2012-08-03.log

--- Log opened Fri Aug 03 00:00:27 2012
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archelssuperkuh: I just launched wget -r on your library, if your nets just slowed to a crawl, feel free to tell me to fuck off.05:09
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delinquentme<406:19
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archelssuperkuh: okay, done06:34
archelsDownloaded: 531 files, 4.3G in 1h 9m 53s (1.05 MB/s)06:34
archels<306:34
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delinquentmewhere do people sell domains?08:02
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kanzuredelinquentme: flippa09:25
kanzure"I am a Bio major at CSULA and I am very excited that I have found this group. I am interested in your projects and I would love to participate and help in any way possible."09:26
kanzure". I am currently interested in all fields of Bio ( or any other science) but I especially like genetic manipulation or any biotechnology. I hope to learn more advanced lab techniques/procedures as well as the knowledge and theory that i is required to perform such experiments."09:26
kanzure"I want to do a simple little experiment to show to the nephews. I'd like to take some E. coli and make them glow by some good ol' fashioned bioluminescence using the pLux gene from Vibrio fischeri. I've done similar recombinant stuff in the lab at school and it's a super straight forward procedure so I thought it'd be fun."09:29
kanzure"Trouble is... Where do I get the plasmids? I cannot find plasmids for the pLux gene anywhere. I thought about ordering a culture of V. fischeri and extracting the gene out via PCR... but I do not have a PCR machine yet. Hell, I don't even know if I can make a plasmid out of PCR products??"09:29
kanzure"But how can I combine that, remove the bad plasmide from that bacterium and insert the glowing genes (but not the saline genes, because the tree shouldn't need salty water to live like the bacterium)."09:30
kanzure"I read about DIYbio in Discover Magazine, and I was instantly in love with the idea of DIY organisms. However, I don't have anything beyond a very basic layman's understanding of how DNA functions..."09:31
kanzure"Where should a noob like me start looking for information? The idea I had was to introduce a gene into a cactus to change it's color, or even make it glow if possible."09:31
kanzure"I'm from the DC area looking to start a project up. I could use some insight and advice on how to get my project going, and if anybody is in the area, people who might be interested hearing about it and collaborating. While I'm still developing my idea, I envision the project sort of iGEM-esque (or maybe that's how all these projects start...),"09:32
kanzure"but would like some input as to how people start their projects; if no formal laboratory facilities are availabe, how/where people purchase lab equipment; and maybe some info on unforseen experimental challenges or technical difficulties people have had."09:32
kanzure"...trying to make myself cognizant of these issues as I develop my project. Thanks for any and all advice in advance."09:32
kanzure"1) Is it worthwhile to take the "reverse genetics" approach, inserting and removing genes with the hope of a meaningful outcome?"09:33
kanzure"2.) I was looking at beginning my research with the Drosophilas and microinjection. Is this a decent starting point for a low-budget? I've built my own functional micromanipulator, but I'm not familiar with pricing for gene synthesis etc."09:33
kanzure"Can anyone help me get into genetic engineering. What can I do? How can I start? The thing I am looking to do with it is (with no aims or goals like to cure cancer) create a living creature, or create biological circuits so that you have living electronics (hack my toys to make them pets!)."09:34
kanzure"What could I do to do a "hello world?""09:34
kanzure"I studied mathematic, and i'm currently studying cognitive science in college. What you people are doing seem pretty interesting. I've always been interested by science. So my question would be naive : where do i start?"09:35
kanzure"I'm getting really interested in DIYBio and hope to do stuff with chlorophyll (green, plant stuff, sorry if that was the wrong word!) and bacteria. Unfortunatly, I have no idea how to get dna into bacteria. I think it involves getting plasmids but I don't know much. Any help at all would be great!!"09:38
kanzureoh right i forgot about http://www.labautopedia.com/mw/index.php/Main_Page09:41
kanzurehttp://www.labautopedia.com/mw/index.php/Category:Automated_liquid_handling_workstations09:43
kanzurehttp://www.labautopedia.com/mw/index.php/The_history_of_automated_liquid_handling09:43
kanzurehttp://www.labautopedia.com/mw/index.php/Early_microplate_automation09:45
kanzure"The procedure was to first add diluent, to all 96 wells with a dropper. The technician holding eight loops at a time would move them from row to row, twirling to obtain mixing, and then transfer 25μL or 50μL to the next row (Figure 3)"09:46
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kanzureoh man, old advertising http://aem.asm.org/content/30/1/local/advertising.pdf09:56
kanzure"The accepted method of cleaning the Microtiter® loop was to flame them to incandescence, then dip them in water. The sudden contraction popped off contaminates. To accomplish this, the Autotiter had a propane burner and a running water bath. At an ASM meeting in Philadelphia someone reversed the connections."09:58
kanzure"The effort to light the burner resulted in a propane-fed flaming torch about three feet high. With the stench of singed hair still prevalent, the Fire Marshall arrived on the scene to remind us open flames were not allowed."09:58
octopinekanzure hmm? http://d.pr/i/IyE8+#.png09:59
kanzure"Morning Star was a large injection-molding house producing eight track cassettes. They and Dynatech (Cooke) created a joint venture to produce microplates in high volume to meet the growing demand. The new company was named CoStar."09:59
kanzure"history of the pipette" http://www.youtube.com/watch?v=IRVFZJ-VLCc10:05
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nmz7871kanzure: labautopedia isnt working, are you harassing their servers?11:43
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kanzureno11:49
kanzurei have copies of those two history pages though11:49
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nmz787'linuz torvalds - nvidia fuck you' http://www.youtube.com/watch?v=iYWzMvlj2RQ13:09
kanzurehttp://www.3ders.org/articles/20120803-first-open-source-powder-based-3d-printer.html13:10
kanzurehttp://blog.makezine.com/2012/08/03/oshw-powder-based-rapid-prototyper/13:10
nmz78796 DPI!!!13:12
nmz787geez13:12
kanzurenmz787: http://diyhpl.us/~bryan/irc/labautopedia-history-of-early-microplate-automation.html13:15
kanzurenmz787: http://diyhpl.us/~bryan/irc/labautopedia-history-of-automated-liquid-handling.html13:15
nmz787kanzure: you gonna get the IMGs?13:59
kanzurei have the images, but i didn't upload them13:59
AdrienGkanzure: http://www.spoonflower.com/welcome14:05
kanzureoh i forgot about chris' "personalpcr" thing.. http://templemanautomation.com/personalpcr/14:15
nmz787man i can't even find a decent google hit for 'new york city overubanization'14:22
nmz787where does a guy go to hate on NYC???14:22
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kanzurehttp://openwetware.org/wiki/TOP10_chemically_competent_cells14:29
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kanzurenmz787: what happened to http://diybioforum.org/wiki/index.php?title=FAQ14:50
nmz787no one ever really used it14:58
nmz787i don't think there was much of anything there anyway... not sure if i backed it up14:59
gnushadiyhpluswiki.git: 21c5bf6 an initial list of better questions for a biohacking faq15:07
gnushadiyhpluswiki.git: 5be2a4a 2012-07-05 Never mind the biologists, here come the biopunks15:07
gnushadiyhpluswiki.git: a004f61 add link to openwetware registration discussion15:07
gnushadiyhpluswiki.git: 22039e0 even more questions in diybio/faq/better-questions15:07
kanzurenmz787: http://diyhpl.us/wiki/diybio/faq/better-questions15:07
kanzureplease add anything you think is missing15:07
kanzurethese were extracted from the mailing list archives15:07
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gnushadiyhpluswiki.git: fee376b fix sterilization typo15:13
kanzurethe faq should probably be segmented into different sections15:14
kanzurethere's usually a big set of questions even for each individual protocol15:14
kanzuree.g. always someone wondering about modifying the calcium chloride transformation protocols15:15
kanzureor the inevitable questions about why their gel runs are smearing15:15
nmz787gels are something of a black art i think15:15
nmz787or maybe the people in the know only publish answers in springer books15:15
nmz787that i haven't found and downloaded yet15:16
kanzurethe most probable reason that your gel smears is that god hates you15:16
kanzurethe second most probable reason is contamination15:16
nmz787hah15:18
nmz787not contam15:18
nmz787no really weird shit can happen15:18
kanzurewell, i had contamination issues when i spent a month running 100s of gels15:19
kanzureto be fair i was doing weird things15:19
kanzuree.g. the problems were mostly upstream in the pcr steps15:19
nmz787tom knight was telling me to do extra DNA precipitations a while ago, that helped things (getting rid of other ions) but it didn't make them perfect15:19
nmz787not just smearing though, wiggly lanes and weird shit15:19
nmz787like someone took a picture of a perfect gel, printed it on transparency plastic, then warmed up the plastic so it got all deformed15:20
kanzure"the weegie board guide to molecular biology (not endorsed by the national spiritualist organization)"15:20
nmz787the new FAQ questions look good15:21
kanzurethey should probably be split up15:21
kanzureinto segments15:21
nmz787we could have been using shitty agarose, though I don't know15:21
nmz787hah, i just noticed one of my own questions15:22
kanzurethe sections could be: gel electrophoresis questions, transformation questions, incubation, all things glowing/gfp, thermocycling/pcr, dna extraction, sequencing, primers and primer design, stochiometry/dilutions/buffers/math, making equipment, buying equipment15:23
kanzurebut this is already way too many subtopics for one person to deal with15:23
nmz787"Are there any poly(T) oligo columns on sale that have a free 3' end"15:23
kanzurethere are some other questions of yours in there15:24
nmz787a bit too technical for a beginner, cory was the only one to reply :P15:24
kanzureoh and then there's lots of software questions, which should be organized somehow15:24
nmz787there could be a question "Do only PhDs answer these FAQ questions"15:24
nmz787geez another one from me... i must be the redheaded stepchild of DIYbio that doesn't get noticed because i'm shoved in the closet under the stairs15:26
kanzurei don't understand that analogy at all15:26
nmz787lol15:26
nmz787you could copy the P is for plasmid google doc that was floating around for the glossary15:26
nmz787'a is for autoclave' https://docs.google.com/document/d/10OlwuiGhIIToPlzpywQhOL0hNyAWdZsR06DPubjlcrM/edit15:27
gnushadiyhpluswiki.git: 5b172a4 possible way to organize these questions15:29
nmz787i've been in the habit of capitalizing Science lately15:30
nmz787like the religious folks do with their deities15:30
kanzureorganizing questions around different methods (gels, blots, precipitation, ...) feels like it's missing the ponit15:32
kanzure*point15:32
kanzurebut they are still important questions15:32
kanzurelike, i can't manually maintain a FAQ for all 4000 protocols on protocols-online.org.. if each protocol gets 10 questions that's 40,000 questions.15:32
nmz787yeah15:36
nmz787i was thinking a lot of the questions are great, and worth taking the time to add answers15:36
nmz787but that it would be hard for someone to search through15:36
nmz787since there are so many15:36
kanzurei have noticed that many people read about diybio in the news15:37
kanzureand then join the mailing list15:37
kanzureand then ask "okay, what do i need to get started"15:37
kanzurewhich is a totally hopeless question..15:37
kanzurethere are just so many possible projects that it's difficult to enumerate them all15:38
nmz787yeah, well, if they need somewhere to get started... we either put them through the PITA many roads..... or we say Carolina Kit15:40
nmz787but even that doesn't give you gel loading or analysis training15:40
kanzurewhy is everyone so interested in gfp? i did the gfp kit in high school and it wasn't that exciting.15:40
nmz787HOWTO use a micropipettor can be a challenge for college students15:41
kanzuregfp is very useful in research projects for other reasons, but by that point you are using it for some practical ends15:41
nmz787I've seen students use them without tips, and heard stories of grad students doing that too15:41
nmz787then again i started biohacking in my kitchen after 9th grade15:41
nmz787but i started with books and long ass FAQs15:42
nmz787which I was fine with15:42
gnushadiyhpluswiki.git: 112166f 9 more questions15:42
gnushadiyhpluswiki.git: e45fbc9 just some questions about open access15:44
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skorkethave you guys heard of/used OMERO?15:46
kanzureno15:46
nmz787nope15:46
kanzureit sounds like an ftp server for microscopy images15:46
skorketmore like a filesystem/management environment15:46
kanzurehuh, maradydd was making her own calcium chloride?15:50
kanzureskorket: you have been pre-selected; we are redoing the diybio faq15:51
kanzureskorket: what questions would you like to see answered?15:51
skorketI won't be representative15:51
kanzurei know15:51
kanzurego ahead anyway :P15:51
skorketwhat kind of questions do you want?15:51
kanzureskorket: any kind15:53
kanzurei know you had some basic microfluidic questions, but questions simpler than that would be cool15:53
kanzureor related.15:54
kanzureskorket: http://diyhpl.us/wiki/diybio/faq/better-questions15:54
skorketwhat are some good resources for biology, diy and diy biology?15:54
gnushadiyhpluswiki.git: 6f859d5 more questions from the diybio mailing list15:54
skorketwho should I go through to get reagents?  Will I run into problems as an individual ordering reagents?15:56
skorketyeah, see, you have most of the questions I would ask on that list in one form or another15:57
gnushadiyhpluswiki.git: a12623a a handful of questions imported from the existing faq16:03
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kanzureybit: happy birthday, old man16:47
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kanzurewhen will "like a roomba stuck in a closet" become an acceptable punchline?17:56
kanzurei fear that roombas have already reached peak popularity17:57
kanzureso the joke might not be that strong17:57
nmz787punchline to what though?17:58
kanzure*shrug*17:58
* kanzure protects his list of zingers (ok, i don't have a list of zingers really)17:59
nmz787mmm hmm18:06
nmz787more like your list of potential punchlines18:06
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gnushadiyhpluswiki.git: 69473a5 rearranging some questions, adding others18:35
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brownieskanzure: i found a bug18:49
browniesclicking on a question does not seem to reveal an answer -_-18:49
kanzureheh18:51
kanzurebrownies: there are answers here http://diyhpl.us/wiki/diybio/faq for some of them18:55
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kanzuredelinquentme: https://www.transcriptic.com/about/jobs18:58
kanzurethought you might like that one.18:58
delinquentmeOOOooOOooOOoO18:59
* delinquentme munches quesidilla18:59
kanzure"illustrated guide to home biology experiments" http://shop.oreilly.com/product/0636920017691.do19:19
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gnushadiyhpluswiki.git: 3e56974 just some introductory books19:24
kanzureyashgaroth: got any better ideas? http://diyhpl.us/wiki/diybio/faq/better-questions19:25
yashgarothyou did all that since yesterday?19:26
yashgaroth"Why are there no really good biology forums?" oh god it's so true :(19:27
yashgarothlooks good to me, should fill in the answers before adding new Qs19:30
kanzureyeah i don't know how to structure it, a lot of these aren't actually "frequently" asked19:31
yashgarothanyone know if the khan academy videos for bio are any good? might as well add a link if they are19:31
kanzurei haven't tried them yet19:32
yashgarothoh and NCBI bookshelf would be good19:32
kanzurethat's mentioned in the actual faq elsewhere19:33
kanzureso, these are just questions that i extracted from the mailing list19:33
kanzurethe number one most frequently asked question is a meaningless one ("how do i get started")19:34
yashgarothdamn they're coming out of the woodwork in that non-biology-native guy's thread19:36
kanzure"Is there a simple kit to order and start with or a book that isn't a textbook?"19:38
kanzurethat isn't a textbook? what does he want, biology by fortune cookie notes?19:38
yashgarothhonestly neither the google group nor diybio.org actually have biology information or links to it, far as I can tell19:39
kanzurethat's true19:39
kanzureand no link to the faq19:39
kanzurei have been debating whether or not i should send out an email about the faq being moved19:40
yashgarothwho owns the group, mac cowell?19:40
kanzurei didn't ask jonathan cline about moving it19:40
kanzuremac cowell and jason bobe19:40
yashgarothyeah a link to OWW and/or the faq would theoretically cut down on the getting started spam...theoretically19:41
kanzurei don't think the oww faq does a good job19:42
yashgarothwell it's better than "welcome to the group! here's a link to a worthless site! ask stupid questions below"19:42
kanzurehaha19:43
kanzurewell, i think i should send out an email about the faq move19:43
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kanzurebut, moving the faq probably makes me an ass19:43
yashgarothit's not like they're doing anything with it19:43
kanzuretrue that19:44
gnushadiyhpluswiki.git: 417c5f6 update internal wiki links in diybio/faq.mdwn19:47
gnushadiyhpluswiki.git: 0ca32ef hmm that diybio.org/projects link looks deprecated19:48
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gnushadiyhpluswiki.git: b6f158b fix some faq interlinking19:51
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kanzurehere is fenn complaining about openwetware registration policies:20:00
kanzurehttps://groups.google.com/forum/?fromgroups#!topic/diybio/50U54BYu9Rw20:00
kanzurehere is mac cowell hating on ikiwiki:20:01
kanzurehttps://groups.google.com/forum/?fromgroups#!searchin/diybio/FAQ/diybio/Whbc4_yQF4s/BZK0-0BaRU8J20:01
kanzureoops i mean20:01
kanzurehttps://groups.google.com/forum/?fromgroups#!searchin/diybio/FAQ/diybio/Whbc4_yQF4s/BZK0-0BaRU8J20:01
kanzurehrm.20:01
kanzurehttps://groups.google.com/d/msg/diybio/Whbc4_yQF4s/FY6bxmlcI3kJ20:01
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delinquentmehttp://imgur.com/gallery/44cYg20:06
delinquentme" Imagine how big that is "20:06
joshcryerExpected porn. Was acceptable.20:07
superkuhI remember that event.20:08
delinquentmelolol20:08
delinquentmeso 1.3 m earths would fit inside the sun...20:09
delinquentmeso yeah that flame is like20:09
delinquentmeplasma ?20:09
superkuhThat comment thread is painful.20:09
delinquentmesubstantially larger that this planet20:09
superkuhThe earth would be the size of one of the small bright dots on the photosphere. Probably 20 could fit across the circumference of that loop.20:10
superkuhEr diameter.20:11
superkuhNot circumference.20:11
superkuhAnyway, the image itself is in 30.4nm light from helium ions in the plasma.20:12
joshcryerI recall a really convoluted video presentation about the magnetic field lines in the core of the sun.20:16
joshcryerSince apparently the surface moves at rates that are counterintuitive or something.20:16
joshcryerBeen awhile since I saw it.20:16
joshcryerSome NOVA doco on the sun.20:16
joshcryerThose big outbursts are caused by magnetic loops and twists that "snap."20:16
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nmz787sooo, downconvert the ultra UV to vis and have some kinda pinhole camera focused on your wall during the day... tracking the sun20:19
superkuhNo. The atmosphere absorbs it.20:19
nmz787seeing the surface of the sun for a wall would be pretty cool20:19
nmz787oh20:20
nmz787lame20:20
* nmz787 goes to get some CFCs20:20
superkuhFor earth bound observations of the photosphere the hydrogen alpha line is best. Or if you care about photospheric magnetic fields then the iron I infrared line at ~1564 nm.20:21
kanzurejrayhawk: how confident are you that pinyshell is safe?20:29
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kanzurenmz787: can you review this email? http://diyhpl.us/~bryan/irc/faq-email.txt20:45
kanzurenmz787: i want to avoid pissing people off20:45
browniesany email longer than 3 sentences is guaranteed to piss someone off20:46
nmz787add cathal to thx list20:46
kanzurenmz787: cathal didn't edit it20:47
kanzureever..20:47
kanzurebrownies: well, it's a complicated history going on here20:47
kanzurebrownies: i wrote this retarded and embarrassing diybio faq on heybryan.org/mediawiki20:47
kanzurebrownies: then mac copied it to openwetware.org20:48
kanzureand it's been there for a few years, where jonathan cline has been updating it with me20:48
kanzureso, in theory, there's no problem with me moving it off of openwetware20:48
kanzure(there are some issues with openwetware like: you have to register and wait for approval to edit)20:48
kanzurebrownies: so there will possibly be some people angry with the fact that i have forked it20:49
browniesi was objecting generally to the wall of text, but, yes, now i see there are several other things that will also probably piss someone off20:49
kanzureit's sorta stupid; jonathan is the only person who has edited it more than i have20:50
kanzureand jonathan probably doesn't give a fuck20:51
nmz787remove this "with the exception of Nathan McCorkle's diybioforums.org version"20:52
kanzurebah20:52
kanzurefine20:52
kanzurei am pretty sure there are some edits there that i am forgetting :)20:52
nmz787its pretty tl;dr20:52
kanzurewell the only thing people should care about is the first link20:53
nmz787tho i did read it20:53
nmz787 "There has also been a trickle of other contributors to the FAQ including:"20:54
nmz787you're saying Cathal didn't ever help with FAQ stuff20:54
kanzureyou can track that by typing: git log --follow diybio/faq.mdwn20:54
kanzureyes20:54
nmz787what about the new stuff20:54
nmz787oh20:55
nmz787ok20:55
kanzuregit log --follow diybio/faq.mdwn | grep "^Author: " | sort | uniq20:55
nmz787yeah I think it's pretty fine20:56
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kanzurenmz787: sent..21:04
nmz787OMG did you just see what Bryan Bishop posted to the DIYbio group?21:04
nmz787insanity21:04
nmz787:P21:04
kanzurecathal sent that?21:05
kanzureactually, where the hell is cathal and why does he never come in here21:05
nmz787huh?21:06
nmz787cathal said nothing!21:06
kanzurecathal doesn't seem to be online21:06
kanzureyes, well, he should be21:06
gnushadiyhpluswiki.git: dcda6fd 21:07
kanzurewhere is JayDugger21:07
jrayhawkpinyshell isn't all that complicated; you should probably man rbash to learn what's going on21:36
nmz787why use that over bash21:36
jrayhawkthat is bash21:36
nmz787pinyshell?21:36
nmz787==bash?21:36
jrayhawkyes. it is bash with set +r. you should probably man rbash to learn what's going on.21:37
kanzurenmz787: pinyshell is the default shell on diyhpl.us for users that register from the wiki21:39
kanzureyou have a more-able account on the server21:40
skorketbiopunk.org hasn't been active in nearly 8 months...21:51
kanzurewhen splicer shows up you should yell at him21:52
kanzurehe sometimes logs in21:52
kanzure(he runs biopunk.org)21:52
skorketnot necessarily his fault...21:52
skorkethey kanzure and nms787, how are you thinking of getting micron precision movement for you laser cutter?21:53
skorketwhoops, I mean nmz78721:53
kanzuremicro stage21:53
kanzurehttp://diyhpl.us/laser_cutter/laser_cutter21:53
kanzurewait21:53
kanzurehttp://diyhpl.us/laser_etcher/laser_etcher21:53
skorketmaybe a bit too expensive, but sparkfun has some steppers that are 0.9 Deg21:55
skorkethow close are you guys to building?21:57
kanzurewell, i have to order parts21:57
kanzureand fenn has to figure out if he wants to build it21:57
kanzureand nmz787 has to figure out where he is living21:58
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skorketin case you're interested: https://www.sparkfun.com/products/1084622:00
skorketcompatible with the a4988 pololu drivers you're using22:01
nmz787i don't think fenn wants to build it. does the austin hackerspace have a machine shop?22:09
nmz787skorket: those motors look pretty good22:09
nmz787would give us 2X resolution22:09
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nmz787skorket: how do i figure out how many oz/in I need22:12
kanzureatx hackerspace is not mnuch of a machine shop22:14
kanzurebtw there's #austinhackerspace22:15
nmz787do you have access to that one?22:17
nmz787oh you're not saying there are two in austin22:18
nmz787well fenn said he might head to austin if he has a car there22:18
nmz787soooo22:18
nmz7873-man hackathon22:18
nmz787for this thing22:18
klafkai was just at the oakland hackerspace22:24
klafkai keep going there for like 10 mins and leaving22:24
browniesoakland has a hackerspace?22:34
brownieswhere?22:34
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klafkasudoroom22:41
klafkaon broadway22:41
klafkahttp://sudoroom.org/22:41
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browniesword, thanks. might drop by sometime.23:13
klafkathey have meetings on mondays23:13
klafkaare you in oakland?23:13
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skorketnmz787, do you mean (oz * in)?23:36
browniesklafka: i'm around, sometimes.23:41
browniesthis is literally the most useless web site in the world23:59
--- Log closed Sat Aug 04 00:00:28 2012

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