the oligos are stuck to the chip | 19:49 |
| kanzure- | er, however that stuff works. It's been a while since I've reviewed it. | 19:49 |
| kanzure- | not if you grow the oligos on beads, or something | 19:49 |
| genehacker | it's bonded via a silane group | 19:49 |
| genehacker | or something like that | 19:50 |
| kanzure- | doesn't have to be. | 19:50 |
| genehacker | I was thinking something like PCR | 19:50 |
| kanzure- | ? | 19:50 |
| genehacker | v | 19:51 |
| genehacker | http://arep.med.harvard.edu/pdf/Tian04.pdf | 19:51 |
| genehacker | here's how they do it currently | 19:51 |
| kanzure- | fenn: clisp -c isn't compiling for me :( | 19:52 |
| genehacker | is there some sort of method to induce double stranded breaks in DNA | 19:52 |
| genehacker | IE you have AAAAAATTTT | 19:52 |
| genehacker | and you want just the AAAAAA part | 19:52 |
| kanzure- | "clisp is a common lisp interpreter. It is easy to use, but does not compile to binary executables." <- oh. | 19:53 |
| genehacker | well I have to go | 19:53 |
| kanzure- | genehacker: surely you know about endonucleases | 19:53 |
| genehacker | no | 19:53 |
| kanzure- | it breaks apart DNA at a specific sequence | 19:53 |
| genehacker | what do they do? | 19:53 |
| kanzure- | it breaks apart DNA at a specific sequence | 19:53 |
| genehacker | with sticky ends? | 19:53 |
| genehacker | I don't want stickyends | 19:53 |
| kanzure- | I think so. yes. | 19:53 |
| kanzure- | what do you want? | 19:53 |
| fenn | why not sticky ends? | 19:54 |
| fenn | can't see how you'd build a decent length sequence otherwise | 19:54 |
| fenn | but anyway you're only synthesizing a single strand | 19:54 |
| genehacker | I want (DNA Sequence I want) seperated(sequence that bonds it to the chip) | 19:55 |
| genehacker | well I gotta go search campus for where the heck my review session is | 19:55 |
| fenn | so, speaking of which kanzure- will you be at the lab a while? | 19:57 |
| kanzure- | no, I'm leaving at 4:15. | 19:58 |
| kanzure- | hrm. I should zip up my modifications to adesign.. | 19:58 |
| fenn | did you ever get it working in interactive mode? | 19:58 |
| kanzure- | before that happens I have to get it to run a bit faster. in the non-interactive mode it's doing something but slowly- campbell says to try to compile it into a binary. | 19:59 |
| kanzure- | my work is largely in bryantest.lisp and any file that has been modified in 2009 (or the last 5 years for that matter) | 19:59 |
| kanzure- | http://adl.serveftp.org/papers/adesign-edited.zip | 20:01 |
| fenn | maybe you should try to acquire a copy of franz lisp | 20:01 |
| kanzure- | comments are sprinkled throughout the files now, somewhat explaining wtf is going on | 20:01 |
| kanzure- | http://www.cs.berkeley.edu/~fateman/lisp-opus38.92.tar | 20:02 |
| kanzure- | that? | 20:02 |
| fenn | franz is a compiler/interpreter/ide | 20:03 |
| fenn | and what campbell used iirc | 20:03 |
| kanzure- | oh. allegro lisp is what he said. | 20:04 |
| kanzure- | http://www.franz.com/downloads/ | 20:04 |
| kanzure- | aha. I see. | 20:04 |
| kanzure- | 43.1 MB .. hrm. | 20:07 |
| kanzure- | jerks. they meant to name the file .tar.bz2 instead of just .bz2 | 20:14 |
| kanzure- | so "compiling" apparently means 'run it as if it was being interpreted' | 20:41 |
| fenn | after compiling it does the same thing, but faster | 20:50 |
| fenn | you can't compile all possible interpreted expressions | 20:50 |
| kanzure- | it doesn't "compile" at all | 20:51 |
| kanzure- | it's just running the interpreted code.. | 20:51 |
| kanzure- | in other words, there's no binary being generated | 20:51 |
| kanzure- | it literally just enters the loop and runs the code. | 20:51 |
| fenn | are you trying to compile your modified version or the original? | 20:52 |
| fenn | because i think we removed a bunch of compile directives | 20:52 |
| kanzure- | should I be using the compile directives? | 20:52 |
| kanzure- | I just made a new project and imported the files into it | 20:53 |
| kanzure- | maybe I should just go dump the software on my quadcore | 21:08 |
| kanzure- | ok, I'm gone. | 21:11 |
| * fenn wonders what kanzure- does without internet access | 21:13 | |
| genehacker | the reason I don't want sticky is because | 21:35 |
| genehacker | I want a sequence that doesn't have the section that is cut in between | 21:35 |
| genehacker | so the guy that claimed to be from the government was this guy | 21:38 |
| genehacker | http://www.european-futurists.org/wEnglisch/aktuelles/2008_08_29_Interview_Nils_Gilman_meldung.php | 21:38 |
| genehacker | Nils Gilman | 21:38 |
| genehacker | posted in Diybio thread too | 21:40 |
| xp_prg | https://noisebridge.net/wiki/Hello_World_in_Synthetic_Biology#Hello_World_DNA_Cell_Based | 21:43 |
| genehacker | invalid security certificate | 21:44 |
| genehacker | let me guess | 21:44 |
| genehacker | it involves GFP | 21:45 |
| xp_prg | yup :> | 21:45 |
| genehacker | does it turn on GFP in response to something | 21:46 |
| xp_prg | yes the binding protein to the promoter reigion of the gene that makes hello world | 21:46 |
| genehacker | ok | 21:47 |
| xp_prg | so do you like the comparison? | 21:48 |
| genehacker | it's ok | 21:52 |
| genehacker | oh ok it looks like in that paper they remove the junk sequence | 21:54 |
| genehacker | or generic primer sequence | 21:54 |
| fenn | re "I want a sequence that doesn't have the section that is cut in between" | 22:57 |
| fenn | it doesn't matter if it's a restriction site or not because you are synthesizing the two complementary strands separately, so te sticky sequence can be watever you want | 22:57 |
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