--- Log opened Tue Jun 10 00:00:30 2014
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00:02 < ||0_-_0||> paperbot http://www.nature.com/nsmb/journal/v21/n6/full/nsmb.2820.html?WT.ec_id=NSMB-201406
00:02 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnsmb.2820
00:04 < ||0_-_0||> paperbot http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2934.html?WT.ec_id=NMETH-201406
00:04 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnmeth.2934
00:04 < ||0_-_0||> paperbot <3 <3 <3
00:04 < gradstudentbot> Okay, someone really needs to do the lab dishes.
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00:35 < nmz787> that zeiss is pretty average for a multi-light source and trinocular (possibly fluorescense) scope
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05:06 < seba-> [14:02] <horsefiend> so i went home, alone, with my wine and maaged to get meth anyway, I used 200mg of it IV and then threw up blood... so i am thinking also that perhaps i am sufffering from something which IV aspirin may be favourable for...
05:06 < seba-> lol
05:07 < nshlol> i don't always practice adultery, but when i do, it's with my bloodstream
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05:14 < seba-> full quote: http://pastebin.com/5NhbP39S
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06:01 < catern> lol
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10:01 < nmz787_i>  I seem to be experiencing a imported function fails to call in exception where the interpreter crashes/closes
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10:06 < kanzure> i am not sure if grammar
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10:07 < kanzure> are you talking about an ImportError?
10:07 < dingo> an exception occured while handling an exception
10:07 < kanzure> https://github.com/docker/libswarm
10:07 < kanzure> "Simulate your entire service topology in a single process"
10:13 < kanzure> an open source embedded microprocessor core https://github.com/atgreen/moxiedev http://www.moxielogic.org/wiki http://www.moxielogic.org/blog
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10:16 < nmz787_i> hmm idk
10:16 < nmz787_i> i'm not reproducing an error in demo
10:21 < archels_> .title http://www.nytimes.com/2014/06/10/health/a-chilling-medical-trial.html
10:21 < yoleaux> archels_: Sorry: that command is a web-service, but its response was too long.
10:21 < archels_> nothing new, but good that this is going mainstream
10:21 < archels_> probably also good news for the cryo crowd
10:22 < archels_> (bearing in mind that Alcor whistleblower blog or whatever it was)
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10:36 < kanzure> gene_hacker: has matt encountered or made a graph grammar for optical train design?
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10:46 < gene_hacker> no
10:46 < gene_hacker> there are expert systems that will beat almost any human at optical system design though
10:46 < gene_hacker> why are you making all your optics yourself btw?
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10:56 < kanzure> gene_hacker: because having a model is a good thing, it lets you simulate before building
10:56 < gene_hacker> why not use a microscope whose properties you know?
10:59 < kanzure> but you don't know- nobody has detailed data about "hey, we're projecting LEDs through microscopes and here's how the images turn out"
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11:33 < kanzure> .title https://www.youtube.com/watch?v=Og9M7xIhW00
11:33 < yoleaux> Virtual Atomic Force Microscope using Interactive MD with LAMMPS and VMD
11:33 < kanzure> cc eudoxia
11:35 < kanzure> gene_hacker: however, your idea is probably better.. looks like nobody has done an accurate simulation of a microscope ever. wtf?
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11:43 < eudoxia> kanzure: you know me too well
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12:03 < kanzure> win 3
12:03 < kanzure> lkdfjdsafja;
12:05 < gradstudentbot> This laproscopic camera is so easy to use.
12:33 < kanzure> .title http://hydracarina.org/910
12:33 < yoleaux> Howto mount an infinity corrected microscope objective on a camera
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12:34 < kanzure> .title http://www.krebsmicro.com/obj_bellows/index.html
12:34 < yoleaux> kanzure: Sorry, that command (.title) crashed.
12:34 < kanzure> "Microscope Objectives on Camera Bellows"
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13:12 < nmz787_i> hmm
13:12 < nmz787_i> cad but no prices http://www.velmex.com/bislide/motor_bislide.html
13:13 < nmz787_i> kanzure: i've come across that hydracarina link before, is a good ref, good reminder of it!
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13:16 < nmz787_i> omg  finally figured out the hanging pipe crap
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13:18 < nmz787_i> if you use popen with pythonw.exe, you have to provide a fd for the stdin arg to popen... also in this case, you can't try doing sys.__stderr__.write(string) because it will cause an error (which you won't be able to see unless you're redirecting stderr in this process to a GUI textbox)
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13:32 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA, banned by the Federal Death Administration (4 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | not intentionally unrepeatable
13:32 -!- Topic set by kanzure [~kanzure@131.252.130.248] [Fri Jun  6 17:48:33 2014]
13:32 [Users ##hplusroadmap]
13:32 [ Adifex      ] [ devrandom     ] [ JayDugger      ] [ rk[1]       ] 
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13:32 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010
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13:33 < dingo> good on you
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13:33 < justanotheruser> welcome back to the mainnet
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13:49 < kanzure> did i die
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13:57 < archels_> paperbot: http://www.nrcresearchpress.com/doi/pdf/10.1139/y94-080
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13:57 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/358920edfa35f8bdfecf8f41d0903c5e.txt
13:58 < archels_> yeah, welcome to hell. there's no free paper access here either
14:02 < justanotheruser> archels_: please hold
14:05 < justanotheruser> hmm, I'm signed in for http://www.ncbi.nlm.nih.gov/pubmed/7954086, but I can't find a download link
14:06 < archels_> well... it's in a 1994 issue of the Canadian Journal of Physiology and Pharmacology
14:06 < archels_> I guess it was a long shot
14:06 < archels_> thanks for trying though
14:06 < justanotheruser> yeah, sorry I couldn't get it
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14:20 < delinquentme> paperbot, http://www.nature.com/ncomms/2014/140610/ncomms5082/full/ncomms5082.html
14:20 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fncomms5082
14:22 < delinquentme> kanzure, paper isn't actually fetching novel papers right now right?
14:22 < delinquentme> "novel papers" = papers which aren't already on libgen
14:23 < kanzure> if it's on libgen, i think it skips it
14:24 < gradstudentbot> My study reveals that people are awesome at memorizing insecure passwords.
14:24 < delinquentme> kk, so that paper isn't on libgen and Mr. Paper failed to get it from nature
14:24 < delinquentme> problem?
14:25 < kanzure> yes it most likely doesn't have the pdf
14:25 < kanzure> .title http://www.sciencedirect.com/science/article/pii/S0378517307010113
14:25 < yoleaux> Size analysis of submicron particles by laser diffractometry—90% of the published measurements are false
14:25 < kanzure> (haha, people can't use microscopes)
14:25 < kanzure> or diffractometers
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14:32 < delinquentme> kanzure, libgen clearly does not.  So paperbot isn't fetching them via shibboleth ?
14:32 < delinquentme> " If libgen doesn't have the paper , why isn't paperbot fetching it an uploading it to libgen ? "
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14:34 < kanzure> paperbot does not have access to shibboleth
14:34 < kanzure> as far as i know
14:34 < kanzure> did someone add that?
14:35 < delinquentme> I thought that was how it was downloading papers
14:36 < delinquentme> I thought he downloaded papers from  nature?
14:36 < kanzure> shibboleth is not nature
14:36 < delinquentme> ... no shit
14:37 < kanzure> so again, paperbot does not have access to shibboleth
14:38 < delinquentme> Why isn't it downloading the papers if its not on libgen?
14:38 < kanzure> probably because it doesn't have access, like any other time it can't download something
14:39 < delinquentme> is this a new thing that has gone wrong ? or has it not had access to nature?
14:39 < kanzure> nature.com is not a single access system
14:39 < kanzure> nobody has /full/ access
14:45 < delinquentme> so paperbot has some access to nature but not this journal
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14:45 < delinquentme> ?
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14:46 < kanzure> who knows- sometimes the restrictions are per paper, per journal, per "year published", per "year accepted", per "number of diagrams"...
14:49 < delinquentme> and this is just per whoevers access we're using at the time
14:50 < delinquentme> you and nmz are jumping into the lasercutter game again?
14:50 < delinquentme> this is dumb that I cant get this paper instantly =/
14:51 < kanzure> i forget if it's a cutter or not
14:51 < kanzure> it points light at things, does that help?
14:51 < delinquentme> ablation ?
14:51 < kanzure> what is it called when you point it at a photoresist.. absorption?
14:51 < delinquentme> I want bioreactors which keep cells alive and make blood
14:52 < delinquentme> yeah probs
14:52 < delinquentme> This whole ' young blood ' just seems a really convincing abstraction for youthfulness in my mind.
14:54 < gradstudentbot> I am sponsored by Thermo Fisher.
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15:05 < heath> what do you call someone who's name is an emoticon? pipe pipe zero underscore dash underscore zero pipe pipe? ppzuduzpp?
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15:18 < FourFire> heath, it's not a verbal name
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15:48 < kanzure> oh yeah, maybe i should convert mcad to python-brlcad https://github.com/elmom/MCAD
15:59 < kanzure> dpk: i think the "fix zotero's translators-scrapers to make them not require gecko or zotero" project is the one i'm most interested in
16:00 < kanzure> dpk: so that i can stop using zotero, and also get the benefit of zotero's community focusing on scrapers for me
16:00 < dpk> okay, that was more or less my plan anyway
16:00 < kanzure> unfortunately this means that it can't be pure python, which is a shame..
16:01 < dpk> i did some preliminary investigation and discovered that JavaScript is a load of cocks, but otherwise the plan is good
16:01 < kanzure> have you written js things before?
16:01 < dpk> just needs a good embeddable-into-both-paperbot-and-zotero scraping framework behind it
16:01 < dpk> yeah
16:01 < kanzure> i would have expected you to know already that js sucks?
16:02 < dpk> my consistent experience has been that JavaScript is a load of cocks, indeed
16:02 < kanzure> well, paperbot can be thrown away and replaced with a js version
16:02 < kanzure> the actual irc bot integration is not important to me.. i mean that is simple to hack up later.
16:02 < dpk> but it's always good to rediscover things in new ways, to help improve understanding of them
16:02 < dpk> in this case i came to a new way of understanding the load-of-cocksiness of JavaScript
16:03 < kanzure> i haven't thought strongly about how i would do the zotero integration
16:03 < kanzure> one way is that you could have commonjs stuff, and just require() a vendorized dependency of scrapers
16:04 < kanzure> another way is that you could have a tool that takes the nodejs/browserify-compatible scrapers and dumps them into a format that zotero is capable of using
16:04 < dpk> well i assume that if it runs in the browser, it can run in Zotero?
16:04 < kanzure> well, no, zotero itself has its own api
16:04 < dpk> in that case i'd be inclined to just browserify the whole thing
16:04 < dpk> oh, right
16:04 < kanzure> https://github.com/zotero/translators
16:04 < dpk> oh, that one
16:05 < dpk> i assumed it just ran on top of the browser's JS libraries
16:05 < kanzure> nah it uses this global called Zotero
16:05 < kanzure> https://github.com/zotero/translators/blob/master/American%20Institute%20of%20Aeronautics%20and%20Astronautics.js
16:05 < kanzure> and it has these doWeb, detectWeb, scrape functions
16:06 < dpk> okay, hmm
16:07 < dpk> i think the first option is probably the better one then
16:07 < dpk> or specify some basic HTTP scraping interface which they can provide a shim for
16:07 < gradstudentbot> The smell of e.coli is so very rewarding.
16:07 < dpk> where does gradstudentbot get these things from? heh
16:07 < gradstudentbot> Argh, what do you mean you don't accept LaTeX submissions??
16:08 < dpk> is it just a database of lines to regurgitate a la fortune?
16:08 < kanzure> yep, but he's surprisingly sentient
16:09 < kanzure> so, they are not going to be willing to send their scraping work over http to some other server
16:09 < kanzure> the scrapers/parsers should definitely be local
16:09 < dpk> right, i'm not proposing that
16:09 < dpk> i mean 'interface' in the sense of 'just write a class/module that has these methods'
16:10 < kanzure> zotero/translation-server has an http server where you submit a json request and get back a json response
16:10 < kanzure> the json response is based on the bibliographic data that the scraper returns
16:10 < dpk> ... i see
16:11 < kanzure> i had to hack it to get it to return the pdf url to paperbot,
16:11 < gradstudentbot> Protip: the lab's attic hasn't been used since 1966. Pretty nice.
16:11 < kanzure> https://github.com/kanzure/translation-server/commit/4d35648672c1ff2d2b6c61308ac7fcb684d63448
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16:12 < kanzure> https://github.com/kanzure/translation-server/blob/4d35648672c1ff2d2b6c61308ac7fcb684d63448/src/server_translation.js
16:12 < kanzure> such a terrible system
16:12 < kanzure> oh huh i didn't know about /refresh
16:14 < dpk> the new library of scrapers would be embedded in translation-server, then?
16:15 < kanzure> translation-server accesses the zotero translators through some environment variable containing a path
16:15 < kanzure> heh
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16:16 < kanzure> translation-server is totally irrelevant to me, i'm only using it because it's a quick way to be using gecko/xulrunner
16:16 < kanzure> to be using xulrunner/zotero, i mean
16:16 < chris_99> anyone know can freecad/brlcad work with autocad files
16:16 < dpk> i see
16:16 < kanzure> it actually doesn't work for all of the zotero translators because some of the translators use frames and link navigation, which xulrunner doesn't support(??) according to simonster
16:16 < kanzure> so some of the translators are failing
16:16 < kanzure> chris_99: dxf
16:17 < kanzure> chris_99: .step .iges are also exportable from autocad, which both freecad (opencascade) and brlcad are able to work with
16:17 < chris_99> aha neat
16:19 < kanzure> dpk, so maybe you're right, standard interface, every zotero translator is just a thin wrapper that someone writes, calls the appropriate sanely-architected scraper
16:19 < kanzure> dpk: but then those sanely-architected scrapers need to be packaged into zotero and available
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16:19  * dpk nkds
16:19 < dpk> *nods
16:20 < kanzure> i wonder how js imports work in xul-related js, is it just require()
16:21 < kanzure> https://github.com/firebug/firebug/blob/master/extension/modules/require.js
16:21 < kanzure> https://github.com/firebug/firebug/blob/master/extension/modules/mini-require.js
16:21 < kanzure> but that's requirejs gah
16:22 < dpk> yeah, fuck requirejs
16:22 < dpk> not doing that
16:23 < dpk> well, maybe if there's literally no other option
16:24 < kanzure> looks like require() is baked in these days
16:25 < kanzure> ok, so it can be a git submodule in zotero/translators.git that references something else that assembles/caches/compiles/dumps the saner scrapers
16:25 < kanzure> each translator in zotero/translators.git can just be a thin wrapper that uses require("./sanestuff/whatever.js") and calls those functions
16:25 < dpk> yeah
16:28 < kanzure> and those would probably be browserify bundle outputs
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16:36 < kanzure> dpk: this was my streaming parser attempt https://github.com/kanzure/papermonk-downloader-plosone
16:37 < dpk> hmm, i didn't see that, only the main papermonk repo
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16:38 < kanzure> i think i have my pipes fucked up =)
16:38 < dpk> i am going to sleep now. i will investigate the Zotero/node thing tomorrow morning and hopefully have a solid plan by the time you show up in (my time) the afternoon
16:39 < kanzure> okie dokie
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16:44 < delinquentme> kanzure, where was it that you said had solid internet infrastructure, high quality research + cheap living?
16:44 < delinquentme> china right?
16:44 < delinquentme> ever thought about living there?
16:45 < kanzure> i'm not opposed to it, but i never put a lot of thought into it
16:46 < delinquentme> I really want to find applications at the junction of simple manufactured objects + programming + electronics and version control
16:52 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=9bd2883f Bryan Bishop: move diybio faq file >> http://diyhpl.us/diyhpluswiki/diybio/faq/software/
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17:27 < heath> delinquentme: ukraine?
17:28 < delinquentme> heath, Im guessing the political stuff doesnt help
17:28 < heath> far cheaper living and internet infrastructure than what i have
17:42 < kanzure> oh yeah, for larger objects you can just blast sound at them to separate them: http://www.elmat.lth.se/fileadmin/user_upload/Publications/04_Analyst_Petersson.pdf
17:44 < kanzure> ugh but did they have to call it "acoustophoresis"?
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17:55 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f1b63a7b Bryan Bishop: various microfluidic designs for diybio >> http://diyhpl.us/diyhpluswiki/diybio/microfluidics/
17:57 < kanzure> yashgaroth: http://diyhpl.us/wiki/diybio/microfluidics/
17:57 < kanzure> yashgaroth: what obvious and important equipment am i forgetting about?
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18:13 < yashgaroth> lemme eat dinner first
18:29 < yashgaroth> ok well I'm not sure what techniques can be used in microfluidics, but let's see...you surely will not be able to pack traditional chromatography resins microfluidically, but monoliths would mostly solve that
18:29 < yashgaroth> how big are the channels typically?
18:30 < kanzure> let's say we're aiming for between 10-100 microns (inclusive)
18:30 < kanzure> and the other dimension can be up to multiple millimeters or centimeters if really necessary
18:31 < yashgaroth> yeah you'd be fitting in traditional beads in single file with those dimensions
18:31 < kanzure> i think you can easily purchase microbeads 1-5 micron diameter
18:31 < seba-> lol
18:31 < kanzure> or make them
18:31 < kanzure> emulsions + curing or something
18:32 < kanzure> chromatography columns require high pressure that i'm not sure would be compatible with these chips. not sure.
18:32 < yashgaroth> ehhhh high pressure chromatography does, but it depends what you want to do
18:33 < yashgaroth> if it's just 'stick DNA to this under condition X and elute under condition Y', you don't need pressure
18:33 < kanzure> antibody purification would be nice
18:33 < gradstudentbot> I think my PI hates me.
18:33 < yashgaroth> purification of antibody, or by antibody?
18:33 < kanzure> of antibody
18:34 < yashgaroth> oh yeah you can do that; high pressure stuff is only for separating out things with a high resolution...purification you don't need pressure
18:35 < yashgaroth> stick recombinant Protein A to/in your channel somehow, run crude stuff over it, wash, knock it off with another buffer
18:35 < delinquentme> yashgaroth, do you have chromatography columns for sale OOC?
18:35 < kanzure> could probably get that protein stuck to microbeads/spheres if not the channel
18:35 < yashgaroth> I may, what you lookin' for bruv?
18:35 < delinquentme> Or have the capability to get heparin sepharose 4B at price reductions ?
18:36 < delinquentme> yashgaroth, a 16/20 GE column
18:36 < yashgaroth> heh I used to have a bunch of heparin sepharose
18:36 < yashgaroth> XK column?
18:36 < delinquentme> yeah. http://www.ebay.com/itm/Pharmacia-Biotech-XK-16-20-chromatography-Column-Excellent-GE-Amersham-/321410626909?pt=LH_DefaultDomain_0&hash=item4ad590f55d
18:36 < delinquentme> yashgaroth, !!!!!!
18:36 < delinquentme> damnit hahah
18:37 < delinquentme> I'd gladly pay you for some if its under market value :D
18:37 < yashgaroth> it won't be, buy it off ebay, that's a good price
18:37 < delinquentme> ah alright. thanks anyhoo
18:37 < yashgaroth> you think I can buy them from GE for less than that? because laffo
18:38 < kanzure> dingo: were you GE or GM?
18:39 < yashgaroth> delinquentme I'm not sure how fully you appreciate that biotech stuff is absurdly expensive
18:40 < delinquentme> yashgaroth, I'm getting hints of it.  The prices of the fibronectin I was gonna purify are obscene.
18:40 < yashgaroth> I thought you was purifying your own fibronectin out of corpses
18:41 < delinquentme> piggie blood
18:41 < yashgaroth> or whatever
18:41 < delinquentme> I was also looking for human femurs for other reasons though
18:41 < yashgaroth> yeah they're good to have around
18:41 < delinquentme> yeah. Could make for a decent bioreactor
18:42 < yashgaroth> well anyway you're gonna need more than a single heparin purification, lotta shit in blood binds heparin
18:42 < delinquentme> I was thinking decellularizing the vasculature and then using that piping system to distribute haematopoetic stem cells
18:42 < yashgaroth> uh huh
18:42 < delinquentme> yeah I've got the protocol ... just no paying clients
18:43 < yashgaroth> you want someone to pay you to dissolve their blood vessels?
18:43 < delinquentme> sorry nah, two separate projects. One was " people who would buy fibronectin "
18:44 < delinquentme> the other is " how to get osteoblasts / HSCs to maintain + product blood "
18:45 < yashgaroth> try high-pressure sales techniques, like stab them and then say 'would you like to buy my miracle wound healing powder?'
18:45 < yashgaroth> if they say no you can still take their money!
18:48 < yashgaroth> anyway kanzure there's also tangential flow filtration, which is awesome, but again adapting it to micro scale would be a challenge
18:48 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=4d334d80 Bryan Bishop: brief mention of tangential flow filtration >> http://diyhpl.us/diyhpluswiki/diybio/microfluidics/
18:48 < yashgaroth> assuming you want cells producing tiny amounts of antibody, you can keep them in a chamber, and then flow that with some back-pressure and push antibodies through the membrane while keeping the cells in one place
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18:49 < kanzure> oh, keeping the cells on-chip makes sense, i was also thinking of just loading up whatever liquid from some other process
18:49 < kanzure> on-chip cell culture makes more sense though
18:49 < yashgaroth> I assumed that's what you were going for, since you'd be making tiny amounts of antibody
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18:50 < yashgaroth> either way, tangential flow/ultrafiltration is the biggest thing to happen in purification since...well, a while
18:50 < kanzure> no idea if it would be tiny or not- add in some parallelism and suddenly you have large cultures producing antibodies
18:50 < yashgaroth> but then why microfluidicize it
18:51 < kanzure> the parts that need to be microsized are the parts that cost an annoying amount
18:51 < kanzure> for doing normal biology lab things
18:52 < kanzure> instead of paying $500 per pcr machine you could just print them out
18:52 < yashgaroth> PCR is an exception because you're regularly working with picograms
18:52 < kanzure> sonoporation can also work on a chip
18:52 < kanzure> separation stuff can work
18:53 < yashgaroth> well I'd focus mainly on DNA then
18:54 < yashgaroth> tangential flow is nice for that, you can separate decently-sized strands away from dNTPs, buffer salts etc
18:54 < seba-> why would a PCR machine cost $500
18:54 < seba-> lol
18:54 < dingo> kanzure: GM
18:54 < kanzure> seba-: yeah it's stupid isn't it? they actually go for $20k
18:54 < kanzure> dingo: damn
18:54 < seba-> kanzure, a PCR machine should be around $150
18:55 < seba-> if you make it at home
18:55 < kanzure> you can make one for <$10
18:55 < seba-> yeah
18:55 < seba-> with various baths
18:55 < seba-> lol
18:55 < kanzure> not even
18:55 < kanzure> the lightbulb method doesn't require multiple baths
18:55 < seba-> ok
18:55 < seba-> i meant $150 for a proper aluminium block/peltier
18:55 < kanzure> proper
18:56 < kanzure> there's all sorts of other equipment that is expensive in a lab that you could build on a flat surface instead
18:56 < seba-> like
18:56 < kanzure> http://diyhpl.us/wiki/diybio/microfluidics/
18:57 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/
18:58 < kanzure> oh i forgot cell sorting
18:58 < kanzure> that falls under separation though
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19:01 < kanzure> hrm, so the really interesting stuff only happens when you can do dna sequencing and synthesis
19:08 < kanzure> "Utau is known mostly as being a free clone of the much more popular and mature Vocaloid software"
19:09 < kanzure> for comparison,
19:09 < kanzure> vocaloid: http://www.youtube.com/watch?v=_JGaQ3g8WU4
19:09 < kanzure> utau: http://www.youtube.com/watch?v=nCqy27QrqZA
19:12 < gradstudentbot> I don't have enough data to form a hypothesis.
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19:20 < kanzure> i gave you *two* samples, isn't that enough
19:29 < seba-> http://phys.org/news95869196.html
19:29 < kanzure> .title
19:29 < yoleaux> Researchers Use Smallest Pipette to Reveal Freezing 'Dance' of Nanoscale Drops
19:29 < seba-> look how big it is
19:30 < kanzure> making tiny tips is hard
19:30 < kanzure> just ask the afm users
19:30 < kanzure> well, annoying, not really hard
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20:13 < nmz787> ok hi
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20:48 < gene_hacker> by doing interesting stuff with DNA synthesis and sequencing do you mean making an ultra-parallel computer for cracking crypto/mining bit coin?
20:49 < kanzure> gene_hacker: microelectronics would be better at mining bitcoin, http://diyhpl.us/wiki/homecmos/bitcoin/
20:50 < kanzure> dna synthesis is too slow for bitcoin mining
20:51 < gene_hacker> probably, but you can still use them to crack crypto
20:51 < kanzure> various SAT problems i guess, yeah
20:51 < gene_hacker> DNA computers are supposed to have some nice scaling laws two
20:53 < kanzure> reason i mentioned dna synthesis "to do anything interesting" is biology reasons
20:53 < kanzure> once you can do dna synthesis you can inject dna into cells and get whatever wacky proteins, antibodies, or whatever you please
20:55 < gene_hacker> but if you convince the bitcoin people that DNA synthesis and sequence is worth it...
20:56 < kanzure> i think we could convince them that asic/microelectronics fabrication is worth it
20:56 < kanzure> there's some math i need to figure out to prove that it's cost effective
20:56 < kanzure> compared to doing an asic batch run at MOSIS or some other wafer fab
20:57 < kanzure> microelectronics fabrication is practically the same method as microfluidics, if you are using contact lithography (which is fine for 1-100 micron features)
20:57 < kanzure> i mean, if you build a mask via photolithography, which you then use to stamp a wafer or w/e
20:57 < kanzure> (or you can possibly laser cut a wafer directly if you cared a lot..)
20:58 < gene_hacker> microelectronics fabrication is quite different than microfluidics fabrication
20:58 < gene_hacker> microfluidics tend to be a lot bigger than most things on a microchip
20:58 < kanzure> you don't need nanometer features for microelectronics
20:58 < kanzure> first few microchips were using 200 micron transistors
20:59 < kanzure> (1960s)
21:02 < kanzure> photomask chemistry might be different, but once you have something the right size (existing mask?) you have more options
21:02 < nmz787> gene_hacker: well there /are/ jumping genes, so i presume eventually we'll be able to edit DNA with DNA programmed stuff
21:02 < kanzure> "eventually" is "not in the next 5 years"
21:03 < gene_hacker> you don't need nanometer feature resolution, but it helps
21:03 < nmz787> gene_hacker: you need the DNA synthesis first though to optimize all the biological 'logic gate' precedent papers that are around
21:03 < nmz787> such that they work when linked into massive systems
21:03 < kanzure> if you have dna synthesis then you can just build proteins/antibodies which are going to be useful and valuable anyway
21:03 < nmz787> of which could be self-editing programs/logic-functions
21:03 < gene_hacker> well logic gates are one way to do it, but there are better ways of solving problems with DNA
21:04 < nmz787> well whatever, there's some operation you want to do that's probably recursive or something
21:05 < nmz787> so you need to verify the base function first, and that process is really slow right now
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21:06 < kanzure> you killed him
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21:08 < kanzure> fenn: summon
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21:32 < fenn> moooooo...
21:34 < kanzure> fenn: reasons not to use belts?
21:34 < kanzure> or am i full of shit
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21:35 < fenn> not for micron resolution; the belts arent precise enough
21:35 < fenn> maybe if you had a linear optical encoder (glass rule)
21:36 < kanzure> nmz787 is trying to convince me about cannibalizing an existing commodity microscope
21:36 < kanzure> instead of building our own stuff, stages, etc.
21:36 < fenn> that sounds easier than building everything
21:36 < kanzure> e.g., place gear on microscope knob, belt, stepper to control
21:36 < kanzure> well, i don't want this to be dumpster diving and repurposing
21:37 < fenn> are there no standard microscope designs?
21:37 < nmz787> fenn: how about a gear to gear from the coaxial stage knob on most any microscope to a geared stepper motor that is microstepping (just cause the microcontroller can) (28byj-48 stepper)
21:37 < kanzure> there's "openlabtools" that you were complaining about, http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/images/microscope.png
21:37 < kanzure> or maybe that was me that was complaining
21:37 < fenn> nmz787: i don't like gears for motion control.. introduces backlash for no good reason, and they're noisy
21:38 < kanzure> nah we can have it play hatsune miku songs when it's stepping
21:38 < nmz787> yeah, but what's a better way?
21:38 < nmz787> i was thinking a one-time calibration
21:38 < fenn> well since this is optical you might be fine with gears and a spring
21:38 < nmz787> go to bottom-left (home) then microstep all the way to the right, then go home, then microstepp all the way to the top.... slowly enough to get images of each microstep
21:39 < nmz787> and also maybe the backlash at each location
21:39 < kanzure> one of the hypothetical advantages of not using an existing microscope that i was contemplating is that you get to make whatever frame you need
21:39 < kanzure> with as much clearance as you want
21:39 < fenn> images of what?
21:39 < kanzure> (none of that weird curvy neck shit. i don't trust those scopes.)
21:39 < nmz787> then either try using that to calibrate, or use it to get good averages for correction factors
21:40 < nmz787> images of a laser printed grid reticle
21:40 < nmz787> laser printers can do something like 20 or 50 micron lines
21:40 < kanzure> so, how much would it cost to buy both the gears/belts and the threaded rod/washers/screws
21:40 < nmz787> seems more accesible than a shelf-bought grid
21:40 < fenn> uh, don't use a laser printer as your reference measurement
21:41 < kanzure> there's cheap slides that provide micrometer calibration for microscopes
21:41 < nmz787> i didn't find any that were the right size and design for cheap
21:42 < kanzure> http://www.amazon.com/AmScope-MR400-Micrometer-Calibration-Microscopes/dp/B005KVGAAS
21:42 < fenn> you could use a reject silicon wafer :P
21:42 < nmz787> its really annoying that I can't even tell if the ebay scopes have infinity objectives on them
21:42 < kanzure> it's based on tube length
21:42 < nmz787> silicon doesn't have a grid on it though
21:42 < kanzure> the 270mm tubes or something are the infinity corrected ones. and presumably the objectives say whether or not they are for that tube size.
21:43 < nmz787> i measured a lot of laser printed lines a while ago when i made a test lithography mask on transparency paper
21:43 < nmz787> film
21:43 < kanzure> erm, *those tubes are the ones that fit infinity corrected objectives
21:43 < nmz787> it was pretty decent
21:43 < fenn> a reject wafer would have a grid of chips on it
21:43 < kanzure> or you can get the $30 slide i just linked to
21:43 < nmz787> yeah but you don't know the dimensions
21:43 < fenn> the slide doesn't cover the whole range of motion
21:43 < fenn> (or does it?)
21:44 < kanzure> "1mm Total Length Subdivided into 100 Divisions, Each Division is 0.01mm Across"
21:44 < kanzure> "Just in case you can't fucking divide"
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21:44 < fenn> let me get out my atm machine card
21:45 < nmz787> No I guess not
21:45 < kanzure> http://www.pyser-sgi.com/graticules/stage-micrometers-calibration-scales-grids/stage-micrometers-grids-s-series/s28-stage-counting-grid-0-01mm-squares-detail
21:45 < gradstudentbot> If I write this paper, then maybe I can use that as my thesis?
21:45 < kanzure> "0.01mm grid / 0.2 x 0.2mm overall"
21:46 < kanzure> hrm
21:46 < nmz787> with 1 to 10 micron features that is still a lot of space
21:46 < kanzure> huh, what about this one?
21:46 < kanzure> http://www.pyser-sgi.com/graticules/stage-micrometers-calibration-scales-grids/stage-micrometers-grids-s-series/s7-england-finder-slide-detail
21:46 < gradstudentbot> I'll need to pull an all-nighter.
21:46 < nmz787> problem might be with breaking out the lines to microtubes
21:46 -!- rayston [~rayston@ip68-106-242-42.ph.ph.cox.net] has quit [Ping timeout: 260 seconds]
21:47 < nmz787> but then again, you could go into open-loop in those regions
21:47 < fenn> is this some magic eye thing
21:47 < kanzure> no i think they just wrote a bunch of numbers in each cell because ??
21:47 < kanzure> it's curious that most micrometer slides are only for a small mm^2 region
21:48 < fenn> numbers would make a lot more sense
21:48 < fenn> they probably just expose photographic emulsion directly on the slide through a microscope
21:48 < kanzure> "if you can't see all the detail at once, there's no point"
21:48 < kanzure> yeah, but you could just move the slide and expose again
21:48 < fenn> but then you have to ensure that each sub-grid is precisely aligned
21:49 < fenn> before you know it you are back at the micron laser plotter
21:49 < kanzure> i shouldn't pussy out by buying both sets of actuators (gears/belts and screws)
21:49 < nmz787> that's called a stepper
21:49 < nmz787> a wafer stepper
21:49 < kanzure> yes i know what a stepper is
21:49 < kanzure> wtf
21:49 < fenn> silicon chips don't have to be precisely aligned to each other
21:50 < fenn> making precise things is easy; making accurate things is easy; making precise and accurate things is hard
21:50 < nmz787> they still use interferometers on the axes
21:50 < nmz787> kanzure: want to start off the night by buying both of those?
21:51 < nmz787> the latter seems like it would be computationally more work
21:51 < fenn> gears belts and screws is three things
21:51 < nmz787> to track
21:51 < kanzure> no prices on the page
21:51 < nmz787> yeah
21:51 < kanzure> so no
21:51 < kanzure> i think we should separate the project into two parts:
21:52 < kanzure> (1) the machine we want to build
21:52 < kanzure> (2) laser diode, lcd projector, dmd projector lithography things through whatever microscopes you already have
21:52 < nmz787> I think that openlabstools had a FOV calculator
21:53 < nmz787> there's also all the software though too
21:53 < nmz787> soft/firm
21:53 < kanzure> #2 would probably mean "buy some photoresist" and maybe a way to mount something
21:53 < nmz787> #2 still needs a reticle
21:54 < kanzure> the full-slide grid? or partial-slide grid
21:54 < kanzure> that amazon one looked ok for basic calibration
21:55 < nmz787> the amazon one would prove the concept i think, and maybe draw others into that part of the project
21:55 < kanzure> what others
21:56 < kanzure> fenn: what material did you think the frame should be made out of?
21:56 < gradstudentbot> Can I take a nap yet?
21:56 < nmz787> "Casio EX-ZR100"
21:56 < nmz787> up to 1000FPS
21:56 < nmz787> but most likely not over USB
21:56 < fenn> the same material as everything else, but preferably cast iron
21:57 < fenn> that's the benefit of using a premade microscope
21:58 < fenn> vibration may not matter in practice though, i have no idea
21:58 < kanzure> nmz787: er, why? amazon does not list this as a linux-compatible camera, so they probably don't think it's important, and they probably didn't check streaming capability
21:58 < kanzure> and it has an lcd hah
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21:59 < nmz787> oh cool
21:59 < nmz787> http://www.raspberrypi.org/new-camera-mode-released/
21:59 < nmz787> 90 FPS
21:59 < fenn> the casio is not a webcam and definitely doesn't stream at 1000fps
21:59 < fenn> it is a neat toy tho
21:59 < kanzure> the openlabtools microscope's frame just seems much easier to work with than a curvy-neck microscope,
21:59 < kanzure> http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/images/microscope.png
21:59 < kanzure> look at all that free space to put crap
22:00 < gradstudentbot> Anyone else think pol II looks like a butt?
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22:01 < fenn> those rod ways are a joke
22:01 < fenn> why build a t-slot frame and then suspend two toothpicks from pieces of plastic
22:02 < kanzure> they had "10 people working on this for 10 weeks"
22:02 < fenn> seriously what is it with people and t-slot cubes
22:02 < kanzure> so i am gonna go ahead and assume they are brain damaged
22:02 < fenn> i hope it works better than a bent paperclip and a drop of water
22:03 < kanzure> t-slot structure has got to be better than attaching to http://www.coslabindia.com/HL-55.jpg
22:04 < fenn> does it have X or Y axis drive? or only motorized Z?
22:04 < nmz787> all axes
22:04 < gradstudentbot> I lost my pipette.
22:04 < nmz787> all 3
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22:06 < nmz787> fenn: so what material then?
22:07 < fenn> if you want to throw huge gobs of cash you could use epoxy granite concrete and linear ways
22:07 < fenn> i'm not sure why they use "crossed roller" ways in optical stuff
22:08 < nmz787> i think the idea is to keep costs practical, i think unde $1k
22:08 < kanzure> over $1k is okay
22:08 < fenn> is that just a way of saying "dovetail slides, but with rollers"?
22:08 < nmz787> fenn: that is your question to answer
22:09 < nmz787> my CAD PIPE is redirected to fenn
22:09 < fenn> my optics experience consists of burning ants with a magnifying glass
22:09 < kanzure> perfect
22:09 < nmz787> i've been trying to learn for a while
22:09 < kanzure> nmz787: do these guys have any good pics of their microscopy in action?
22:09 < fenn> so i was thinking a solar sand sinterer would be cool
22:09 < nmz787> i have all the optical parts for the openlabtools scope i believe
22:09 < nmz787> there was 1 or 2 pics
22:09 < fenn> one with better optics than that projection screen tv fresnel lens
22:09 < kanzure> because the bug on this page sucks http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/Optics/
22:09 < kanzure> this is just a fucking awful pic to advertize your microscope
22:09 < nmz787> showing chromatic aberration i believe
22:10 < nmz787> either from lack of oil, or from using the wrong tube lens
22:10 < nmz787> i think/hope it was chromatic
22:10 < fenn> a dobsonian telescope would probably work for fine sintering
22:10 < kanzure> and i hate how nobody does calibration or takes measurements
22:10 < nmz787> as using laser is monochromatic so wont mess up like that
22:10 < kanzure> well that's fine, but that bug is way bigger than 1 micron
22:10 < kanzure> or 10 microns
22:11 < kanzure> or 100...
22:11 < fenn> is there supposed to be a video or something?
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22:11 < nmz787> i dont think so
22:12 < kanzure> http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/media/OLT_Microscope.mp4
22:12 < fenn> nevermind, i dunno why it didnt render at all in dillo
22:13 < nmz787> https://groups.yahoo.com/neo/groups/Microscope/conversations/topics/33567
22:13 < kanzure> .title
22:13 < yoleaux> Yahoo Groups
22:13 < kanzure> fuck you yahoo groups
22:14 < fenn> can't they fix chromatic aberration by using an RGB LED and taking separate pictures?
22:14 < fenn> or is that too high tech
22:14 < gradstudentbot> Yeah, but his PI wrote his dissertation.
22:15 < fenn> am i a genius or is everyone just a moron
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22:15 < kanzure> neither, you are simply stuck in the seventh circle of super hell
22:16 < kanzure> copy of their video (their server was downloading too slow for me..) http://diyhpl.us/~bryan/irc/openlabtools-microscope/OLT_Microscope.mp4
22:16 < nmz787> it wouldn't work well for living subjects
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22:16 < fenn> oh well, you would either get motion blur from 1/30 framerate or 1/90 framerate
22:16 < fenn> assuming your stepper can refocus fast enough
22:17 < kanzure> were you holding off on the stepper mount plates because we didn't know which stepper?
22:17 < nmz787> unless you synched and stopped just before the exposure
22:18 < kanzure> this video is way too big for what it is showing
22:18 < fenn> http://www.designworldonline.com/When-to-Choose-Crossed-Roller-Bearings/
22:19 < fenn> ugh it's not streamable?
22:20 < fenn> "Cage creep can be prevented by studs that roll into the raceways depressions.
22:20 < nmz787> fenn, actually their video says 8-bit RGB LED
22:20 < nmz787> so they simply failed to get HDR images
22:20 < fenn> <insert sarcastic WWF methamphetamine reference here>
22:20 < nmz787> or HD-focus
22:21 < fenn> Z-stacking is pretty common in macro photography; i figured it was also standard practice in computer-controlled microscopy
22:21 < nmz787> fenn: is 3d-printed bad for material?
22:21 < fenn> yes
22:21 < fenn> but the rod ways are particularly bad
22:21 < nmz787> fenn: i think you understimate CNC-scopy
22:21 < nmz787> wait
22:21 < nmz787> overestimate
22:21 < fenn> superestimate
22:21 < kanzure> actually-estimate
22:21 < nmz787> ultraestimate
22:22 < kanzure> i don't think these guys were getting microscopic resolution
22:22 < fenn> yeah they should have taken photos of a CD or something
22:22 < kanzure> and besides, if they were really serious, they would submerge the whole machine in oil to prove their determination
22:22 < fenn> not "this hairy bug i pulled out of my butt-crack"
22:23 < nmz787> that 80/20 t-slot seems pricey
22:23 < fenn> that is openmakerbeamslot
22:23 < kanzure> *beamslut
22:23 < fenn> sirbeamsalot
22:23 < kanzure> ah without the slut shaming. nice.
22:24 < nmz787> decaocular microscope with interleave raspberry pi cameras each at 90FPS
22:24 < nmz787> ULTRA
22:24 < nmz787> DECA
22:24 < nmz787> LAURYL
22:24 < kanzure> are you okay?
22:24 < fenn> sulfonuramidoscope?
22:24 < nmz787> oh, wait DOCECYL
22:24 < nmz787> DODECYL
22:24 < nmz787> **
22:25 < nmz787> fenn: please make some recommendations before the night is through, or at least some things that might be the right direction if you aren't interested enough to spend more time on this
22:26 < nmz787> we need you fenn!
22:26 < nmz787> (or at least I think we do)
22:26 < fenn> buy a microscope with a vertical camera port
22:26 < fenn> add a beam splitter for whatever extra crap you want to add
22:27 < fenn> i know you lose power but i doubt laser power is the limiting factor
22:27 < nmz787> for the custom job, would 3D printing be useful for design/prototyping stage?
22:28 < nmz787> what about for lense holders?
22:28 < nmz787> even for them just prototyping
22:28 < fenn> you can just buy this stuff
22:28 < nmz787> are CNC mills as easy to get parts out of as a 3D printer?
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22:28 < nmz787> is the design strategy different, or just the CAM file?
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22:28 < kanzure> you give the machine shop your cad file, never a cam file
22:28 < nmz787> CAM compiler
22:29 < fenn> no, and yes, and no
22:29 < fenn> cnc is a lot harder to think about than 3d printing
22:29 < fenn> that's kinda the point
22:29 < fenn> if it were easy we wouldn't need 3d printers
22:29 < gradstudentbot> I don't remember the paper, but someone definitely did that.
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22:31 < fenn> huh that crossed roller way is pretty neat
22:32 < fenn> it's just a 90 degree v-groove
22:32 < fenn> someone should do a t-slot thing like that
22:33 < kanzure> it would be nice to do the machine shop run al lat once
22:33 < kanzure> *all at once
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22:34 < fenn> i'm not sure what you are planning on machining; all this is pretty standard microscope stuff, no?
22:34 < kanzure> i am very confused about priorities
22:34 < fenn> you need: a camera mount, a laser mount, a motorized stage
22:34 < kanzure> the xy stage needs to be mounted to something
22:34 < kanzure> and the z has to be mounted somewhere
22:34 < nmz787> and a microscope in between
22:35 < fenn> the laser has independent focus mechanism, so why do you need a Z
22:35 < kanzure> microscope tube and objective can be mounted on the z
22:35 < nmz787> with adjustments everywhere for focus and if its our build I'd think tilt
22:35 < nmz787> or that would all need to be precisely machined stuff so the angles were right
22:35 < kanzure> oops, stage would have z
22:35 < kanzure> you want z for the normal reasons you have z on a microscope
22:36 < kanzure> i don't see why it would be different just because you have a laser in use for less than 100% of the time?
22:36 < nmz787> well there are two laser routes, one is beam splitter in the microscope (laser down the ocular of a bino scope)
22:36 < nmz787> and a bluray module mounted next to the objective
22:36 < nmz787> two different tests
22:36 < kanzure> huh?
22:37 < nmz787> adjustable focus laser mated to a binocular scope's right-eye ocular... camera on the other ocular
22:37 < kanzure> blah oculars..
22:38 < kanzure> is that really necessary
22:38 < nmz787> well we could call that area something else
22:38 < nmz787> the tube lens i suppose
22:38 < nmz787> lenses
22:38 < kanzure> like why do we have to have pieces that are fitted for human eyes- who cares
22:38 < nmz787> that was just my labelling from the cannibalizing idea
22:39 < nmz787> don't you care about robot eyes (cameras and lasers)
22:39 < kanzure> these just seem annoying: http://www.microscope.com/media/catalog/product/cache/2/image/9df78eab33525d08d6e5fb8d27136e95/m/e/meiji_mt6000_fluorescence_microscope_eyepieces.png
22:40 < fenn> you can pull them out of the tube they sit in
22:40 < fenn> then it's just like a camera port
22:40 < kanzure> ah
22:40 < fenn> the ocular lenses usually help in mounting a webcam though because webcams have similar focal length and focusing range as human eyes
22:41 < fenn> or so i hear
22:41 < fenn> you also should be able to pop off the rubber thingies
22:41 < kanzure> good
22:41 < nmz787> yeah, maybe a set screw
22:41 < kanzure> why are there only two?
22:41 < kanzure> why not 8
22:41 < fenn> because we're humans, not spiders
22:42  * nmz787 nods
22:42 < kanzure> ugh
22:42 < nmz787> shew spider!
22:42 < fenn> if you want to shoot lasers or use a camera, you're expected to use a microscope with a camera port
22:42 < kanzure> yeah but i think we need more than just a trinocular microscope
22:42 < fenn> but those tend to cost a lot more for reasons that are beyond my comprehension
22:43 < kanzure> "because nobody knows how to insert a prism"
22:43 < fenn> they tend to be much bigger and have more stuff
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22:44 < kanzure> "elbow" http://www.truetex.com/zeiss_opmi_elbow_3.jpg
22:44 < kanzure> http://www.truetex.com/zeiss_opmi_elbow_2.jpg
22:44 < fenn> that is not what i mean
22:45 < kanzure> i know
22:45 < fenn> i'm talking about  https://en.wikipedia.org/wiki/File:Microscope_And_Digital_Camera.JPG
22:45 < kanzure> .title http://www.truetex.com/micad.htm
22:45 < yoleaux> Making Digital Camera Microscope Adapters
22:46 < nmz787> tri would only be needed for ....
22:46 < nmz787> idk, if the computer was broken?
22:46 < nmz787> we wanted another color laser
22:46 < fenn> a penny would have been a good test of the british microscope
22:46 < nmz787> a spectrometer port
22:46 < fenn> oh but it's transmission, nevermind
22:47 < gradstudentbot> I was searching for a new particle that alters gene expression, didn't find it, but didn't refute it's existence either. But then some other asshole professor at another school found it.
22:47 < fenn> most of that truetex stuff is for mounting the camera to anything else
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22:49 < fenn> honestly a lot of it can be done with a piece of pvc pipe
22:49 < kanzure> that page has a bunch of content
22:49 < fenn> but "optics!" and "high quality!"
22:49 < kanzure> pvc pipe sounds good to me
22:49 < fenn> yeah i've read it before
22:50 < kanzure> lolwtf "Adapters incorporating optical elements are more complex and typically cost $500 to $950, including the optical elements. Complete kits for medical and scientific instruments, with custom mechanical, optical, and electronic components, range from $800 to $6000."
22:51 < fenn> are you going to believe the guy who makes his living selling adapters
22:51 < kanzure> i am sure that's what he sells them for...
22:51 < kanzure> what a booming market
22:52 < kanzure> literally dozens of microscopes aorund the globe
22:52 < fenn> you fail at sarcasm
22:52 < kanzure> hm? of course i'm not going to believe him
22:52 < kanzure> but also his market sucks
22:52 < fenn> not everyone can make the next snapchat
22:53 < kanzure> that doesn't mean you should support the microscope monopolists
22:53 < kanzure> isn't it just zeiss, olympus, nikon that are making "the good ones"?
22:53 < kanzure> everything else does not seem to be micro
22:54 < fenn>  I modify the the Microsoft Lifecam Cinema (720p HD) and Microsoft Lifecam Studio (1080p HD) cameras for scientific and medical instrumentation. The Lifecams are USB cameras with amazing high-definition video performance, especially considering their street price of about $50 to $100. They also have the rare virtue among webcams of being housed in a cylindrical metal shell, so they can be easily
22:54 < fenn> fitted into the cylindrical geometry typical of optical instrumentation, in many cases with no modifications, using a relatively simple mechanical adapter.
22:54 < nmz787> I think someone asked for this a while ago, maybe gene_hacker http://diyhpl.us/~nmz787/pdf/Efficient_Assembly_of_Threaded_Molecular_Machines_for_Sequence-Specific_Synthesis.pdf
22:54 < gene_hacker> oh no, I was posting that
22:55 < kanzure> fenn, wouldn't it be better to just skip all the weirdo tubes, adapters, etc. completely, and just use your own pvc pipe stuff..
22:55 < fenn> i'd rather start with a cylindrical camera at least
22:58 < fenn> "Just tested the Microsoft Lifecam Studio; it works out of the box on
22:58 < fenn> Ubuntu 10.10 (both video and microphone worked perfectly). I tested
22:58 < fenn> using cheese, camorama and skype."
22:58 < nmz787> I haven't had time to sit and read this one http://diyhpl.us/~bryan/papers2/paperbot/Reproductive%20ectogenesis%3A%20The%20third%20era%20of%20human%20reproduction%20and%20some%20moral%20consequences.pdf
22:59 < fenn> "One thing I did notice is that when I run v4l2ucp, the "Exposure,Auto"
22:59 < fenn> setting has four modes (Auto, Manual, Shutter Priority and Aperture
22:59 < fenn> Priority) but only Manual and Aperture Priority work (the other two
22:59 < fenn> result in a dialog saying "Unable to set Exposure,Auto; input/output
22:59 < fenn> error"."
22:59 < kanzure> http://www.amazon.com/Microsoft-LifeCam-Studio-1080p-Webcam/dp/B0042X8NT6
22:59 < fenn> manual exposure is what you want anyway
22:59 < nmz787> raspberry pi cam should work
22:59 < nmz787> i feel like i saw someone using the GPU for opencv stuff too
22:59 < kanzure> CAM?
23:00 < kanzure> the point was that this camera is already fitted to the right ports
23:00 < nmz787> maybe I am wrong about using GPU accell, maybe it was just for grabbing the video/images
23:00 < nmz787> that binary blob
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23:00 < kanzure> hm, maybe the concept of having multiple people working on design is stupid
23:00 < kanzure> it is clear that there is no ability to get coherent
23:01 < kanzure> and then you end up with stupid shit
23:01 < fenn> burbledeeburbledeebahbahblooo
23:01 < kanzure> like openlabtools' stuff
23:01 < fenn> haven't you heard of "design by committee"
23:01 < kanzure> it's not a committee if... well. uh.
23:01 < nmz787> i think there aren't enough ppl on this 'team'
23:01 < kanzure> is it?
23:01 < fenn> it's the latest executive mangement craze, patterned after the "waterfall pattern" pattern
23:01 < kanzure> hahaha yeah add more people, that'll help
23:01 < kanzure> (it wont)
23:02 < nmz787> i am serious
23:02 < nmz787> there isn't enough discussion
23:02 < nmz787> not enought input
23:02 < nmz787> not enough direction
23:02 < nmz787> (you cried for it earlier)
23:02 < kanzure> i have no idea what i could say to convince you otherwise
23:02 < nmz787> get some more ppl who know CAD, know CNC, know optics
23:03 < kanzure> all three of us know cad
23:03 < kanzure> i don't think anyone knows optics
23:03 < nmz787> what CAD tool should be used?
23:03 < kanzure> brlcad
23:03 < kanzure> python-brlcad if possible, but not necessary
23:03 -!- Burninate [~Burn@pool-173-66-15-196.washdc.fios.verizon.net] has quit [Ping timeout: 276 seconds]
23:03 < kanzure> openscad is not end of world
23:03 < kanzure> but sorta is
23:03 < fenn> brl-cad does ray tracing but does it know about chromatic aberration?
23:04 < kanzure> i asked brlcad about that and he said - uh
23:04 < kanzure> well
23:04 < fenn> "try it and find out!"
23:04 < kanzure> 10:10 < brlcad> kanzure: it won't do some optical effects like spectrum diffraction (prism effects)
23:04 < fenn> ok
23:05 < kanzure> 10:13 < brlcad> ray tracing theory doesn't generally including wave effects like diffraction and interference
23:05 < kanzure> 10:13 < brlcad> our multispectral library might have that capability, but I honestly haven't looked at it in many years
23:05 < kanzure> 10:13 < brlcad> our multispectral library does track packets of spectrum as they propagate, but I don't know to what extent
23:05 < fenn> so you can actually ray trace a hyperspectral image?
23:05 < kanzure> 10:16 < brlcad> fwiw, I don't believe povray does diffraction either
23:06 < kanzure> 10:22 < brlcad> mildly relevant: http://brlcad.org/gallery/renderings/lightbulb/lightbulb
23:06 < kanzure> 10:23 < brlcad> had a rendering of a gci-modeled fresnel lens that was modeled in brl-cad, but I can't find the optical rendering
23:06 < kanzure> 10:23 < brlcad> kanzure: we also have http://brlcad.org/xref/source/src/proc-db/lens.c which might be interesting
23:06 < kanzure> 10:24 < brlcad> (it's one of brl-cad's dev tools, creates lens geometry)
23:06 < fenn> well i remember seeing the magnified LED in the ronja animation
23:07 < fenn> so the newtonian optics seems to work well enough
23:07 < nmz787> wouldn't the chromatic effect just be a LUT of color vs refractive index?
23:07 < kanzure> jblake recommends pbrt (physics-based ray tracer)
23:08 < fenn> that light bulb has some weird triangular artifacts
23:10 < kanzure> well, at minimum, lens.c looks interesting
23:10 < kanzure> even if not using their ray tracer
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23:13 < fenn> huh so OLT microscope is top-lit (not transmission)
23:13 < fenn> also they have no condenser lens
23:14 < fenn> i wonder if anyone who designed that had ever actually used a microscope before
23:14 < fenn> i also don't see any X or Y actuation
23:16 < nmz787> fenn: for laser/DMD litho stuff we wouldn't need a condenser
23:16 < kanzure> fenn: i would prefer not to do a committee
23:16 < kanzure> let's go with a benevolent dictator model
23:16 < kanzure> malevolent dictator also okay
23:18 < fenn> sample lifecam studio output http://fennetic.net/irc/cam1080a.mp4 http://fennetic.net/irc/cam1080b.mp4 from com/shop/usb-microscope-1080p-for-smt-soldering/51-lifecam-studio-1080p-microscope-lens-mod-kit
23:18 < fenn> gah
23:19 < fenn> http://www.diyinhk.com/shop/usb-microscope-1080p-for-smt-soldering/51-lifecam-studio-1080p-microscope-lens-mod-kit.html
23:19 < nmz787> the benefits of higher framerate for the raspicam are quite a lot i think
23:20 < fenn> too bad the lifecam is rolling shutter, why is everything rolling shutter
23:20 < fenn> nmz787: yeah probably.. i am also just kind of interested in good small hackable webcams
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23:23 < nmz787> yeah
23:23 < nmz787> the raspi+cam was $40 when i got it
23:23 < nmz787> it seemed pretty bad for low-light use, but I never even took the film off the lens so idk how well it was focused/aligned
23:23 < fenn> is it rolling shutter? (wobbly jello effect when shaking)
23:23 < nmz787> but I imagine enough to do grid reticle stuff
23:24 < nmz787> yeah I think so
23:24 < nmz787> pulsed light can get around that
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23:37 < kanzure> in fact, i think the number of designers should be reduced
23:40 < nmz787> the night is almost over and we didn't spree at all
23:40  * night nods
23:40 < fenn> back to my whale watching then
23:40 < kanzure> huh?
23:41 < kanzure> because the design kept changing
23:41 < kanzure> suddenly there are belts
23:41 < kanzure> this is why i am suggesting the number of designers be reduced
23:41 < kanzure> fenn: could you just scribble the rest of it out
23:42 < fenn> i still dont even know what you're building tbh
23:43 < fenn> a laser plotter with micron resolution?
23:43 < kanzure> what is a "plotter"
23:43 < fenn> draws lines
23:43 < kanzure> so, there are a number of techniques for microfabrication that seem to all use the same hardware (other than the write method itself)
23:43 < fenn> exposes film with light
23:43 < nmz787> you are the only one to mention belts, sir
23:43 < kanzure> you wanted a gear, what are you putting on the gear
23:44 < fenn> you could direct drive the fine focus knob
23:44 < nmz787> nothing goes on a gear
23:44 < nmz787> it meshes with adjacent gears
23:44 < kanzure> and what do those adjacent gears mesh to -_-
23:44 < nmz787> the XY knobs are coaxial kno
23:44 < kanzure> fenn: yes, light of various types: LEDs, laser, LCD projector, DMD projector
23:44 < nmz787> tho
23:45 < fenn> ok it would seem to be prudent to just use a microscope then, and develop each of these things as a microscope attachment
23:45 < kanzure> also with a camera port
23:45 < nmz787> they don't mesh to anything else, one gear on the X shaft, on on the Y shaft... one on each of the two stepper motor shafts
23:46 < fenn> unless there is some reason to use all N of them at once
23:46 < nmz787> find some glue or metal or 3d printed thing, sticks, chewing gum... to mount them so they mesh
23:46 < nmz787> a motor to an axis-gear
23:46 < kanzure> fenn: camera should be always-on
23:47 < kanzure> fenn: as far as i can tell, the light sources will never be used at the same time, and probably could be switched out if the designer is clever enough with mounts
23:48 < kanzure> where's the spec sheet for which optical mount connectors you need
23:49 < kanzure> for interfacing with the existing microscopes?
23:49 < fenn> michael broxton would know all of this stuff
23:49 < kanzure> and i don't understand why the design is different now
23:49 < kanzure> last time we looked at the laser cutter, it was not in a commodity microscope
23:49 < kanzure> but now it is?
23:50 < fenn> because before you wanted a huge slide with over 9,000 meters of continuous channel
23:50 < kanzure> wasn't it only a few cm?
23:51 < fenn> the specifications were lacking then too
23:51 < fenn> s/slide/microfluidics sandwich/
23:51 < kanzure> what do you think a microfluidics sandwich is?
23:51 < nmz787> delicious
23:51 < fenn> the word "slide" is overloaded in this context
23:52 < kanzure> all of the microscope projector lithography things are using "slides"
23:52 < nmz787> https://www.youtube.com/watch?v=C7HaQucL9pg
23:52 < kanzure> spin coated with photoresist
23:52 -!- petrushka [~asakharov@24.60.79.55] has quit [Quit: quit]
23:52 < fenn> i believe nmz787 was pushing for that form factor last(?) year and you wanted something bigger
23:53 < fenn> has anyone seen katsmeow around?
23:53 < kanzure> she appeared once last year
23:54 < nmz787> i would still love a better than backlash-filled design, but i think we need to get an iteration done with something that is at least accessible
23:54 < kanzure> what the fuck does "accessible" mean
23:54 < fenn> ability to test theories against experiment
23:55 < nmz787> UPS can deliver it anywhere in the world in 5 to 14 days
23:55 < nmz787> microscopes and those $3 steppers and gears are accessible
23:55 < kanzure> okay, so what are the new design parameters?
23:55 < nmz787> cheap is accessible
23:56 < nmz787> if we do it and it turns out to do 1 micron lines but they're all jerky then we can try a $200 or $400 stage or whatever fenn's thing will cost
23:56 < nmz787> with the super awesome slides and bearings
23:56 < nmz787> if the thing gives us 100 micron lines we know
23:56 < nmz787> maybe it will give 10 micron lines
23:56 < nmz787> or 20 and be OK with respect to squiglyness
23:56 < kanzure> that sounds a lot like "engineering by not being sure about anything"..
23:57 < nmz787> we don't know, so lets start with something that some other hacker dudes can easily replicate and augment/respin
23:57 < nmz787> lets get /some/ data point
23:57 < fenn> yes we should be trying to at least design within an order of magnitude
23:57 < kanzure> or, how about we fucking know things
23:57 < nmz787> or we're just mentally masturbating
23:57 < kanzure> knowing things is not masturbating...
23:57 < nmz787> knowing them and talking about dong them someday is
23:57 < nmz787> i want someday to be yesterday
23:57 < kanzure> you can't just buy random pixie dust and things magically work
23:58 < kanzure> i am so confused
23:58 < nmz787> and either move on to another project, or come back to it later with a fresh mindset, and in the mean time let it be there for inspiration to others
23:58 < kanzure> so you are opposed to estimation for engineering design, or am i strawmanning you?
23:59 < fenn> i think he is just designing by what's available rather than starting with detailed specs and trying to find the perfect thing
23:59 < nmz787> .dic strawmanning
23:59 < kanzure> fenn: where "perfect" is "within an order of magnitude" ?
23:59 < nmz787> .ud strawmanning
23:59 < fenn> strawmanning = putting words in someone's mouth
23:59 < nmz787> .wik strawmanning
23:59 < yoleaux> "A straw man, also known in the UK as an Aunt Sally, is a common type of argument and is an informal fallacy based on the misrepresentation of the original topic of argument. To be successful, a straw man argument requires that the audience be ignorant or uninformed of the original argument." — http://en.wikipedia.org/wiki/Straw_man
--- Log closed Wed Jun 11 00:00:14 2014