| --- Log opened Mon Aug 08 00:00:15 2011 | ||
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| delinquentme | so what are the difficulties associated with unwrapping DNA? | 05:13 |
|---|---|---|
| foucist | delinquentme: well generally speaking, when a dna is duplicated, there's a pile of enzymes that unfold the dna, split it apart, and then others that copy each strand | 05:27 |
| foucist | but i don't think the strands end up completely separate, it happens in multipe spots along the dna and moves along | 05:27 |
| foucist | so as it finishes it gets wrapped up again | 05:27 |
| foucist | or some shit | 05:28 |
| delinquentme | lol | 05:28 |
| delinquentme | comparatively... is DNA as a molecule .. fragile? | 05:28 |
| foucist | i'm actualy mixing up the rna transcription and dna duplication parts in that explanation! | 05:28 |
| foucist | kinda | 05:28 |
| foucist | it's probably pretty stable in its folded up form | 05:29 |
| foucist | there's like 3-levels of folding | 05:29 |
| foucist | so it's basically tiny when folded | 05:29 |
| foucist | but HUGE when unfolded | 05:29 |
| foucist | long rather | 05:29 |
| foucist | long as hell | 05:29 |
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| delinquentme | yeah | 05:44 |
| delinquentme | histones | 05:44 |
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| delinquentme | hey so everyone else thinkgs im crazy ( whats new) .. i want to fit an electron microscope into a cm^3 .. where to start? | 06:08 |
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| kanzure | "before you put him anywhere, i would recommend making him edit his "cover letter" for grammatical and spelling errors. it comes off very unprofessionally and that might rub a serious academic the wrong way" | 07:05 |
| kanzure | " i'm not sure whether such a meandering, causal letter will get a reply from an excessively busy research professor, unless it is a simple: "thank you for your interest, maybe you should go get a degree."" | 07:05 |
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| delinquentme | so is it possible that a lab who has sequencing equipment would want additional sequence alignment power? | 07:48 |
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| drazak | who's in DIYBio Vancouver? | 08:18 |
| archels | delinquentme: electron microscope into a cubic cm? The acceleration voltages involved would probably be quite high. | 08:33 |
| delinquentme | archels, so one of the ideas i had on the matter was to "cascade" as much as possible across parallel sample scans | 08:33 |
| delinquentme | IE if i want to scan 40 samples in parallel ... i could easily place all those samples within the same vacuum chamber .. and im wondering if the same could be done for the electron gum | 08:34 |
| delinquentme | gun** IE one big one .. then just disperse the electrons and focus to individual samples | 08:34 |
| archels | Oh so now you don't want just an electron microscope in 1 cm^3, but you also want to it image 40 samples in parallel? | 08:36 |
| archels | Also, big is not that big given the size constraint. :) | 08:37 |
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| delinquentme | kanzure, on aubreys reply lol | 08:58 |
| delinquentme | i thought that academics are all about the massive run ons and endless sentences? | 08:59 |
| foucist | delinquentme: what was the email about | 09:04 |
| delinquentme | foucist, my place within aging research | 09:04 |
| foucist | at the forefront.. duh! | 09:05 |
| foucist | jk | 09:05 |
| foucist | hmm | 09:05 |
| foucist | delinquentme: what are you studying in school? | 09:06 |
| foucist | in uni | 09:06 |
| foucist | delinquentme: i think nanotech & some combo of medical/bio is good | 09:06 |
| foucist | go for a dual degree in MD/Phd in Biochemistry or some such | 09:06 |
| foucist | so you get the medical and phd awesomenezz | 09:07 |
| foucist | and go straight into rezearch | 09:07 |
| delinquentme | did business marketing | 09:07 |
| delinquentme | i dont like school | 09:07 |
| delinquentme | i'm self taught basically from the ground up | 09:07 |
| foucist | yeah skool sucks | 09:07 |
| foucist | yeah | 09:07 |
| foucist | so how do you want to contribute then? i.e. do you plan to study bio and sutff on your own? | 09:08 |
| foucist | study research papers, do experiments? or what | 09:08 |
| delinquentme | basically i want to look over biologists shoulders and take notes | 09:08 |
| delinquentme | and then come up with ways to automate what they're doing | 09:08 |
| delinquentme | in software or hardware | 09:08 |
| foucist | ah | 09:08 |
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| Tyrant | delinquentme, have you talked directly to SENS people? (not aubrey) | 10:28 |
| delinquentme | Tyrant, nah cant say i have | 10:29 |
| delinquentme | isnt he the main dude | 10:29 |
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| Tyrant | delinquentme, he's the "main dude" in the sense that he's their figure head. if you want to do work in the labs though the best people to talk to are theo nes that work their, they have quite a bit autonamy about who they get as interns, etc. | 12:06 |
| Tyrant | also I know the sens lab in the bay area is using a tecan for which they could use quite a few modifications | 12:07 |
| delinquentme | hmmm | 12:31 |
| delinquentme | i think if i had my choice | 12:31 |
| delinquentme | halcyon would be #1 | 12:31 |
| delinquentme | thoughts Tyrant ? | 12:31 |
| Tyrant | I dont think theres much youd be able to do at halcyon | 12:32 |
| delinquentme | specifics? | 12:32 |
| Tyrant | well their current problem isn't throughput or automation | 12:33 |
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| Tyrant | and working on their transmission electron microscope requires a very advanced understanding of its operation | 12:33 |
| delinquentme | oh! there are public statements of the tech they're currently working on?? | 12:34 |
| Tyrant | their big problem right now is a lack of metalorganic chemists | 12:34 |
| Tyrant | in the thiel network, yes | 12:34 |
| delinquentme | thats one of the things i was looking for ... bc damn if all these biotech companies were like "This is what we are trying to solve" | 12:34 |
| delinquentme | it would make it hella easy to be like " ok lets start here" | 12:34 |
| delinquentme | thiel network O_o;;; | 12:34 |
| delinquentme | ? | 12:34 |
| Tyrant | the network surrounding sens, halcyon, etc. etc. | 12:35 |
| delinquentme | i mean how'd you get access to this info | 12:35 |
| Tyrant | im a thiel fellow | 12:35 |
| delinquentme | @_@ | 12:35 |
| delinquentme | waiiit you're one of the 20 under 20?? | 12:35 |
| delinquentme | sorry wait | 12:35 |
| Tyrant | yeah | 12:35 |
| delinquentme | http://en.wikipedia.org/wiki/Organometallic_chemistry | 12:36 |
| Tyrant | the info isnt very difficult to get from bryan anyway | 12:36 |
| delinquentme | ^^ thats what they're after right | 12:36 |
| Tyrant | yeah | 12:36 |
| delinquentme | Tyrant, were you the guy building the HPLC machine? | 12:36 |
| Tyrant | yea | 12:36 |
| delinquentme | oh shit! | 12:36 |
| delinquentme | hahah god IRC is so bad ass!!!! | 12:36 |
| delinquentme | wow awesome to meet you | 12:37 |
| Tyrant | where do you live? | 12:37 |
| * delinquentme shakes | 12:37 | |
| delinquentme | pittsburgh | 12:37 |
| Tyrant | ah | 12:37 |
| Tyrant | you need to go to the bay area for sens/halcyon/etc. | 12:37 |
| delinquentme | frankly im interested in anyone who has stated purposes of human life extension | 12:37 |
| delinquentme | anywhere | 12:37 |
| Tyrant | I think what you're looking for is a startup that works on it | 12:38 |
| Tyrant | and thats bay area | 12:38 |
| delinquentme | yeah man i've been in a startup for a while now and startup is definitely what im after | 12:38 |
| Tyrant | A startup in pittsburg? :P | 12:38 |
| delinquentme | yeah haha | 12:38 |
| delinquentme | they're here | 12:39 |
| delinquentme | they're modest you know | 12:39 |
| delinquentme | but im just | 12:39 |
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| delinquentme | meh. like ive got this exhaulted image of what a startup founder should be | 12:39 |
| Tyrant | theres no single image of a startup founder | 12:40 |
| delinquentme | absolutely | 12:40 |
| delinquentme | however theres passion | 12:40 |
| Tyrant | generally that and hard work are the only global traits | 12:41 |
| delinquentme | yah =] i wont say anymore | 12:42 |
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| delinquentme | Collaborative Drug Discovery (CDD) << thoughts anyone? | 16:21 |
| klafka | hey | 17:09 |
| klafka | in what sense? | 17:09 |
| delinquentme | have you heard of em... and if you've got thoughts :D | 17:15 |
| klafka | oh it's a thing | 17:16 |
| klafka | no | 17:16 |
| klafka | what is really collaborative about it | 17:19 |
| klafka | it's like 'do your drug research in the CLOoooOOOooOOoooud | 17:19 |
| delinquentme | lol are you sure? | 17:20 |
| delinquentme | their website seems to be about collaborative drug discovery | 17:20 |
| klafka | https://www.collaborativedrug.com/ | 17:26 |
| klafka | ? | 17:26 |
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| delinquentme | yar! | 17:27 |
| klafka | i guess the public part | 17:28 |
| klafka | is open | 17:28 |
| delinquentme | klafka, have you ever removed parts of DNA from an organism? | 17:29 |
| klafka | sure | 17:29 |
| delinquentme | oh | 17:29 |
| delinquentme | bamf | 17:29 |
| delinquentme | whats that process involve? | 17:29 |
| klafka | um well i only did it from bacteria | 17:30 |
| delinquentme | so yeah how would i do that with ecoli | 17:30 |
| klafka | umm, i'm pretty sure I put a ligase in LB broth + ecoli and spun them in a centrifuge | 17:30 |
| delinquentme | LB ? | 17:31 |
| klafka | the culture medium | 17:31 |
| delinquentme | and spinning them in a centerfuge? | 17:31 |
| klafka | yeah | 17:31 |
| delinquentme | what does that contribute to the exchange / removal of genes? | 17:31 |
| delinquentme | energy? | 17:31 |
| klafka | it is used to separate DNA from the other crap in the cell | 17:31 |
| delinquentme | OHHHhhhhhh | 17:32 |
| delinquentme | so youre busting the organism open .. grabbing its DNA .. then you'd do the replacements | 17:32 |
| delinquentme | derp this is actually miniprep stuff isnt it? | 17:32 |
| klafka | yeah | 17:32 |
| klafka | yup | 17:32 |
| klafka | this is just standard dna purification + amplification proces | 17:32 |
| klafka | s | 17:32 |
| delinquentme | reading this article w church talking about creating an ecoli "chassis" | 17:33 |
| delinquentme | IE removing as much of the DNA as possible to support a living ecoli organism | 17:33 |
| evolv | I did it from birds and nonaviant reptiles | 17:33 |
| delinquentme | and then using that guy to ker-chunk functional DNA snippets to do stuffs | 17:34 |
| delinquentme | so then after you sub the plasmids in ... you just incubate | 17:34 |
| delinquentme | and if stuff grows >> great success? | 17:34 |
| delinquentme | i feel like im missing some part | 17:35 |
| delinquentme | subbing in the plasmids >> electroporator :P | 17:36 |
| klafka | sort of like what venter did | 17:37 |
| delinquentme | yeah but theres complexity that im missing there | 17:40 |
| delinquentme | is it the same process to get a organism to take up a new chunk of DNA as it is to get it to ditch some of its existing DNA? | 17:40 |
| delinquentme | surely replacing ... would be different than " drop these basepairs and reconnect" | 17:41 |
| klafka | no | 17:54 |
| klafka | usually organisms only get rid of DNA if you lyse the cells | 17:55 |
| klafka | you can get organisms to take up DNA much easier | 17:55 |
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| delinquentme | http://benkrasnow.blogspot.com/2011/03/diy-scanning-electron-microscope.html | 18:09 |
| delinquentme | check it! | 18:09 |
| delinquentme | klafka, correct me if im wrong but after lysing a cell that organism is no more | 18:09 |
| delinquentme | right? | 18:09 |
| klafka | well if it's single celled | 18:10 |
| delinquentme | you can selectively lyse cells? | 18:10 |
| delinquentme | i assumed that when you lyse .. all the stuff pops | 18:10 |
| QuantumG | presumably you could | 18:10 |
| delinquentme | i guess i didnt follow klafka's statement on why multicellular wouldnt die from lysing? | 18:11 |
| QuantumG | I expect he was presuming also :) | 18:12 |
| klafka | haha well i mean you can lyse cells only locally | 18:13 |
| klafka | for instance | 18:13 |
| klafka | or you can remove the cells from a multi-celled organism then lyse them | 18:13 |
| QuantumG | or just shoving a pin into your finger... | 18:14 |
| klafka | right | 18:16 |
| klafka | hence locally | 18:16 |
| delinquentme | -_________- | 18:20 |
| delinquentme | tagged my electron microscope post for relocation on stack over flowwww woot woot | 18:23 |
| QuantumG | so what sort of resolution _do_ you get? | 18:28 |
| delinquentme | QuantumG, on the DIY electron microscope? | 18:28 |
| delinquentme | or? | 18:28 |
| QuantumG | ya | 18:28 |
| delinquentme | oh i didnt get all the way through the video | 18:29 |
| delinquentme | this is strictly a concepting excercise | 18:29 |
| QuantumG | oh, I thought this was you | 18:29 |
| delinquentme | oh no | 18:29 |
| delinquentme | its sweet that we'd expect that from this channel though huh :D | 18:30 |
| delinquentme | QuantumG, what do you do on the daily? | 18:30 |
| QuantumG | well, I was actually about to say that I'm thoroughly impressed. :) | 18:30 |
| delinquentme | my heads abuzz with thoughts of venters work, with churches work, with left coast biotech startups .. man .. its wild right now | 18:30 |
| klafka | hey so have we gotten any farther with the 5 man project? | 18:31 |
| delinquentme | klafka, nope not that i know of .. i proposed we work on some of the life sciences challenges | 18:31 |
| delinquentme | really I wish i had everyones resumes | 18:31 |
| delinquentme | like i've got mine handy if youd like it | 18:31 |
| delinquentme | .. wait are you part of the 5? | 18:32 |
| klafka | kanzure said i can by | 18:32 |
| klafka | be | 18:32 |
| klafka | oh i can send you mine | 18:32 |
| klafka | what's your email? | 18:32 |
| delinquentme | carlcrott@gmail.com | 18:32 |
| delinquentme | yeah ill shoot you mine | 18:32 |
| delinquentme | you guys have heard of the OpenPCR right? | 18:33 |
| delinquentme | i was wondering what it would cost to make their heating block 96 well | 18:33 |
| delinquentme | any ideas? | 18:33 |
| delinquentme | i feel kind of rude asking tito outright | 18:33 |
| klafka | not offhand | 18:33 |
| klafka | i guess the one thing my resume doesn't show that is relevant to this channel is i have quite a bit of bio experience | 18:34 |
| klafka | i'm 6 classes shy of a bs in bioinformatics (6 classes that are like 40,000 total though :() | 18:34 |
| delinquentme | klafka, ignore that chat invite.. was getting punchy | 18:35 |
| klafka | ah | 18:35 |
| delinquentme | 40 grand? | 18:35 |
| klafka | eh no maybe 25k | 18:35 |
| delinquentme | feck | 18:35 |
| delinquentme | dude seriously | 18:35 |
| delinquentme | simplifying bio education | 18:35 |
| klafka | i think i t's like 2500 or 4k a class | 18:35 |
| delinquentme | esp on the high end | 18:36 |
| delinquentme | fuck everything about those college courses | 18:36 |
| klafka | heh | 18:36 |
| klafka | that was when my father decided to no longer pay for my education | 18:36 |
| delinquentme | ... PS are you guys enrolled in the free stanford AI class? | 18:36 |
| klafka | so i got my one bs | 18:36 |
| klafka | no | 18:36 |
| klafka | i've watched most of andrew ng's ml class, and i've taken a bunch of ML / pattern recognition classes | 18:36 |
| klafka | maybe i should watch it though, it's like peter norvig | 18:37 |
| klafka | he's kind of awesome | 18:37 |
| delinquentme | http://www.ai-class.com/ | 18:37 |
| delinquentme | klafka, have you dont any bayesian implementations in ruby? | 18:38 |
| delinquentme | done** | 18:38 |
| klafka | aah no, i've thought about it | 18:38 |
| klafka | i've done stuff that is not really Bayesian but not really frequentist either | 18:39 |
| klafka | although i'm fairly familiar w/ Bayesian learning | 18:39 |
| delinquentme | i read a bit about it | 18:39 |
| delinquentme | its just probabalistic models right? | 18:39 |
| delinquentme | ba ba ba balistic | 18:40 |
| delinquentme | lulz | 18:40 |
| klafka | um Bayesian learning? well it does imply a probabilistic model, but it's a specific type of one | 18:41 |
| delinquentme | dude turns out i derped on sending this one girl my resume | 18:41 |
| klafka | it's one where you integrate over all possible priors | 18:41 |
| klafka | er | 18:41 |
| klafka | not priors | 18:41 |
| delinquentme | assumptions | 18:41 |
| klafka | but over the entire space | 18:41 |
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| delinquentme | damnnnn some reason my resume it taking forever to send | 18:45 |
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| kanzure | sup | 19:07 |
| klafka | oh deli oh you left | 19:07 |
| klafka | hey kanzur | 19:07 |
| klafka | e | 19:07 |
| kanzure | reading backlog.. | 19:09 |
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| kanzure | klafka: hey, how about a lego design sharing site | 19:27 |
| kanzure | delinquentme: do you like that project idea? | 19:27 |
| kanzure | ybit: you? | 19:27 |
| kanzure | Nam-Ereh-Won: would you be ok with that? | 19:27 |
| kanzure | foucist: or you? | 19:27 |
| klafka | hmm lego sharing could be cool | 19:28 |
| kanzure | like for leocad designs | 19:28 |
| kanzure | there's no modern site for doing this, last i checked | 19:28 |
| kanzure | also a plugin to leocad to download it, or an iphone/android client to view designs | 19:28 |
| klafka | i see | 19:29 |
| klafka | can we interface it with a social network and then develop algorithms to recommend you other leocad designs? | 19:30 |
| klafka | :P | 19:30 |
| kanzure | sure why not | 19:30 |
| klafka | heh | 19:30 |
| kanzure | we can also do GAs on designs | 19:30 |
| kanzure | and other wacky shit.. | 19:30 |
| klafka | oh fun | 19:30 |
| kanzure | fenn wrote a lot of lego-related code for skdb "back in the day" | 19:30 |
| kanzure | http://diyhpl.us/cgit/lego/ | 19:31 |
| kanzure | we can also enlist mike rayhawk for some graphic design http://mikerayhawk.com/ | 19:31 |
| Nam-Ereh-Won | oooh | 19:38 |
| Nam-Ereh-Won | and the projects could generate bricklink shopping lists | 19:38 |
| delinquentme | lego sharing | 19:47 |
| kanzure | yeah there's some pretty good individual-lego-buying sites out there | 19:48 |
| delinquentme | ahah well i dig legos .. examples? | 19:48 |
| kanzure | uh.. i don't remember any of them off the top o my head | 19:49 |
| kanzure | fenn might | 19:49 |
| klafka | i am not really too familiar with legos | 19:55 |
| klafka | well | 19:56 |
| klafka | i assume you're talking about not the normal legos | 19:56 |
| foucist | kanzure: limited market.. | 19:57 |
| kanzure | there's no market whatsoever | 19:58 |
| kanzure | but the market isn't the oint | 19:58 |
| kanzure | klafka: mostly the normal legos | 19:58 |
| klafka | oooh ok | 19:58 |
| kanzure | foucist: it's just a project to get on the ol' resume | 19:58 |
| foucist | kanzure: there's a lot of other moer useful things you could do tho perhaps | 19:59 |
| kanzure | like what | 20:00 |
| delinquentme | now cant you just make these on the lego website? | 20:16 |
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| kanzure | delinquentme: what? | 20:30 |
| kanzure | i said a lego sharing site | 20:30 |
| klafka1 | kanzure | 20:32 |
| klafka1 | you know what would be cool | 20:32 |
| klafka1 | 'how well will my laptop run linux' | 20:32 |
| klafka1 | you give the website specs/model name/number | 20:32 |
| klafka1 | it (if given a model name/number) crawls for specs, asks for confirmation, and returns any potential driver issues | 20:32 |
| delinquentme | i say we start a website that lets people run genetics expiriments that look cool in test tubes | 20:35 |
| delinquentme | it would be like DIY bio lab decorative expiriments | 20:35 |
| klafka1 | man installing scipy on this linux vbox | 20:36 |
| klafka1 | fuun | 20:36 |
| klafka1 | building atlas atm | 20:36 |
| kanzure | delinquentme: that makes no sense | 20:37 |
| kanzure | "that letsp eople run genetic experiments".. they are already able to do that | 20:37 |
| kanzure | what are you talking about, specifically? | 20:37 |
| delinquentme | http://dbprng00ikc2j.cloudfront.net/work/image/323776/mf2ji7/testtube_plants.jpg | 20:41 |
| kanzure | delinquentme: are you the type of person that doesn't tend to think in complete thoughts or sentences? | 20:42 |
| delinquentme | lol | 20:43 |
| QuantumG | this _is_ the ADHD channel | 20:43 |
| delinquentme | im tracking down images | 20:43 |
| delinquentme | and i just helped my little bro make his PS3 gamertag ... pedobear | 20:43 |
| delinquentme | =/ | 20:43 |
| delinquentme | my name is on the account | 20:43 |
| uniqanomaly | pedolicious | 20:44 |
| uniqanomaly | haha | 20:44 |
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| delinquentme | test tube bonsais >_< | 20:47 |
| delinquentme | http://static3.depositphotos.com/1000708/115/i/950/depositphotos_1157988-Leaf-buds-in-test-tube.jpg | 20:47 |
| delinquentme | we could make hippy fodder | 20:47 |
| delinquentme | embed plant seeds into tapioca balls | 20:48 |
| delinquentme | they could throw it and greenify the world | 20:48 |
| delinquentme | http://lh4.ggpht.com/-9C9XBxNXuUc/STGNmfsxyTI/AAAAAAAATmo/JzqJTGLTFQY/IMG_3578.JPG | 20:48 |
| delinquentme | how hard is it to engineer flourescent algae | 20:49 |
| delinquentme | i know other groups have done it | 20:49 |
| kanzure | in a month? | 20:49 |
| delinquentme | get test tubes with a few shades of glowing algae? | 20:49 |
| kanzure | what the hell man | 20:49 |
| kanzure | :( | 20:49 |
| kanzure | you guys don't even live together | 20:49 |
| delinquentme | out source that shit! | 20:49 |
| delinquentme | infact there was a kickstarter with GFP | 20:50 |
| delinquentme | that'd be hot :D | 20:50 |
| delinquentme | umm derp? | 20:56 |
| delinquentme | The rationales behind the comparison of sequences may be manifold. | 20:56 |
| kanzure | are you a hidden markov model bot | 21:12 |
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| delinquentme | bayesian | 21:13 |
| delinquentme | noper! | 21:13 |
| delinquentme | lol im reading the bioinformatics tut on the max planck society website and that "manifold" was on there | 21:14 |
| delinquentme | http://www.wired.com/dangerroom/2011/06/pentagons-new-factory-your-dna/ << darpa grants? | 21:17 |
| delinquentme | i think they've got a few bucks | 21:17 |
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| ybit | current project is to make a site for a local jewelry store, i think $2000 is a good asking price. they don't want to pay by the hour | 23:53 |
| ybit | a friend of mine is giving me a template he used when freelancing, i think he got it from legalzoom.com | 23:54 |
| ybit | that should give me enough money to get in school | 23:54 |
| ybit | i've got enough now, but that will pay for me to actually live | 23:55 |
| ybit | ..so no lego repo for now | 23:56 |
| --- Log closed Tue Aug 09 00:00:16 2011 | ||
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