2010-07-07.log

--- Log opened Wed Jul 07 00:00:17 2010
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bdeskkanzure: i think there are between 0 and 1000s of sequenced genomes, depending on what you call sequenced.  http://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes  http://www.genome.gov/1000215402:42
bdeskit is possible to do interesting genetics research without sequencing a genome.02:42
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Brunshai03:25
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Brunshttp://000chan.org/b/src/12781781357.gif04:10
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kanzurevia nicholas roberts: http://permaculture.tv/pathways-to-sustainable-self-governance-democratic-open-source-food-and-manufacturing-networks/07:31
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kanzure"Have you ever compiled git from source? See the number of dependencies? It can't have a Windows client without puting a shitload of mingw32 dlls in the PATH. And since gcc can't behave itself when on Windows there are no manifest files anywhere and you can broke other applications compiled with a different version of mingw32. Install QtCreator and later install TortoiseGit to replicate this."07:39
ENKI-][that's kind of funny07:40
ENKI-][i compile git from source all the time07:40
kanzure"As of January 2009 there has only been one human feeding study conducted on the effects of genetically modified foods" wut?07:43
kanzureENKI-][: on windows?07:43
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JayDuggerGood morning, everyone.07:53
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ENKI-][kanzure: i don't compile anything on windows. i can't afford it07:57
JayDuggerGood night, everyone.08:20
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kanzurehttp://charlespax.com/2010/04/27/motorized-conveyor-belt-sneak-peek/08:32
kanzure"Help DIYgenomics crowd-source clinical trials" guh?08:33
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bdeskkanzure: what is wrong with that?08:56
kanzurebdesk: the diygenomics quote? nothing08:57
kanzurejust news to me :)08:57
kanzurealso i make lots of weird sounds (guh, buh, meh, bleh, blah, eh, aroo, ..)08:57
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bdeskwhat exactly is a crowd sourced clinical trial?09:06
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kanzuregood question. uh..09:06
bdeskdo not all clinical trials use crowds?09:06
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kanzurewell, a quick google shows that some of it just means "using the web to get participants for the clinical trial"09:06
kanzure(recruitment)09:07
bdeskwhat do they usually use?09:08
bdeskjunk mail?  random telephone calls?09:08
kanzurehm. http://openthoughtspace.pbworks.com/Personal-Genome-Analysis 09:09
AJollyLifebdesk: subway ads09:09
kanzurebdesk: dunno, that's a good question09:09
AJollyLifeused to see them all the time when i was living in chicago09:09
kanzureas far as i know, clinical trials most often acquire participants who are in need of some cash09:09
AJollyLifenever got a single phone call or mailing, but i saw the ads all the time riding public transportation09:09
kanzureusually via flyers on the street09:09
kanzureyes09:09
kanzurealso, on occassion there are ads on cable television for the we-really-need-something-obscure like a particular type of schizophrenia patient09:10
bdeskso the people in clinical trials ride public transportation and watch non-prime-time cable television.09:12
ENKI-][this is a terrible audience.09:13
kanzurebdesk: http://www.socialwish.com/wish/4-diygenomics-crowd-sourced-clinical-trials09:13
ENKI-][you would get a more representative sample posting clinical trial ads on /b/09:13
kanzureso, melanie is asking for $72.75 to fund one person's "clinical trial" for diygenomics?09:14
kanzureapparently diygenomics is a "startup"?09:14
kanzure"More information about Thermotyp, our Open Source PCR Machine09:15
kanzurehttp://otyp.es/videos "09:15
kanzurehttp://vimeo.com/12330301 "What makes traditional themal cyclers so expensive (and what is Otyp doing differently)?"09:16
kanzure" James from Otyp gives a little more detail about what makes conventional PCR machines (thermal cyclers) so expensive, and how using open technologies, and mass produced parts designed to be used with traditional computers, Otyp is going to be making Thermotyp, an open source PCR machine. "09:16
kanzurethis is from the same group doing the "hello world" synthetic biology thing on kickstarter (it hasn't been getting any money, though)09:16
kanzurehttp://otyp.es/09:16
kanzurehttp://kck.st/8YAkI309:17
kanzurethermotyp block v004 http://thingiverse.com/thing:324009:18
kanzure" The most recent edition of Otyp's open source PCR machine block, Thermotyp. Follow the development of Thermotyp through kickstarter or on otyp.es  "09:18
kanzurelooks like it's just a tube holder.. but at least they have some files released09:19
kanzure" Block2 v004.igs "09:19
kanzureholy fuck! an IGES file!09:19
kanzurethis guy just became my best friend09:19
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kanzurehm.. genome_Andrew_Hessel_Full_20100702181249.txt.zip10:08
fennyou made a test tube holder at one point, forget why.. http://www.thingiverse.com/thing:231110:08
kanzureyou?10:09
fennshould be redone in openscad i think10:09
kanzurei had this terrible idea about an hour ago10:10
fennfrom the otyp.es guy10:10
fenni don't make anything anymore :(10:10
* fenn pushes some bits around10:10
kanzurethe idea was to make an in-browser openscad-like javascript thingy with raphaeljs10:10
fennyarr, get in there, bits!10:11
kanzurehttp://raphaeljs.com/scape/ it seems capable10:11
kanzurethe rendering would be with svg10:11
fennwhy not opengl?10:11
kanzurea right-hand side for typing out javascript stuff (my_sphere.blah)10:11
kanzuredo you mean webgl?10:11
fennwhateverthefuckgl10:11
kanzurethe only browser that supports webgl is like chrome on windows10:11
fennjava3d then10:12
fennor just send a friggin screenshot every 2 seconds10:12
bdeskkanzure: soon everything will be in the browser.  also inside facebook, probably.10:12
kanzurefenn: right10:12
fennlet's start a secret group inside facebook that you have to join in order to look at any of the content10:13
fennthen invite people to lots of parties, but only give them links to this group10:13
kanzurehuh? why?10:14
kanzuredoesn't that make us assholes?10:14
fennkanzure did you ever check out the sage interactive web notebook?10:14
fenn(yes)10:14
kanzureno but i saw something similar before so i just assumed..10:14
bdesksagenb.org10:14
bdeskSage is awesome.10:15
bdeskkanzure: add this to your omnibase:  [bdesk: "Sage"]10:15
kanzurecheck this out: http://2.latest.sympy-gamma.appspot.com/nb/10:15
kanzurehttp://sagenb.org/ seems to complain about a proxy error10:16
bdeski actually like sympy more because it is less than a gigabyte to install.10:16
bdeskkanzure: works for me10:17
kanzurethis sympy-notebook thing would be way better if it took a clue from etherpad10:18
kanzureand then was based on R instead (or something)10:18
kanzureso that you get mathematicians doing collaborative math proofs/theorems/etc. in an understandable syntax10:18
bdeskno, sympy is good.  it can maintain the math in symbolic form like mathematica and unlike R.  but only to a limited degree.10:18
kanzureright10:19
kanzurei guess i was referencing the large number of libraries available via CRAN10:19
bdeski think there are R web thingies.  but they are probably full of bobby tableses10:19
bdeskhttp://www.math.montana.edu/Rweb/10:20
kanzurenow warp it with etherpad, pastebin and a mathematica notebook :P10:20
kanzurewell, not a mathematica notebook10:20
bdeskkanzure: how did you find the sympy notepad?  the planet sympy blog is down.10:21
kanzuresince that tries to preserve traditional math syntax10:21
kanzurebdesk: i'm on the sympy-dev mailing list10:21
bdeskah10:21
bdeskisn't google wave supposed to own all this?10:22
kanzuresupposedly.10:22
fennwave never had anything to do with math10:24
kanzurefenn: the collaborative, interactive aspect thing10:24
fennoh. i thought the point of the web notebook was so you didnt have to install a gigabyte of dependencies10:24
kanzureit is, but it would be even more helpful if you could share your current notebook state with ohters10:25
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bdeski do this with my collaborators; i use cgi web programming and they use email.10:28
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fennme too; i use awesomesauce and they use weaksauce10:35
* fenn goes back to pushing bits around10:36
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jrayhawkkanzure: Is there something like the Open Source Definition or the DSFG published for hardware designs?11:11
jrayhawkIt seems like that such a thing would help with your "nobody has any idea what 'open' means" problem11:13
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kanzurejrayhawk: no, there isn't11:23
kanzureand i do agree something like the DSFG doc is desperately needed11:23
kanzurei talked with some lawyers, and they suggested the traditional "working group" model11:23
kanzurein particular for scenario planning11:23
kanzureand then once we bundle up the scenarios, we can make some generalized statements11:24
bdeskwhat is an example of a scenario?  someone wants to make a startup with your microfluidic techs?11:24
kanzurebdesk: example is: joe makes an "open source hardware" project for a thermocycler, sells a few kits that he throws together11:25
kanzurethen, amy comes along and starts selling kits as well with the same designs11:25
kanzurei want that to be possible11:25
kanzurebut there are variations on this scenario, like, amy makes some modifications, and then *doesn't* distribute the designs11:25
kanzureor where amy doesn't distribute designs at all (even when she doesn't modify the designs)11:25
bdeskso that would be ok if she is not distributing the modified techs, right?11:26
kanzurethat=?11:26
bdeskthat=amy makes some modifications and then doesnt distribute the deisngs.11:26
kanzureah, i see11:26
kanzureright, that's how it goes with open source software too11:27
kanzure(in general)11:27
bdeskyes that is the analogy i was thinking of11:27
kanzureamy makes some mods to the designs, builds her own hardware for herself, but doesn't distribute the changes/diff.. that's fine as far as i can tell11:27
kanzurebut if it goes commercial, that's when things get messy11:27
bdeskwhat if it is in her garage11:28
kanzureso anyway, this sort of scenario planning is what i think we should do11:28
bdeskok11:28
kanzurewhat if what is in her garage?11:28
kanzureher piece of hardware that she builds?11:28
bdesknvm11:28
kanzurejrayhawk: how does ikiwiki protect against spam attacks?11:29
bdeskkanzure: there is this on the reprap forum http://forums.reprap.org/read.php?58,4087411:31
bdesk'gpl for hardware is bad11:31
bdesk'11:31
jrayhawkYou have the option of requiring a per-wiki password for signup, which you can creatively turn into a turing test by stuffing it somewhere obvious.11:34
kanzureyeah, they're just pointing out that the gpl isn't really compatible11:34
kanzurebdesk: in that thread they suggest TAPR or CC but that just shows that they don't know the situation all that well..11:34
jrayhawkFor Piny I just make the account creation procedure sufficiently complicated and obscure that spammers are unlikely to try.11:34
kanzurejrayhawk: your anti-spam measures don't look good :(11:35
jrayhawkYeah, I might fix that someday. Maybe.11:35
kanzure"As far as I can tell, nothing currently legally prevents someone from withholding the hardware design files, when they modify and making electronics, mechanical parts, and kits for, or like, RepRap devices for sale or donation to others."11:35
kanzure"Even more, if they should write their own software and documentation, from the way I read RepRap licensing, they can feel free to create their own fully proprietary RepRap machines so long as they don't call it a RepRap; in fact, I believe this has already been done, has it not? "11:36
kanzure"Ah. My point is that it is the responsibility of the FLOSS-legal community to address this matter. I believe RMS can fix the GPL so that it does address hardware. address"11:36
kanzure^ now that's definitely wrong11:36
jrayhawkI don't actually have world-writable wikis implemented yet, but that might come soon.11:36
bdeskoh, i would have thought the reprap group could make a good license.11:37
bdeskor find one or whatever.11:37
kanzurethis explains it well: "11:37
kanzure"Any material that can be copyrighted can be licensed under the GPL. GPLv3 can also be used to license materials covered by other copyright-like laws, such as semiconductor masks. So, as an example, you can release a drawing of a hardware design under the GPL."11:37
kanzure"However, if someone used that information to create physical hardware, they would have no license obligations when distributing or selling that device: it falls outside the scope of copyright and thus the GPL itself."11:37
bdeskkanzure: ok so GPL itself is not directly useable for the hardware in a way that satisfies your scenarios.  but are the goals for reprap licensing the same as your hardware licensing goals?11:38
kanzureyes absolutely11:40
kanzuresebastien baillard has been in here a few times in the past11:40
kanzure"From how I interpret the OHL, the intent is to restrict your ability to distribute the hardware devices by licensing the use of copyrighted material used to make that device"11:41
kanzure"You are not allowed to modify or use a copy of copyrighted material to produce hardware unless you include that copyrighted material and the modifications you make. In this sense, OHL is still leveraging copyright law. I'm not sure there is enough precident to say whether this can be enforced. "11:41
jrayhawkDid you want me to set up an ikiwiki on Gnusha for you to play with?11:41
kanzureehh11:41
kanzurejrayhawk: i'm trying to figure out if that's a good idea or not11:42
jrayhawkI assume you don't *really* want a world writable wiki, and handing out access credentials on an individual basis is more in line with your trust model.11:43
kanzurebdesk: look at the last post in that thread (on page 2)11:44
kanzurejrayhawk: my internal trust model is about as fucked up as .. well, it's just all broken, to say the least11:45
bdeski dont know what is om or dman11:45
kanzuredman is a typo11:45
kanzureom is http://openmanufacturing.org/11:45
kanzureor more specifically http://groups.google.com/group/openmanufacturing11:45
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kanzurehttp://en.wikipedia.org/wiki/Patentleft12:55
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kanzurejonathan cline is asking me for $10k/mo for 4 years with an early termination clause12:59
kanzurehe sounds expensive :)12:59
kanzure"The 1931 regulations abolished the private ownership of intellectual property rights. Instead of being able to independently exploit her invention in a commercial way, the inventor now received a nominal remuneration in exchange for permanently assigning her invention and the accompanying intellectual property rights to the state."13:03
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cluckjthat's pretty expensive13:03
cluckjdon't you get a brothers-in-arms discount?13:03
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kanzurehttp://www.africafocus.org/docs04/wipo0411.php the world intellectual property organization13:10
kanzure"#  Private interests misappropriate social and public goods, and lock up the public domain. "13:10
kanzurei would have guessed something named WIPO would be *for* IP13:10
kanzure"A 1967 Convention sought to encourage creative activity by establishing WIPO to promote the protection of intellectual property. The mission was expanded in 1974, when WIPO became part of the United Nations, under an agreement that asked WIPO to take "appropriate action to promote creative intellectual activity," and facilitate the transfer of technology to developing countries, "in order to accelerate economic, social and cultural developme13:11
kanzure"As an intergovernmental organization, however, WIPO embraced a culture of creating and expanding monopoly privileges, often without regard to consequences."13:11
kanzureah, nevermind.13:11
kanzurehttp://www.wipo.int/ip-development/en/dacd.html "Development Agenda Coordination Division (DACD)"13:13
kanzureguess they just setup a separate part of their group to handle argentina's claims :P13:13
kanzurehttp://www.futureofwipo.org/futureofwipodeclaration.html13:16
kanzureinteresting list of signatures: http://www.futureofwipo.org/signatures.html13:16
kanzurelessig, doctorow, .. and lots of other random names13:17
kanzurehttp://www.idrc.ca/openebooks/454-3/ Implementing WIPO's Development Agenda13:21
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fennand now you know why pcb/chip etch patterns are called 'artwork'13:31
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kanzurehttp://biohouston.org/13:46
kanzuremakerbot on cbs news: http://www.cbsnews.com/8301-501465_162-20009744-501465.html13:48
kanzuresomeone wants to know the makerbot stock ticker symbol: http://answers.yahoo.com/question/index?qid=20100705182337AAhBY6S13:48
fennthey aren't a public company afaik13:49
kanzureright13:49
kanzurehm the question on yahoo answers was from two days ago13:49
fennhype is always a good investment, until it's not13:49
kanzureso i suspect it was unrelated to CBS News13:49
kanzuresinginst.org will be releasing the software i worked on in 2008 under the gpl tomorrow13:53
kanzurefor http://theuncertainfuture.com/13:53
fennwhy do it tomorrow when you can do it today? :)13:53
kanzurethey had to ask the contributors (like me) if we were all ok with the licensing13:54
kanzureso they gave a deadline for responses to be collected13:54
fenndidnt you steal some code from some webpage?13:54
kanzurethey ended up not using it13:54
kanzureand instead some java developer (rolf) got involved13:54
kanzureso, of course, everything switched to java..13:54
fennewww13:54
kanzureget this: we (by we i mean everyone else but me in the group) were thinking of applying to ycombinator :/13:55
kanzurefor that project13:55
fennsure, applying is fine. i hope they didnt expect anything to come of it though13:55
kanzurewe had probability distributions of our certainty of getting accepted to yc and everything!13:55
fennwas it just like 'omg we're in silicon valley 111'13:56
kanzureno it was more like anna/steve drawing graphs to prove how smart they were and that yc would thus let them in13:56
kanzureor something13:56
fennwell, it's not a university13:57
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kanzureah here's the paper on theuncertainfuture.com14:01
kanzurehttp://singinst.org/theuncertainfuture.html14:01
kanzurehm i wonder why i didn't get on that paper14:01
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Brunsanyone wanna donate 18 hundred?15:19
Bruns:315:19
Brunslol15:28
BrunsI am about to make 900 dollars from one computer15:28
Brunshaha15:28
Brunsand its a compaq15:29
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Brunshttp://000chan.org/news.php17:45
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JayDuggerGood evening, everyone.17:56
bkerohttp://gizmodo.com/5581377/solid+state-systems-could-sequence-a-genome-for-100?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+gizmodo%2Ffull+(Gizmodo)&utm_content=Google+Reader18:07
* kanzure nods18:12
kanzurebkero: have you seen the AFM-DNA-sequencing papers?18:12
kanzureoh wait, this is a nanopore article18:13
bkeroYea18:13
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kanzurewut? http://openfarmtech.org/index.php/OSE_License18:23
kanzurethat was from http://openfarmtech.org/weblog/?p=201218:25
kanzuredrill press: http://openfarmtech.org/weblog/?p=203718:25
kanzuresomehow michael koch convinced marcin to use openpario :(18:25
kanzurehttp://openpario.mime.oregonstate.edu/projects/drillpress/documents18:25
kanzurethe original replab blog post: http://openfarmtech.org/weblog/?p=125418:26
Brunsfood backed currency? won't work in Ethiopia that is for sure.18:26
kanzurehere's the dxf file: http://openpario.mime.oregonstate.edu/attachments/2227/drill_press_v0.1.dxf18:26
kanzurei'm not sure how the "OSE License" is a license..18:26
JayDuggerWhy complain about open+pario?18:28
kanzureJayDugger: it's yet another "project management" suite-on-a-website18:28
JayDuggerYeah, so/18:28
kanzureuh18:28
JayDuggers/\//?18:28
kanzurewhy not just put the files under a standard revision control system18:28
JayDuggerSeriously?18:28
kanzureyes18:29
JayDuggerI think that would work better, but it lies pretty far from current practice.18:29
kanzuregoogle wave seems to be doing it (er, or do they have some proprietary bullshit under the hood?)18:29
JayDuggerToo big a change in tools, regardless of advantage, deters adoption.18:29
JayDuggerMS Project sucks eggs, but it, like the rest of office, remains a common vice.18:30
kanzureJayDugger: openpario was pitched as a competitor to an skdb-on-the-web thing18:30
JayDuggerOh? 18:30
kanzurefrankly it seems completely inappropriate for the task at hand18:30
JayDuggerI didn't know that.18:31
kanzurewell, openpario didn't originate like that18:31
kanzurebut i mean, that's how it was injected into the openmanufacturing community as far as i can tell18:31
kanzurefenn: i forget, what was marcin's understanding of dependency resolution as being a priority?18:31
BrunsI know what you all wanna do18:32
Brunsis donate to my site :D18:32
JayDuggerHmm...18:38
JayDuggerhttp://openpario.mime.oregonstate.edu/projects/foodcommonshydro18:38
JayDuggerThat intrigues me.18:38
JayDuggerI wonder if it works well with salt-water hydroponics.18:39
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kanzureis there anything on it on the appropedia page18:40
JayDuggerUNK--FF is slow.18:40
JayDuggerNot really.18:42
JayDuggerA superficial glance--rainwater collection for hydroponics.18:42
JayDuggerNot too helpful.18:42
JayDuggerIt would be different if I had some real estate, but I don't.18:44
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Alystairgod I really wish I had a topic summizer for IRC so I wouldn't have the urge to go check what's been talked about in the last X minutes/hours19:02
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kanzureAlystair: you could just uh, ask people19:28
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Alystairbut I thought you were a fan of automation19:41
kanzurei am :) just, sometimes you abuse other people until they spontaneously turn into programs19:48
kanzureor something19:48
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kanzurewb quantumkat 19:49
JayDuggerGood night, everyone.19:51
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fennAlystair: you could run a k-means clustering on the last n lines and only return a cluster name or statistically improbable phrases20:43
kanzure< P3P: CP="This is not a P3P policy! See http://www.google.com/support/accounts/bin/answer.py?hl=en&answer=151657 for more info."20:55
kanzurehrm20:56
kanzurefenn: i think it would be fun to run statistically improbable phrases over the logs20:56
cluckjsomething like fishtastic or flippymagig20:56
kanzureif curl doesn't support P3P i'm going to be pissed20:58
kanzurewell my youtube scraper didn't work out as planned21:45
kanzureweird cookie rerouting stuff going on21:45
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genehackerwhy are you trying to scrape youtube?22:04
bdeskfor its insightful comments22:05
AJollyLifei do belive this is the first ive ever heard someone say youtube and insightful comments together.22:09
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--- Log closed Thu Jul 08 00:00:17 2010

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