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| QuantumG | kanzure, you around? | 04:05 |
|---|---|---|
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| QuantumG | I don't think you have this one: http://www.springerlink.com/content/r75jv1650l0q0758/ | 04:19 |
| QuantumG | looks neat | 04:19 |
| jcluck | Ian_Daniher cool idea about NEB :) | 04:36 |
| kanzure | QuantumG: yes i'maround | 04:52 |
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| cluckj | hopefully I'll see some of you at the diy bio boston meetup | 05:56 |
| cluckj | cya | 05:56 |
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| kanzure | ew, why is steve klabnik on the openscad mailing list? | 08:04 |
| * kanzure hopes cloudfab.com isn't going towards openscad.. | 08:05 | |
| pmetzger | howdy, kanzure. | 08:06 |
| pmetzger | trying out a new client this morning... | 08:06 |
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| pmetzger | did anyone answer fenn's question to his satisfaction last night? I went to bed.... | 08:10 |
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| kanzure | fenn seems to have disappeared | 08:18 |
| kanzure | ever since he started that job :( | 08:18 |
| pmetzger | who is fenn? | 08:18 |
| kanzure | http://fennetic.net/ | 08:19 |
| pmetzger | I didn't quite get whether I was talking at too low or too high a level when he asked that question... | 08:20 |
| kanzure | honestly it sounded like chem 101 :P | 08:23 |
| pmetzger | my idea of what chem 101 is like is rather distorted at this point. :) | 08:24 |
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| kanzure | esther dyson writing about diygenomics.org http://healthsymptomsfacts.com/i/Esther-Dyson-about-Genomics/ | 09:09 |
| kanzure | oops | 09:10 |
| kanzure | http://scienceroll.com/2010/06/18/esther-dyson-about-genomics/ | 09:10 |
| kanzure | there's an nyc quantified self? http://go2.wordpress.com/?id=725X1342&site=scienceroll.wordpress.com&url=http%3A%2F%2Fwww.meetup.com%2FNYQuantifiedSelf%2F&sref=http%3A%2F%2Fscienceroll.com%2F2010%2F06%2F18%2Festher-dyson-about-genomics%2F | 09:10 |
| kanzure | er | 09:10 |
| kanzure | http://meetup.com/NYQuantifiedSelf/ | 09:11 |
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| kanzure | hmm how'd this get here? | 09:24 |
| kanzure | http://brlcad.svn.sourceforge.net/viewvc/brlcad/brlcad/trunk/src/proc-db/spiral.pl | 09:24 |
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| kanzure | pmetzger: do you have a copy of "Extropy: A Journal of Transhumanist Thought"? | 09:57 |
| kanzure | http://blog.ponoko.com/2010/06/21/boitech-tools/ | 09:58 |
| kanzure | http://blog.ponoko.com/2010/06/21/biotech-tools/ | 09:58 |
| kanzure | "xerox machine for DNA" ugh | 09:59 |
| kanzure | my head hurts :( | 09:59 |
| pmetzger | kanzure: I have copies of every issue of Extropy. | 10:01 |
| pmetzger | At first it was "Vaccine for Future Shock". | 10:02 |
| kanzure | are they physical or digital issues | 10:07 |
| kanzure | hm lots of biotech videos: http://article.wn.com/view/2010/06/15/Cipla_ups_biotech_play_via_stake_buys/ | 10:11 |
| kanzure | pmetzger: digital or physical? | 10:11 |
| pmetzger | physical. | 10:12 |
| kanzure | drats | 10:13 |
| pmetzger | this is 20+ year old paper. | 10:13 |
| kanzure | nobody has a digital copy of these articles | 10:13 |
| pmetzger | I even own the issues that have been placed in the memory hole. | 10:13 |
| kanzure | i'd be willing to type some of them up, but.. | 10:13 |
| pmetzger | I suspect Max and esp. Natasha would be vigorous in pursuing copyright violations. | 10:13 |
| kanzure | really? i think they want these articles up on the web as much as anyone | 10:14 |
| pmetzger | no. they want everyone to forget they ever existed. | 10:14 |
| kanzure | uh.. why? | 10:14 |
| kanzure | btw i've been talking with natasha recently and everything you're saying sounds contrary, but it's entirely possible that i've misinterpreted her | 10:14 |
| pmetzger | Then ask her for a copy of issue 3 of extropy. | 10:15 |
| pmetzger | see what she says. | 10:15 |
| kanzure | how about a copy of all of them | 10:15 |
| pmetzger | or even just to see the first few issues. | 10:15 |
| pmetzger | issue #3 in particular went down the memory hole. | 10:15 |
| pmetzger | but I suspect all the early ones would now be considered things they don't want online. | 10:15 |
| kanzure | they live down the street | 10:23 |
| kanzure | this is stupid | 10:23 |
| kanzure | they probably have archives of everything just sitting around | 10:23 |
| pmetzger | certainly they do. | 10:23 |
| kanzure | i just sent them an email proposing i go over and just spend a day typing up the articles | 10:23 |
| kanzure | it's not like i'm a slow typist | 10:23 |
| pmetzger | okay. :) | 10:23 |
| pmetzger | they're well typeset, OCR will work fine. | 10:23 |
| kanzure | bah | 10:23 |
| kanzure | it takes longer to scan a page, i would think | 10:23 |
| pmetzger | it is a bit rough, late 1980s mac stuff, but... | 10:24 |
| kanzure | eww macs? :( | 10:24 |
| kanzure | well i guess that was one of the only options back then | 10:24 |
| pmetzger | I'm assuming it was a mac. I think it was. | 10:24 |
| pmetzger | Probably Max's or Simon!'s. Maybe Tom's. | 10:25 |
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| kanzure | updated: http://openwetware.org/wiki/DIYbio/FAQ#Has_DIYbio_been_in_the_news.3F | 10:38 |
| kanzure | cluckj: you might be interested in that | 10:38 |
| kanzure | pmetzger: you too maybe | 10:38 |
| kanzure | "The free Mobile Gulf Observatory (MoGO) app turns you and your iPhone(TM(TM) | 10:40 |
| kanzure | into a ' Citizen Scientist' helping us track the environmental impact of | 10:40 |
| kanzure | the BP" | 10:40 |
| pmetzger | Around here, the only BP spills are at gas stations. :) | 10:40 |
| fenn | yes i meant "probability density" though that's a silly way to think about it. I don't care about an analytical solution; I guess VMD is the ticket: http://www.ks.uiuc.edu/Research/vmd/current/images/c60_orb104b.png http://www.ks.uiuc.edu/Research/vmd/current/ | 10:43 |
| kanzure | Southeast Citizen Science Project: how oil spill | 10:44 |
| kanzure | affects ghost crabs (& birds that feed on them) http://bit.ly/9c0M3G | 10:44 |
| pmetzger | Probability density is the QM way to think of it. It is a probability density. | 10:45 |
| pmetzger | Electrons have no position until you measure the position. | 10:45 |
| pmetzger | VMD displays the output of programs like GAUSSIAN and GAMESS, yes. | 10:46 |
| pmetzger | though there are all sorts of things you may want to see. for example, the probability density doesn't show you where the wave function is positive and where it is negative. | 10:47 |
| pmetzger | (The real part of course.) | 10:47 |
| pmetzger | if you want to understand things like the Woodward-Hoffman rules, you need to visualize *that*... | 10:48 |
| fenn | i've never even heard of "woodward-hoffman rules" | 10:49 |
| fenn | is this like a resonance? | 10:49 |
| pmetzger | no. | 10:51 |
| fenn | rawr. chemistry has too many made up words | 10:51 |
| pmetzger | https://secure.wikimedia.org/wikipedia/en/wiki/Woodward-Hoffmann_rules | 10:51 |
| fenn | ah, see I wasn't in the wrong with "electron density" http://www.ks.uiuc.edu/Research/vmd/current/ | 10:51 |
| pmetzger | so does computer science. it is hard to discuss a technical subject without macros to summarize complicated concepts. | 10:51 |
| fenn | erm, i mean http://en.wikipedia.org/wiki/Molecular_geometry#3D_Representations | 10:51 |
| kanzure | pmetzger: cool, max is going for it | 10:52 |
| pmetzger | orbitals and electron densities are different. | 10:53 |
| fenn | they are? | 10:53 |
| pmetzger | so an orbital is for ONE electron. | 10:53 |
| pmetzger | or a pair with opposite spin. | 10:53 |
| pmetzger | but an atom has many electrons in different orbitals. | 10:54 |
| pmetzger | so you can mean many different things when you are colloquial about it | 10:54 |
| pmetzger | the probability density of a single electron, of all the electrons.... | 10:54 |
| pmetzger | it helps to be very specific about what one means. | 10:54 |
| fenn | well basically i was upset with the simplistic representation of molecules with balls and sticks, but didn't realize i had to jump up to a whole new level of sophistication/cantankerousness just to get anything beyond that | 10:56 |
| pmetzger | different representations are good for different things. | 10:57 |
| pmetzger | 2D reps are often good enough for organic chemists, given how they think. | 10:58 |
| kanzure | "We actually have licensed copies for most all of the CAD-related STEP application protocols, but thanks anyways. ARL got us copies of the specification several years ago so we could develop our STEP importer, which we just finished implementing last year. We've taken over the NIST SCL as part of that project and have been making improvements to it in order to support the latest specification." | 10:58 |
| * kanzure <3 brlcad | 10:58 | |
| kanzure | (that was sean) | 10:58 |
| pmetzger | getting full accurate representations of things like d or f based orbitals gets fun. | 10:58 |
| fenn | so they now have a working step importer? | 10:59 |
| pmetzger | hard to visualize wacky stuff like that | 10:59 |
| kanzure | fenn: apparently. i'm sniffing around to see if it's true | 10:59 |
| kanzure | they were using the NIST SCL thingy that i was trying to compile yesterday | 10:59 |
| pmetzger | things like delta bonds happen as well. :) | 10:59 |
| pmetzger | https://secure.wikimedia.org/wikipedia/en/wiki/Delta_bond | 10:59 |
| pmetzger | and do you want a representation to show orbital symmetry (which is critical to bond formation) or to ignore it and just show probability distributions? | 11:00 |
| pmetzger | these are all considerations when you're trying to view something. | 11:00 |
| pmetzger | sometimes, just seeing balls and sticks is *easier* than a more literally accurate representation because it gives a person with a particular background a clearer view of what's where, and their intuition does the rest. | 11:00 |
| fenn | well, most people don't have any "intuition" | 11:01 |
| fenn | they just see balls and sticks | 11:01 |
| pmetzger | You can't do work without intuition anyway. | 11:01 |
| fenn | you can't develop intuition unless you've seen wtf you're trying to visualize | 11:01 |
| pmetzger | without chemical intuition, you don't get that you should be watching out for the behavior of the lone pair on a nitrogen, say. | 11:01 |
| pmetzger | and the visualization won't show you that. | 11:01 |
| fenn | it's not "intuition" dammit | 11:02 |
| pmetzger | it is. | 11:02 |
| fenn | bah | 11:02 |
| pmetzger | you build it by doing loads of problems. | 11:02 |
| pmetzger | it is like having a sense of what type of integration trick to try for a particular integral. | 11:02 |
| pmetzger | "oh, this probably needs integration by parts"... | 11:02 |
| pmetzger | you build a big database of ideas in your head as you work with some difficult domain | 11:02 |
| pmetzger | "intuition" is as good a word as is easily available for that. saying "experience" doesn't give the right flavor. | 11:03 |
| pmetzger | anyway, you look at a molecule, and if you have the right kind of background, you can see "ah, that's a tertiary carbon with high steric hinderance, I bet that SN1 chemistry happens there" | 11:03 |
| pmetzger | and with too many things cluttering the picture you won't pick that up. | 11:04 |
| pmetzger | or you see a carbonyl group and you think about the carbonyl chemistry that can happen at the spot. | 11:04 |
| fenn | i've noticed that it suddenly became hard to remember the meaning of the kanji when ubuntu decided to upgrade and changed the font... | 11:04 |
| pmetzger | Anyway, people without the background won't know what sort of reactions can happen, and for people with it, the most "realistic" notion of an electron probability density around the molecule would conceal what they need to see to figure the chemistry out. | 11:05 |
| pmetzger | so often, people use very primitive visualizations because they're sufficiently uncluttered to show the right things. | 11:06 |
| pmetzger | sorry to make it sound hard. unfortunately, to some extent it is. | 11:06 |
| pmetzger | Organic chemists typically do things like not labeling the carbons and leaving the hydrogens entirely off the diagram to make it easier to see the important parts. :) | 11:08 |
| kanzure | fenn: also, they have the entire complete set of ISO 10303 thanks to their military connections | 11:08 |
| kanzure | !! :) | 11:08 |
| pmetzger | this is BRL-CAD? I thought people said it wasn't useful... | 11:08 |
| kanzure | it isn't | 11:09 |
| fenn | the entire complete set? | 11:09 |
| kanzure | but they have some pretty wacky connections with the military | 11:09 |
| kanzure | fenn: at least the STEP-related portions.. but i'll check/ask | 11:09 |
| fenn | i thought ARL pretty much WAS the military | 11:10 |
| pmetzger | I wonder how long it would take a dedicated team to clone AutoCAD... | 11:10 |
| kanzure | advanced research lab? i thought the military is more than military | 11:10 |
| fenn | army research labs | 11:10 |
| kanzure | pmetzger: you want a team to clone Solidworks. screw autocad | 11:10 |
| kanzure | fenn: have you used solidworks yet? | 11:10 |
| pmetzger | I've used neither. | 11:11 |
| kanzure | pmetzger: also, i was once working on this weird hack to use solidworks DLL files from python running under wine. a lot of the symbol names and class names in solidworks are the same as in OpenCASCADE | 11:11 |
| kanzure | corporate acquisitions or something, i bet | 11:11 |
| fenn | i liked the old manuals where they described each tutorial as a "mission" | 11:12 |
| pmetzger | I'm pretty ignorant when it comes to using actual mechanical CAD systems. I've never done a project on one. | 11:12 |
| kanzure | "okay soldier, watch out for the compiler errors, and don't mess with -Wall" | 11:12 |
| pmetzger | so my opinions about them may be cheerfully ignorant. | 11:12 |
| fenn | i think i played around with solidworks once, or maybe it was inventor.. | 11:12 |
| pmetzger | I mentioned AutoCAD only because it is the one many people seem to use, not out of knowledge. | 11:16 |
| kanzure | solidworks was the once that looked like this: http://upload.arabsbook.com/imgcache/SolidWorks-2008-Unveiledne8dzzjgL7.www.arabsbook.com.jpg | 11:16 |
| fenn | i thought this was nifty: //secure.wikimedia.org/wikipedia/en/wiki/Delta_bond | 11:18 |
| fenn | grarr | 11:18 |
| fenn | http://brlcad.org/w/images/4/4f/Vehicle_Tire_and_Wheel_Creation_in_BRL-CAD.pdf | 11:18 |
| fenn | i want "surface normal vision" | 11:19 |
| pmetzger | if BRL-CAD is used enough to need tire creation primitives, but it isn't usable, how do people manage? | 11:23 |
| fenn | there are a small number of highly trained army personnel that do nothing but use brl-cad all day | 11:24 |
| fenn | (highly trained in the use of brlcad that is) | 11:25 |
| fenn | it's a great geometry kernel, it just sorely needs a real UI | 11:25 |
| pmetzger | so are all the "bones" there and it is just a UI issue? | 11:25 |
| * fenn has discovered the hot chocolate machine at work | 11:36 | |
| fenn | internet connection and near-infinite amounts of on-demand low grade chocolate.. now if only they would stop pestering me about this camera sensor stuff | 11:38 |
| kanzure | "now if only i could get them to stop making me actually do stuff" | 11:39 |
| pmetzger | work is the curse of the drinking class. | 11:45 |
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| fenn | i eat cake too | 11:52 |
| kanzure | oh ok, cake too :) | 11:53 |
| kanzure | hot damn i might get the rest of the specs from the brlcad peeps | 11:53 |
| fenn | thanks to my quantitative diary, i can say that i've actually done 33 minutes of "work" today | 11:53 |
| fenn | this was really a bad thing when doing telecommuting with flex hours | 11:53 |
| fenn | because i only billed for actual work | 11:54 |
| kanzure | yeah when people are actually honest with how much "work" they do, it gets a bit mind-boggling | 11:54 |
| fenn | when you figure what stuff actually costs vs the price, it balances out | 11:54 |
| AJollyLife | you mean im not supposed to just answer e-mails/tweet/hang out in irc all day at work? | 12:10 |
| fenn | for a lot of people, that's actually their job | 12:10 |
| fenn | consider for example a typical "customer relations" position | 12:11 |
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| kanzure | http://wiki.makerbot.com/open-source-ftw | 12:19 |
| fenn | er, how did they go from "open source yay!" to "you must buy your parts from us"? | 12:25 |
| fenn | i wonder if that was a response to "some people just hang out and tweet all day at work" | 12:26 |
| kanzure | "it's totally possible for you to do it without us and get all the parts yourself, we're ok with that and for personal use (ie: not selling it)," | 12:26 |
| kanzure | the link was not a response to that.. the link is random (in comparison) | 12:27 |
| kanzure | "Anyhow, the main idea here is that if you're going to make it to sell, please talk to us so we can support you and you can support us and so your project will contribute to the community." | 12:27 |
| kanzure | so, it just sounds like "we won't be happy if you sell it independent of us" | 12:27 |
| fenn | yeah, that's how it sounds | 12:27 |
| kanzure | "# If you're selling them, you need to license the MakerBot name from us." | 12:28 |
| kanzure | but it doesn't sound like a legal threat | 12:28 |
| kanzure | (does it?) | 12:28 |
| fenn | yes, but i'm ok with that | 12:29 |
| fenn | it's the actual intended purpose of trademarks after all | 12:29 |
| kanzure | sorry i meant "you must buy your parts from us" didn't sound like a legal threat | 12:29 |
| kanzure | i'm ok with trademark stuff too, that's fine imho | 12:29 |
| fenn | it's not like sun suing sparkfun because they supposedly infringed on their "SPARC" trademark | 12:29 |
| kanzure | woah wtf | 12:29 |
| kanzure | they did that? | 12:29 |
| fenn | heh, they sent some scary letter demanding money, i dunno if they actually sued or not | 12:30 |
| kanzure | that's amazing | 12:30 |
| fenn | indeed | 12:30 |
| fenn | http://www.sparkfun.com/commerce/news.php?id=300 | 12:31 |
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| fenn | btw, i went camping this weekend, that's why i was disappeared | 12:48 |
| fenn | kanzure did you ever find the package i ordered from sparkfun just before hplus summit in december? | 12:52 |
| fenn | i want to play around with sensor fusion; i should probably just get a wiimote from ebay or craigslist | 12:52 |
| fenn | but having a real gyro or accelerometer chip would be educational | 12:52 |
| kanzure | yes, i think so | 12:53 |
| kanzure | i never opened it up to confirm stuff | 12:53 |
| fenn | that's ok | 12:55 |
| fenn | wow the gyro chips were only $8 | 12:56 |
| fenn | btw did i mention the recent-ish discovery by meredith scheff @ noisebridge that you can just feed copper-clad kapton through a laser printer and it prints fine | 12:57 |
| pmetzger | kapton? | 12:58 |
| fenn | heat resistant plastic film | 12:58 |
| fenn | so anyway i don't need to get a solid ink printer at least | 13:01 |
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| kanzure | http://brlcad.org/tmp/spirot.png | 13:31 |
| kanzure | http://brlcad.org/tmp/spirot2.png | 13:32 |
| kanzure | looks like chris got the rotations working on my old spiral.pl script | 13:32 |
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| * kanzure listens to http://www.di.fm/mp3/vocaltrance.pls | 13:35 | |
| kanzure | time to get back to work on step.py | 13:35 |
| jrayhawk | this is not a good song | 13:36 |
| kanzure | i agree :( | 13:37 |
| kanzure | it should be over soon. i hope. i pray. | 13:37 |
| jrayhawk | you should be listening to my radio station | 13:37 |
| kanzure | what do you stream | 13:37 |
| jrayhawk | a delicate mix of animaniacs and gangster rap at all times | 13:37 |
| kanzure | sounds intoxicating | 13:37 |
| * fenn grumbles about arc-length parameterization | 13:39 | |
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| fenn | jrayhawk: might i suggest adding some french rap and ievan polka to the mix | 13:39 |
| jrayhawk | I have a small snippet of psytrance polka in there somewhere | 13:40 |
| jrayhawk | and yes, i do have french rap, too | 13:40 |
| pmetzger | MC Solar? | 13:41 |
| kanzure | jrayhawk: it doesn't sound like animaniacs fyi | 13:41 |
| kanzure | can you fix it and put something good on? kthnxbai | 13:41 |
| pmetzger | pardon, missing an a. | 13:41 |
| pmetzger | MC Solaar | 13:41 |
| jrayhawk | indeed | 13:41 |
| kanzure | joe's stream is like listening to the internet cry out in pain constantly | 13:42 |
| kanzure | ok, there it goes, switched over to something else | 13:42 |
| kanzure | jrayhawk: do you have the mp3 or album that xmms 1.2 was shipped with? | 13:43 |
| pmetzger | Everyone outside of France who has french rap in their collection has MC Solaar. | 13:43 |
| jrayhawk | I doubt it. | 13:43 |
| pmetzger | it seems like it sometimes. :) | 13:44 |
| jrayhawk | pmetzger: good call, I do indeed have that. | 13:44 |
| pmetzger | http://blog.makerbot.com/2010/06/21/icookie-baking-for-the-new-generation/ | 13:48 |
| kanzure | mota does openmaterials.org | 13:51 |
| kanzure | which, has no materials data :( | 13:51 |
| kanzure | jrayhawk: your musical tastes confuse me | 13:51 |
| kanzure | now i'm imaginging all this french rap stuff while you're doing system admin stuff | 13:52 |
| kanzure | chmod +x that shit | 13:52 |
| jrayhawk | fuck tha IEC | 13:53 |
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| fenn | pmetzger, if only those kids were as good at engineering as they were at marketing | 13:58 |
| kanzure | all the cute chicks go into marketing | 13:59 |
| pmetzger | which kids? | 13:59 |
| fenn | mota, hoeken, et al | 14:00 |
| kanzure | right | 14:01 |
| kanzure | yeah a lot of these people are *amazing* at marketing and self PR | 14:02 |
| fenn | ahem | 14:03 |
| kanzure | hm? | 14:03 |
| fenn | so i think alex lightman/whoever was bullshitting about the number of viewers at hplus | 14:03 |
| kanzure | i agree | 14:03 |
| kanzure | alex fails at pr because it's so easy to see through ;) | 14:03 |
| fenn | i saw about 250 on average watching the stream, according to ustream | 14:04 |
| fenn | nah, people are shallow and easily misled, that's what marketing is about | 14:04 |
| pmetzger | with enough marketers, all people are shallow. | 14:07 |
| pmetzger | (to distort ESR.) | 14:07 |
| fenn | "with enough assholes, all arguments are shallow" | 14:11 |
| pmetzger | :) | 14:13 |
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| pmetzger | fenn: so anyway, if you look at: http://www.ks.uiuc.edu/Research/vmd/current/images/c60_orb104b.png | 14:21 |
| pmetzger | it doesn't show any of the pi bonds in the system, and it makes you think everything is a clean sigma bond | 14:22 |
| pmetzger | it isn't a realistic depiction of the bonding orbitals or of the overall electron probability density | 14:22 |
| pmetzger | so it is easy with programs like this to view "the wrong thing" if you're not careful too.. | 14:23 |
| pmetzger | you always need to know what you're doing... | 14:23 |
| pmetzger | Wild. Did a google search for something else and exhumed this... http://www.wired.com/wired/archive/2.10/extropians.html | 14:33 |
| kanzure | yeah that was a popular article back in the day | 14:33 |
| pmetzger | I'd forgotten Ed Regis had written that. | 14:33 |
| pmetzger | Ever read "The Great Mambo Chicken and the Transhuman Condition"? | 14:34 |
| kanzure | i have a copy laying around, i flipped through a few of the chapters once | 14:34 |
| kanzure | fenn: do you know the guy who wrote the config file for the puma500 in emc2? | 14:35 |
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| fenn | what's his name? | 14:42 |
| kanzure | no, i'm asking you | 14:42 |
| fenn | no, i'm asking you | 14:42 |
| kanzure | er uh | 14:42 |
| fenn | looks like it was added by alex joni | 14:43 |
| kanzure | know him? | 14:43 |
| fenn | yeah, he's alex_joni on freenode, in #cam and #emc | 14:44 |
| fenn | idle 1 day | 14:44 |
| kanzure | better than you | 14:45 |
| kanzure | "idle 2 weeks" or some shit :P | 14:45 |
| kanzure | (sometimes) | 14:45 |
| fenn | heh. where's my brain implant | 14:45 |
| fenn | i think this wearable computer is going to have to be waterproof | 14:45 |
| kanzure | and humidity proof | 14:45 |
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| fenn | and squashed-in-a-backpack-in-a-trunk-proof | 14:46 |
| kanzure | and jocked-up-on-since-i'm-a-nerd-proof | 14:46 |
| fenn | so i got my 2 kg of shapelock (PCL/CAPA) yesterday | 14:47 |
| fenn | kanzure i've been thinking about that and also plan to build a retractable baton/stun gun/mace/flashlight thing | 14:47 |
| kanzure | hah | 14:48 |
| fenn | a nice 5W cyan lumiled ought to blind the shit out of anybody at night | 14:48 |
| kanzure | Steve Canfield and his marvellous mechanical joint http://selenianboondocks.com/2010/06/cjoint1/ | 15:02 |
| kanzure | wtf | 15:02 |
| kanzure | QuantumG: what are you doing in the comments there? :) | 15:02 |
| QuantumG | it's a space site | 15:03 |
| QuantumG | and Kirk is a bitter old bastard | 15:03 |
| fenn | i was just looking at canfield joints recently, they're used on the momentum exchange tether design http://www.youtube.com/watch?v=mPx1Nq80jm8 | 15:04 |
| QuantumG | that's Kirk's | 15:05 |
| fenn | er, why yes it is | 15:05 |
| kanzure | i think the world just collapsed in size a little | 15:06 |
| kanzure | did you feel it? | 15:06 |
| fenn | i'm used to it | 15:06 |
| QuantumG | yeah, Kirk is probably more famous for his Thorium energy work | 15:06 |
| fenn | canfield joint reminds me of a cross between a helicopter cyclic and a deltabot | 15:08 |
| QuantumG | first time I looked at it I thought "wow, imagine that at a nano scale." | 15:08 |
| fenn | i should put one on thingiverse | 15:08 |
| QuantumG | kanzure, my "are you around?" question last night was going to be: what can DIY microfluidics do so far? | 15:12 |
| kanzure | a lot of microfluidics is DIY btw | 15:12 |
| kanzure | but do you mean things that were done without academic funding? | 15:13 |
| kanzure | i mean.. everything in the literature is mostly PDMS stuff that the researcher poured himself | 15:13 |
| QuantumG | DIY to me means someone without funding could whip it together, yeah | 15:14 |
| QuantumG | any gentle introduction to PDMS around? :) | 15:14 |
| fenn | i dont see what's so hard about pdms.. it's basically like pcb fab right? | 15:14 |
| kanzure | it's easier than pcb fab imho | 15:15 |
| fenn | pdms == poly dimethyoxy silicone == silicone casting rubber | 15:15 |
| fenn | dimethyl siloxane, wah | 15:15 |
| QuantumG | what do DIYBio people call HOWTOs? :) | 15:16 |
| fenn | protocols? | 15:16 |
| kanzure | protocols | 15:17 |
| fenn | or if you want to be realistic, "instructables" :( | 15:17 |
| kanzure | :( | 15:17 |
| QuantumG | might I suggest that HOWTO be reserved for DIY and have the detail of both? :) | 15:17 |
| QuantumG | anyway, is there a protocol or an instructable for DIY PDMS? | 15:18 |
| kanzure | yes, let me dig something up | 15:18 |
| fenn | 17:05 < QuantumG> that's Kirk's | 15:18 |
| kanzure | http://www.biomemsrc.org/biomems/documents/pdmscasting.pdf | 15:19 |
| fenn | sorry, windows is being a little bitch | 15:19 |
| fenn | http://www.vanderbilt.edu/viibre/documents/PDMS_Molding_and_bonding.pdf | 15:19 |
| kanzure | chemicals: Sylgard 184 base, Sylgard 184 curing agent, Acetone, 2-Propanol | 15:20 |
| QuantumG | k, so what can you do with PDMS? | 15:20 |
| kanzure | Weighing Scale, Vacuum Chamber, Curing Oven | 15:20 |
| kanzure | wtf a vacuum chamber? | 15:20 |
| fenn | "su-8 100mm silicon wafer" sounds a bit more involved than pcb etching | 15:20 |
| kanzure | QuantumG: pretty much anything you see here: http://designfiles.org/papers/microfluidics/ | 15:20 |
| kanzure | hrm | 15:20 |
| fenn | vacuum is only for removing bubbles | 15:20 |
| kanzure | yeah, especially if you have to spin down the wafer or something | 15:20 |
| kanzure | QuantumG: except not the papers that are about different ways of doing microfluidics | 15:21 |
| kanzure | i.e. there are some papers about "alternatives to PDMS" | 15:21 |
| kanzure | and obviously those aren't about.. uh. nevermind. | 15:21 |
| QuantumG | can you build stuff that can count cells? | 15:21 |
| kanzure | i think you would need optical circuitry as well on top of it? | 15:21 |
| kanzure | or maybe something like resistive capacitance sensing? | 15:21 |
| QuantumG | or electrical | 15:21 |
| kanzure | :) | 15:21 |
| kanzure | fenn: i don't remember wafers being required.. | 15:22 |
| QuantumG | how do you control the flow? electrical valves of some sort? | 15:22 |
| kanzure | some people do hydraulic valves | 15:22 |
| kanzure | and have separate channels for controlling various valves | 15:22 |
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| fenn | i think they just use silicon as the substrate because it fits in the photolithography machine | 15:24 |
| fenn | kanzure do you know if the laser pump idea works for actuating hydraulic valves? | 15:25 |
| fenn | though you wouldnt really need valves if you had a laser pump... | 15:26 |
| kanzure | heh | 15:26 |
| * fenn chases his tail and it falls off | 15:26 | |
| kanzure | damn furries | 15:26 |
| kanzure | get off my lawn | 15:26 |
| QuantumG | anyone done magnetic separation of fluids in PDMS? | 15:26 |
| fenn | magnetic separation of fluids? | 15:27 |
| kanzure | Capture of DNA in microfluidic channel using magnetic beads - increasing capture efficiency with integrated mixer http://designfiles.org/papers/microfluidics/Capture%20of%20DNA%20in%20microfluidic%20channel%20using%20magnetic%20beads%20-%20increasing%20capture%20efficiency%20with%20integrated%20mixer.pdf | 15:27 |
| fenn | like, liquid oxygen? (only magnetic fluid i konw of) | 15:27 |
| kanzure | Discrete magnetic microfluidics on superhydrophobic surfaces using magnetic fields http://designfiles.org/papers/microfluidics/Discrete%20magnetic%20microfluidics%20on%20superhydrophobic%20surfaces%20using%20magnetic%20fields.pdf | 15:27 |
| QuantumG | k, I'll read all these and see if I get knowledge :) | 15:28 |
| fenn | i wonder if mark hayes is related to sean hayes (arizona state, last paper) | 15:28 |
| kanzure | QuantumG: i don't suggest reading the last two links i pasted | 15:28 |
| kanzure | the pdms pdfs that fenn and i pasted links to are worth reading | 15:28 |
| QuantumG | yup, that's the plan | 15:29 |
| fenn | oh, "sean hays" nevermind | 15:29 |
| fenn | curses, my name hashing algorithm has been revealed! | 15:29 |
| kanzure | fenn: did you read in here the other day when i found out about the "cancer-resistant mice" and livly.org? | 15:31 |
| kanzure | i was pretty upset | 15:31 |
| fenn | hm? | 15:32 |
| fenn | no, i didnt | 15:32 |
| fenn | gimme the dirt | 15:32 |
| kanzure | http://designfiles.org/~bryan/chats/bioinformatics-and-livly.log | 15:35 |
| kanzure | it's not all relevant- you'll have to skip around to the points where i'm sending messages i guess | 15:35 |
| QuantumG | wow, those two pdfs are pretty far away from a HOWTO | 15:35 |
| kanzure | which ones | 15:35 |
| kanzure | the pmds ones or the designfiles.org links | 15:35 |
| QuantumG | pdmscasting.pdf and PDMS_MMolding_and_bonding.pdf | 15:35 |
| kanzure | yeah, science protocols are notoriously terrible | 15:36 |
| kanzure | gee don't you want SKDB and instruction generation? :) | 15:36 |
| fenn | tl;dr: jon wants $100k to sequence a mouse genome, so what? | 15:37 |
| kanzure | fenn: including the mice stuff in that log, btw. that's part of the relevance. | 15:37 |
| kanzure | um, well you missed it then | 15:37 |
| kanzure | livly.org going corporate? after taking equipment donations as a non-profit? | 15:37 |
| QuantumG | ignoring how many of the words I have only a vague idea of: weight boat, desiccator | 15:38 |
| QuantumG | that's fine, I can learn that.. | 15:38 |
| QuantumG | neither of them say anything about making patterns in the mold.. | 15:38 |
| QuantumG | oh, another word: Tare | 15:39 |
| kanzure | usually it's a photolithography setup over a thin layer of SU8 to make a mold | 15:39 |
| kanzure | however, there are many alternatives to this sort of PDMS setup | 15:39 |
| kanzure | wax printing http://designfiles.org/papers/microfluidics/Rapid%20prototyping%20of%20microfluidic%20devices%20with%20a%20wax%20printer.pdf | 15:40 |
| kanzure | laser-patterned tape http://designfiles.org/papers/microfluidics/Rapid%20prototyping%20of%20microfluidic%20systems%20using%20a%20laser-patterned%20tape.pdf | 15:40 |
| kanzure | paper+tape http://designfiles.org/papers/microfluidics/Three-dimensional%20microfluidic%20devices%20fabricated%20in%20layered%20paper%20and%20tape.pdf | 15:40 |
| kanzure | here's an article from wetPONG that isn't up any more | 15:40 |
| kanzure | http://designfiles.org/papers/microfluidics/wetPONG%20%c2%bb%20Homemade%20Microfluidics%20using%20adhesive%20tape.html | 15:40 |
| kanzure | "homemade microfluidics using adhesive tape" | 15:40 |
| kanzure | actually, read that one. :) | 15:41 |
| QuantumG | ok, so say you've got your PDMS.. now you need to inject a fluid right? you just use a syringe? | 15:41 |
| kanzure | there's also shrinky dinks: | 15:41 |
| kanzure | http://designfiles.org/papers/microfluidics/Shrinky-Dink%20microfluidics:%203D%20polystyrene%20chips.pdf | 15:41 |
| kanzure | http://designfiles.org/papers/microfluidics/Shrinky-Dink%20microfluidics:%20rapid%20generation%20of%20deep%20and%20rounded%20patterns.pdf | 15:41 |
| kanzure | well, yes and no | 15:41 |
| kanzure | you could use a syringe, a syringe pump, a pipette, but also sometimes an eye dropper depending on what you're doing | 15:42 |
| kanzure | for instance, if you're doing surface tension devices, you can just use an eye dropper | 15:42 |
| kanzure | http://www.youtube.com/watch?v=1HrRuaLFGmY | 15:42 |
| kanzure | i'm not too sure about fluid inputs when you're using a pump to control hydraulic valves or something | 15:42 |
| QuantumG | how wide is that channel? | 15:42 |
| kanzure | whitesides did this really hawt review on ways to control valves in microfluidics | 15:42 |
| kanzure | QuantumG: in the youtube video? i dunno. the youtube description for that vid has a citation to a paper, though | 15:43 |
| kanzure | and the paper probably says | 15:43 |
| kanzure | now, that's surface tension- which doesn't use a pump, or any valve control | 15:43 |
| kanzure | kind of like the sharpie microfluidics stuff http://groups.google.com/group/diybio/msg/1197606e3c3dc439 (no pumps or whatever) | 15:43 |
| kanzure | at one point i was getting kind of crazy and was using a piece of hair and drawing sharpie over it, to get a straight 100micron channel width.. heh | 15:44 |
| kanzure | A screw-actuated pneumatic valve for portable, disposable microfluidics http://designfiles.org/papers/microfluidics/A%20screw-actuated%20pneumatic%20valve%20for%20portable,%20disposable%20microfluidics.pdf | 15:45 |
| kanzure | A simple pneumatic setup for driving microfluidics http://designfiles.org/papers/microfluidics/A%20simple%20pneumatic%20setup%20for%20driving%20microfluidics.pdf | 15:45 |
| kanzure | a review of microvalves http://designfiles.org/papers/microfluidics/Review%20-%20A%20review%20of%20microvalves%20-%202006.pdf | 15:45 |
| kanzure | re: paper-based microfluidics; Bioactive paper provides a low-cost platform for diagnostics http://designfiles.org/papers/whitesides/Bioactive%20paper%20provides%20a%20low-cost%20platform%20for%20diagnostics.pdf | 15:46 |
| kanzure | on that same note re: paper as the substrate; Diagnostics for the Developing World - Microfluidic Paper-Based Analytical Devices http://designfiles.org/papers/whitesides/Diagnostics%20for%20the%20Developing%20World%20-%20Microfluidic%20Paper-Based%20Analytical%20Devices.pdf | 15:46 |
| kanzure | FLASH - A rapid method for prototyping paper-based microfluidic devices http://designfiles.org/papers/whitesides/FLASH%20-%20A%20rapid%20method%20for%20prototyping%20paper-based%20microfluidic%20devices.pdf | 15:47 |
| kanzure | Low-Cost Printing of PDMS Barriers to Define Microchannels in Paper http://designfiles.org/papers/whitesides/Low-Cost%20Printing%20of%20PDMS%20Barriers%20to%20Define%20Microchannels%20in%20Paper.pdf | 15:47 |
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| kanzure | i don't seem to have the whitesides review of pneumatic valves- it might have been a quake paper. | 15:48 |
| kanzure | at any rate, 'review of microvalves' might be sufficient if you want to go that route | 15:48 |
| QuantumG | so what can you do with it? | 15:48 |
| kanzure | it=? | 15:49 |
| kanzure | a valve? | 15:49 |
| QuantumG | what applications are there that have been done at a DIY scale? | 15:49 |
| kanzure | analyte mixing & simple chemistry experiments (look! it changes colors!), fluid actuation, unintentional bacteria culture, PCR (but i don't know if a DIYer did one or not yet) | 15:50 |
| QuantumG | was about to ask that :) | 15:51 |
| kanzure | there's lots of papers in /papers/microfluidics/ on PCR riggups | 15:52 |
| kanzure | one that i like is a spiral where the four corners have a different heat or cooling source | 15:52 |
| kanzure | but there's also some others like laser-based heating/cooling of a droplet with your polymerase and dNTPs and DNA etc. | 15:52 |
| kanzure | (not very microfluidic if you're just using a laser + petri dish, i guess.. but the droplet is tiny, does that count) | 15:53 |
| QuantumG | you could use it as part of a microfluidic system | 15:53 |
| kanzure | sure | 15:53 |
| kanzure | that's what fenn was talking about earlier, actually | 15:53 |
| kanzure | laser-induced force on a microdroplet http://designfiles.org/papers/microfluidics/Laser-induced%20force%20on%20a%20microfluidic%20drop%20-%20origin%20and%20magnitude.pdf | 15:54 |
| kanzure | non-contact based manipulation with lasers http://designfiles.org/papers/microfluidics/Non-contact%20Mesoscale%20Manipulation%20Using%20Laser%20Induced%20Convection%20Flows%20-%20480%20nm%20(infrared)%20laser.pdf | 15:54 |
| kanzure | PCR + lasers: http://designfiles.org/papers/microfluidics/PCR%20-%20Nanodroplet%20real-time%20PCR%20system%20with%20laser%20assisted%20heating.pdf | 15:54 |
| kanzure | another one: http://designfiles.org/papers/microfluidics/Petri%20dish%20PCR%20-%20laser-heated%20reactions%20in%20nanoliter%20droplet%20arrays.pdf | 15:54 |
| kanzure | whole blood pumped by laser-driven micropump http://designfiles.org/papers/Whole%20Blood%20Pumped%20by%20Laser%20Driven%20Micropump.pdf | 15:55 |
| kanzure | Diode laser generated ultrasound for human blood cell lysis http://designfiles.org/papers/Diode%20laser%20generated%20ultrasound%20for%20human%20blood%20cell%20lysis.pdf | 15:55 |
| kanzure | i <3 lasers | 15:55 |
| pmetzger | "do not stare into laser with remaining eye." | 15:56 |
| kanzure | pmetzger: have you seen the papers on acoustic shockwaves generated by lasers? | 15:57 |
| kanzure | "laser-induced cavitation" | 15:57 |
| kanzure | or "laser-based ultrasound" | 15:57 |
| QuantumG | damn you Keanu Reeves! | 15:57 |
| pmetzger | I've vaguely heard that you could induce shockwaves with lasers but no, haven't read anything on the subject. | 15:57 |
| pmetzger | It is a bit far from my normal stomping ground... | 15:57 |
| kanzure | well, if you ever get interested in it: http://designfiles.org/papers/Aspects%20of%20laser-generated%20acoustic%20shock%20waves%20in%20air.pdf | 15:58 |
| pmetzger | for now I have too much to learn. :) | 15:59 |
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| kanzure | jrayhawk: http://www.di.fm/mp3/vocaltrance.pls is play dj doboy, which is slightly better than the other stuff. try now? | 16:19 |
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| jrayhawk | This is neither animaniacs nor gangster rap. People listen to such a thing? | 16:31 |
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| kanzure | meredith sez: "so apparently the royal society is making their entire archive all the way back to 1665 available for free until july 30th" | 16:37 |
| kanzure | time to write a scraper! | 16:37 |
| kanzure | http://royalsocietypublishing.org/journals | 16:37 |
| pmetzger | please! | 16:37 |
| kanzure | bwahaha | 16:37 |
| kanzure | does anyone have a lot of storage space i can abuse with a few hundred gigabytes of downloads | 16:38 |
| kanzure | also preferably with a good connection | 16:38 |
| kanzure | designfiles.org is quickly running out of storage space | 16:38 |
| jrayhawk | So long as you don't do it too fast, you can use your Bart vserver. | 16:38 |
| kanzure | wah-hey, fantastic | 16:38 |
| kanzure | now i just need to make sure i do it with metadata | 16:39 |
| jrayhawk | I guess you could also use cysteine, at which point we don't really care about bandwidth usage at all. | 16:39 |
| kanzure | ok great | 16:40 |
| jrayhawk | Actually, yeah, that'll work out better. Let me go increase the raided volume size | 16:40 |
| jrayhawk | Okay, you can shove that stuff somewhere in /torrents/. Probably not in /torrents/tmp, we tend to delete that on occasion. | 16:43 |
| kanzure | heh | 16:43 |
| jrayhawk | I just added another 200G | 16:43 |
| kanzure | okay, that sounds like it should do it | 16:43 |
| kanzure | "An Accompt of the Improvement of Optick Glasses" 1665 | 16:44 |
| kanzure | gah meredith was doing a blanket wget on it... | 16:47 |
| kanzure | DON'T DO THAT | 16:47 |
| kanzure | just fyi :) | 16:47 |
| fenn | what's with the weird time limit | 16:53 |
| kanzure | maybe they are challenging me | 16:54 |
| fenn | aside from the coolness of the word "tortuosity", why do we care about laser shockwaves in air? | 16:54 |
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| ybit3 | how to make su-8? | 16:58 |
| kanzure | heh pretty cool.. browsing through some of the archive pages | 16:58 |
| ybit3 | http://designfiles.org/papers/microfluidics/SU-8%20a%20low-cost%20negative%20resist%20for%20MEMS.pdf doesn't give very good details | 16:58 |
| kanzure | * Anthony van Leeuwenhoeck | 16:58 |
| kanzure | An Extract of a Letter from Mr. Anthony Van Leeuwenhoeck, F. R. S. Dated October the 12th. 1713. Concerning the Fibres of the Muscles, &c. | 16:59 |
| * kanzure knows that name :) | 16:59 | |
| kanzure | ybit3: most people buy it :( | 16:59 |
| ybit3 | kanzure: the whitesides paper mentioned that they used a home-made version of it but don't reference a paper or anything | 16:59 |
| ybit3 | the patent: http://www.google.com/patents?id=8943AAAAEBAJ&printsec=abstract&zoom=4&source=gbs_overview_r&cad=0#v=onepage&q&f=false | 17:07 |
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| kanzure | how should i organize this scrape? | 17:34 |
| kanzure | should i do journal/volume_id/paper_name.pdf? | 17:35 |
| QuantumG | http://arxiv.org/ftp/arxiv/papers/0908/0908.0575.pdf | 17:35 |
| QuantumG | neat | 17:35 |
| kanzure | egeste: gah he's scratching at windows to get out (like a gerbil) | 17:36 |
| kanzure | it's kind of pathetic | 17:36 |
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| egeste | kanzure: when do you think he'll be ready to go outside? | 17:47 |
| kanzure | soon. a week or so? | 17:48 |
| egeste | he's going to love it | 17:48 |
| kanzure | egeste: i am hesitant about the heat, though :/ | 17:48 |
| egeste | well | 17:48 |
| egeste | as long as he knows he can come home to ac and food | 17:48 |
| egeste | he'll be fine | 17:48 |
| kanzure | sure. | 17:48 |
| kanzure | right now he's perplexed about the other cat in the window (his reflection) | 17:49 |
| egeste | lol | 17:49 |
| kanzure | however, he doesn't fall for the mirror | 17:49 |
| egeste | yeah, he's not too bright in taht regard | 17:49 |
| kanzure | http://createdigitalmusic.com/2010/06/22/velosynth-bicycle-mounted-synth-is-open-source-hackable-potentially-useful/ | 17:49 |
| kanzure | http://hackaday.com/2010/06/22/ti-makes-a-big-bid-for-the-hobby-market/ | 17:49 |
| kanzure | $4.30? hrm | 17:51 |
| kanzure | "Mouser (the vendor TI points to from the wiki) is currently showing 9,848 have been pre-ordered and the first 398 will ship July 5th. I'm guessing an order now will take a while to ship." | 17:52 |
| bkero | haha | 18:02 |
| bkero | Yea | 18:02 |
| bkero | How could TI not expect this? | 18:02 |
| fenn | http://www.designaside.com/wp-content/uploads/2009/12/josh-keyes02.jpg | 18:39 |
| fenn | i'm always stupendified by the number of people at QS meetups | 18:39 |
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| kanzure | hi Alystair | 18:45 |
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| mheld | hey y'all | 18:47 |
| pmetzger | hola. | 18:48 |
| mheld | how's it going, pmetzger? | 18:50 |
| pmetzger | not so bad. :) | 18:57 |
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| kanzure | http://diyvictoria.com/ | 19:20 |
| kanzure | hm it's not there yet | 19:20 |
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| kanzure | http://brlcad.org/wiki/Spiral | 19:35 |
| kanzure | fenn: i think this is why i vowed to stop writing shit in perl | 19:37 |
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| kanzure | http://www.protohat.com/ | 21:47 |
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| fenn | i chatted with josh perfetto today and i think your concerns about livly are unfounded | 23:22 |
| fenn | first of all they never had any money, and secondly "livly" itself is more or less defunct | 23:22 |
| fenn | jon got some venture funding to investigate his cancer mouse, "immunepath", and eri is steering the biohackerspace stuff towards biocurious | 23:23 |
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| fenn | http://www.mapofscience.com/poster.html | 23:56 |
| jcluck | where the hell am I on there D: | 23:58 |
| jcluck | there are no yellow dots near the green ones! | 23:58 |
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