2013-10-25.log

--- Log opened Fri Oct 25 00:00:04 2013
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archelshttp://www.pnas.org/content/early/2013/10/02/131269111009:34
archelsCortical columns are thought to be the elementary functional building blocks of sensory cortices. Here we show that the cellular architecture of cortical “barrel” columns in rodent somatosensory cortex is not stereotypic, but specific for each whisker on the animals’ snout.09:34
archelsOur findings challenge the concepts underlying contemporary simulation efforts that build up large-scale network models of repeatedly occurring identical cortical circuits.09:34
* archels guffaws09:34
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@kanzurearchels: well that sounds like good news10:07
ParahSailinpaperbot: http://www.pnas.org/content/early/2013/10/02/131269111010:12
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Cellular%20organization%20of%20cortical%20barrel%20columns%20is%20whisker-specific.pdf10:13
@kanzuregeeze what a ridiculous dsl for python http://pythonhosted.org/should_dsl/available_matchers.html10:13
@kanzureoh cool paperbot did the right thing for once10:14
@kanzurearchels: it's good news because that means we just have to stare at slices of cortex and then make models10:14
ParahSailinwhoa what syntax is that | shit10:14
@kanzurei assume black magic10:14
ParahSailinis that quasiquoting or something?10:14
ParahSailinor is that overloading of or?10:15
ParahSailinlol10:15
ParahSailinyeah, gross10:16
ParahSailinwtf people10:16
archelskanzure: it does not bode well for strongly reduced/simplified models though10:21
archelsI suppose 'columns' can still be somewhat elementary building blocks, but it's becoming ever less likely10:22
ParahSailinkanzure: whats been going on with paperbot?10:24
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@kanzureParahSailin: nothing :(10:32
@kanzurearchels: yeah but this is good news because maybe people will now actually believe the brain's structure is fucking relevant10:32
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ParahSailinkanzure: did sci-hub cut us off?10:40
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@kanzureParahSailin: no idea, i haven't investigated11:08
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delinquentmepaperbot, http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=1011:24
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/9b1a919b4d9ef597248fe3e910704bb4.txt11:24
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delinquentmepaperbot, http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=125006&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F8843%2F27977%2F01250065.pdf%3Farnumber%3D12500611:30
paperbothttp://libgen.org/scimag/get.php?doi=10.1109%2F10.12500611:30
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@kanzureapparently brlcad is used by lots of windows users :(12:57
@kanzurehttp://sourceforge.net/projects/brlcad/files/stats/os12:57
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fennarchels: if you can teach a blind man to use a cane, does it matter that mice have specially evolved processing circuits for whiskers?13:48
fennif the goal is to simulate a mouse brain, why bother with abstraction at all, just digitize actual mouse brains13:50
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@kanzurefenn: the fascination with trying to do brain things without looking at brains is really curious14:00
@kanzurefenn: also i found your doppleganger and it is weird14:00
fennwell it depends on your idea of "brain things"14:00
fennwhich doppleganger? there are several14:00
@kanzurejquast has many of your physical mannerisms14:01
@kanzureworked as a sysadmin for a long time, started doing linux things in '97ish or earlier14:01
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fennsymptoms of late stage progression of the disease14:02
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@kanzurenah he is missing that disease; that's where the similarity stops i think14:02
fennhe really likes serial ports14:05
ThomasEgii see no problem with liking seiral ports. they often saved my day when everything else failed. simple, robust, easy to work with.14:06
fenni don't disagree14:07
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@kanzurei wonder if people have been trying to do abstractions because they are too lazy to figure out how to deal with all the data from scanning14:09
@kanzureor maybe they just don't have all of the neuron types characterized14:10
@kanzurebut that seems like a fairly blunt list of things to do.. a rare feat in research.14:10
@kanzure"now we have to character 300 types of neurons" => great.. scale up some drones. get the dishes going.14:10
@kanzure*characterize14:10
fennprobably because their scan data isn't big enough or high enough resolution14:10
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fenndingo: are you jquast?14:12
dingoi am! crap, who are you!14:13
fennyour government-assigned super snooper14:13
fennwell anyway apparently we were cloned from the same vat14:15
dingoah14:17
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dingoyes aparently we wave our hands around the same way14:19
fennoogedy boogedy boo14:19
fenni am not a crook14:19
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delinquentmepaperbot, http://www.ncbi.nlm.nih.gov/pubmed/2279070214:23
paperbothttp://libgen.org/scimag/get.php?doi=10.1016%2Fj.aca.2012.06.00214:24
@kanzurefenn: i'm not happy about how a lot of that research data is not available, though14:33
@kanzurefenn: i'm also disappointed with the computational models available so far14:33
@kanzurefenn: i don't want to end up with merk-style books ("here is your billion tables of neuron properties, have fun assholes")14:34
fennthe data sets would be in the hundreds of terabytes though, how do you make that 'available'?14:34
@kanzureso, i don't actually mean "all possible data"14:35
fenndingo: any thoughts on terminal based calendar programs? i've been using calcurse and am less than impressed14:35
@kanzureeven the abstract thought ("data based on evidence") is a step up from the current situation14:35
@kanzurelike, even just something based on the physical reality14:35
@kanzurethe yales NEURON program for example provides some rudimentary modeling capabilities14:35
@kanzureinstead of talking about brain regions they should use ids that refer to entries on a ncbi.nlm.nist.nih.gov site, and then those ids can have properties and things based on, you know, data14:36
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fennbut that's not "natural language", i mean humans don't generally speak out loud in long digit sequences or urls14:38
fennthey want to say, "the frobenius frobnicator is laterally impelled to digitate your mom"14:38
fennwhereas RDF or (potentially) lojban might be less ambiguous14:39
fennremember how hard it was just to define what counted as a chair?14:40
@kanzurei don't care; it's their jobs to be internally consistent14:40
fennthere's always going to be ontological incompatibility14:40
@kanzurei don't care if they use multiple ontologies14:41
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dingofenn: i just use 'cal', no, but i am working a lot with the 'blessings' project for python if you care to author one of your own :-)14:43
dingocould help you w/that14:43
dingotrying to get keyboard input submitted upstream14:43
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fenndingo: i meant more like an appointment book, but yeah i might scratch something out once i start making appointments again14:44
dingoi'm very much a terminal programer14:45
fennwhat's "trying to get keyboard input submitted upstream" mean exactly?14:46
dingothe 'blessings' project on pypi doesn't support keyboard input yet14:47
dingo'blessings' is to 'curses' for python as 'requests' is to 'urllib2'14:47
@kanzureobv. you should just use urwid14:47
dingothey have different goals, very different14:48
dingourwid:14:48
dingo move_cursor_to_coords(size, x, y)14:48
dingo    Set the cursor position with (x,y) coordinates. Returns True if move succeeded, False otherwise.14:48
dingoblessings:14:48
dingo print term.move(x, y)14:48
fennurwid looks more like the "dialog box" thing on a linux install14:49
dingourwid is definitely not 'requests', its more like 'twisted' or something worse14:49
dingoin that the interface is very very involved14:49
fennwhat i've seen so far of x84/blessings is closer to my impedance :)14:50
dingoyeah trying to get this pull in first: https://github.com/erikrose/blessings/pull/4314:51
dingoyou can word-wrap colored text, or center, rjust/ljust, something urwid can't do, either, i dont think14:52
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archelsfenn: I agree whole-heartedly15:04
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sbaughfenn: i'm also looking for a working terminal based calendar program - namely one that works with caldav15:13
sbaughi'm almost resigned at this point to eventually switching to emacs and using org-mode15:14
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delinquentmeLemminkainen, http://spectrum.ieee.org/tech-talk/biomedical/devices/teeny-tiny-pacemaker-fits-inside-the-heart16:00
delinquentmeso just on the topic of the thing where execution > ideas ( always ) ... theres a reason that its not all about execution.16:00
delinquentmeits necessary truly, but its also a sentiment passed around the startup scene because thats what VCs want to perpetuate.16:01
fenndelinquentme: i think you got "spray on bio films which could be applied to 6DOF arm robots" from the hit hollywood movie "the terminator"16:13
delinquentmefenn, sure these are just meant to be throw out ideas16:14
delinquentmesomething meant to incite conversation .. I guess it worked but not exactly as I had expected16:14
@kanzurewhy are you "throwing out ideas"16:14
@kanzureokay.. that's not how conversation works.16:14
delinquentmekanzure, bc unimpressed with speed of things. even in SV16:15
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fenni think the issue is they aren't fully formed ideas16:16
delinquentmecorrect16:16
fenna random number generator, great, but when it can be outperformed by a solid state device that costs 10 cents, why bother?16:16
delinquentmebut its also a big negative when I cant get feedback from networks16:17
ParaSa1lini think you dont have enough domain knowledge to produce any somewhat-formed ideas16:17
delinquentmeIts also a HUGE negative for all of us when IRL social networks have a bit better interplay16:17
@kanzureno, we'd be just as annoyed at you in person16:18
delinquentmeI want to see more collaborations happening online ... and esp if we want to see anyone do something in here well one method is clearly better than another16:18
delinquentmeParahSailin, sadly you fall into the category of kissing ass and really non-novel thought forming16:18
delinquentmekanzure, nah you're pretty benign in person16:18
ParaSa1lindo you have anything to contribute to a collaboration other than entropy source?16:18
delinquentmeParahSailin, go jump off a bridge16:19
delinquentmeseriously.16:19
fennyeah we don't really need to use a human as an entropy source, there's chatbots like gradstudentbot that can do that16:19
* fenn looks around and shrugs16:19
delinquentmeI dont even think you've posted up your RL creds and you're flamingly good at critiquing other ideas when not introducing anything novel.16:20
ParaSa1linmaybe a human would be a cryptographic quality entropy source16:20
fenndelinquentme: it's obnoxious when you do a drive-by idea tossing16:20
delinquentmefenn, well I suppose thats where RL would win out.16:20
ParaSa1linmeh, anywhere here knows who i am if theyre paying attention16:21
delinquentmeIf you want that to be the case ( where RL at least we're not flaming assholes to one another )16:21
delinquentmewell continue along the current path16:21
delinquentmeParahSailin, you said you interned at sens16:21
@kanzurethis is not about "irc versus in person"16:21
delinquentmekanzure, http://en.wikipedia.org/wiki/Online_disinhibition_effect16:22
@kanzurei assure you i do not suffer from in-person disinhibition16:22
@kanzureor.. erm.. the other way around.16:22
delinquentmeyes. Im assured.16:22
@kanzureokay, so now that it's not "irc vs in person", maybe you'll listen16:23
delinquentmethats an interesting projection onto the vagueness of the statement16:23
fennirc is pseudonymous, not anonymous </pedantry>16:23
delinquentmeTLDR: I really hope that IRC would be a place where discussions can be made16:23
delinquentmeIt feels hostile16:23
delinquentmeif thats what you're going for16:23
@kanzureyou're really not bringing up discussions though16:24
fennbecause you tend to disrupt conversations and steer them towards random ends16:24
@kanzurei don't see why you don't understand any of us16:24
fennor at best show up and drop a turd in the middle of the room and run off16:25
delinquentmeAh man. I guess this is what happens when I just dont behave / think in process like the rest of you huh?16:26
delinquentmecoooool ! little circle jerk boys club16:26
fennthen when someone challenges your idea, you rail about the unfairness of the world and double standards16:26
delinquentmeTheres a distinct difference between useful and unuseful crits16:27
delinquentme" thats stupid RTFM "16:27
fennbut you never RTFM16:27
delinquentmeyes because thats a shitty response16:27
@kanzurewhat16:28
delinquentmethats the academic upbringing lazy response.16:28
@kanzurereading things?16:28
fredox"there are no stupid questions, only stupid people"16:28
delinquentmeits " I don't want to think so you should read this 10k page manual "16:28
fennnot reading things and wanting people to spoon feed it to you is the lazy attitude16:28
delinquentmefenn, I assume out of anyone in here that you've worked in a lab space.16:29
delinquentmeSo tell me about how everyone knows everything else.16:29
delinquentmetell me about how the skillsets are totally complete and homogenous.16:29
delinquentmedo you see the point I'm trying to make here?16:29
fennum, you want me to try to extrapolate their educational histories from what i've read on IRC?16:30
delinquentmeDo you want it to be collaborative and " fill in the blanks where I can for my kin "16:30
delinquentmeor do you want this " I'm too busy to be bothered "16:30
@kanzurefenn: i think there's a deeper underlying bug here16:30
@kanzurefenn: like it's not just spoon feeding; like maybe he has a completely bonkers "theory of knowledge"16:30
fennkanzure: i think it's just a feeling of entitlement16:30
ParaSa1linmaybe hes just not effective in researching answers to simple questions16:31
delinquentmekanzure, I'm saying if someone doesn't know something it cant hurt that bad to fill in their misunderstandings16:31
delinquentmeMAYBE thats what a collaboration should be?16:31
@kanzurewe never agreed to collaborate on your fake project16:31
delinquentmeParahSailin, if it was a simple question then all the more reason you should have answered it no?16:31
delinquentmekanzure, then dont.16:31
delinquentmefucking ignore me if it makes you feel better.16:32
fenndelinquentme: so, i learned electronics over IRC from an EE. i would read articles and projects on the web, and when i didn't understand things i would ask for clarification about why they did something a particular way. often the response was to go read a wikipedia article on some subject, which i did16:32
delinquentmefenn, totally and thats fine.16:33
fenni never railed about how unfair it was that they didn't copy and paste the article sentence by sentence into the client16:33
delinquentmeBut its also built in that the individual who has the knowledge is too busy to explain it.16:33
delinquentmeI mean WHY do programming abstractions work ?16:33
delinquentmeBecause we're not repeating work.16:33
delinquentmeWhy does knowlege have to be so substantially different?16:33
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fennexactly, which is why you should read the link instead of whining about how they aren't helping16:33
ParaSa1linhm "completely bonkers theory of knowledge"16:34
fennwe dont want to repeat the work of typing in a wikipedia article16:34
delinquentmeParahSailin, go for it. That was a well articulated thought16:34
fenni believe we have a no-philosophy rule here16:35
delinquentmeis it possible there are time efficiencies built into querying an individuals vrs an article?16:36
entelechiosyeaaaaa outta all the irc channels ive been in i woulda hoped this would be one free of sophistry16:36
delinquentmeefficiency.16:36
@kanzureoh great, waste my time so that you don't have to read16:36
delinquentmekanzure, clearly its been put to world changing ends.16:36
@kanzureif you wont read papers and articles then why would you read what i type16:36
delinquentmekanzure, topic specificity.16:36
fennthere's an inherent asymmetry in human bandwidth; it's easier to read than to write16:36
delinquentmefenn, as is there in forming new knowledge vrs querying existing!16:37
fennit's the same thing16:37
fennuh, i mean "forming new knowledge" is the same as "querying wikipedia"16:37
fenndamn english16:38
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fennalright who tricked me into reading the "theory of knowledge" article on wikipedia?16:40
* fenn casts about balefully16:40
fredoxjust say no to wikipedia16:41
fennnoooooo16:41
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fenni want to put wikipedia on a nook e-reader, with offline access and decent formatting16:42
fennsurprisingly, this hasn't been done16:42
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fredoxa wikified version of the merck index would be nice16:43
fenndid anyone download it when it was online?16:43
fennthe merck index16:44
fredoxi have a copy of the old cd16:44
fredoxsearch paradigm is pretty shit16:44
fennoh, so do i, apparently16:44
ParaSa1linmerck index is on libgen16:45
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fennfredox: that would be hard to maintain because you'd have to keep it online and vulnerable to attack, otherwise it would be distributed and downstream edits would get lost because wiki revision control sucks16:47
fennyou'd have to use something like ikiwiki at a minimum to prevent splintering16:48
fredoxeven just a rip of the database and putting it in useful format would be nice16:49
fredoxi use the old paper book version more than the cd16:49
fennaccording to some random page i found on the web, "An MSI file is actually an SQL database, for all practical purposes."16:52
fennbut this is out of my area of expertise16:53
fenncan one use the cd without installing anything?16:54
@kanzuresomeone converted wikipedia to git16:54
@kanzureso that repo is floating around somewhere16:54
fredoxfenn: not that i'm aware of16:55
fredoxbut then i dont do database stuff much16:57
delinquentmefenn what do you want to know on MSI files?16:58
delinquentmeif you want me to try and build a DB from it let me know.16:59
delinquentmeOk perhaps this would be more of the liking of the general population here17:01
delinquentmeExperiment design on wiring up beta cells to start attempting to produce insulin ?17:02
fennmdb-tables TheMerckIndex.mdb17:03
fennAbsorptions BPs CASNames CASRNs Densities DerivTexts DerivTypes FlashPoints IndexesOfRefraction ManufacturerNames17:03
fennraphs MPs Names OpticalRotations PartitionCoefficients PKas Toxicities TradeNames17:03
dingo23:42 < fenn> i want to put wikipedia on a nook e-reader, with offline access and decent formatting17:05
dingothere is one17:05
dingoan offline, 2x AA battery17:05
fredoxdelinquentme: i think most people here are working on lots of their own projects, so group collaboration is not something that usually happens17:05
fenndingo: yeah and i don't like it, for various reasons17:06
delinquentmefredox, that sucks. Looks like the best project collaborations are then restricted to fleshspace17:06
fennit's missing articles, bad interface, can only do wikipedia, etc17:06
delinquentmeI'd love to the the *opposite* trend.17:07
fennfwiw lots of people telecommute17:10
delinquentmethey're also paid to be cordial17:10
fennthe trick is building entire organizations online; i don't think anyone's figured out how to do that without any money, and the people who have money tend to want to do things in meatspace17:11
fenneven EFF has physical offices17:11
delinquentmefenn, IDK i happened to observe it around playing games17:12
delinquentmewhich happen to be something of "working towards a common end"17:12
Lemminkainenthen gamify your MVE17:12
delinquentmeIDK I guess I see it mirrored here17:12
fennLemminkainen: market value of equity? what?17:12
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Lemminkainenminimum viable experiment17:13
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fenni dont think he has anything viable :\17:14
Lemminkainenit's worth encouraging someone to act even if they're unsure of what action to take17:15
fenni disagree17:15
fennthat just leaves us all with a bunch of blinking LEDs and popsicle sticks and hot glue17:15
LemminkainenI'd rather see a hundred enthusiastic people get turned onto the process of experimentation and actualization of their ideas than to have them be turned away frustrated17:15
delinquentmeaction here can be both research as well as building things.17:15
delinquentmefenn,  I think you're advocating research .. Lemminkainen could be as well.17:16
Lemminkainenresearch and then experimentation17:16
fredoxdepends if you're volunteering to do stuff for other people17:18
fennso, in the context of online collaborations, a minimum viable experiment is what?17:18
* fenn is imagining a "pimp my lab bench" social photo-sharing website17:19
fennbarf17:19
Lemminkainenha17:19
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Lemminkainenonline collaboration in science has a very useful component often missed: replication17:20
Lemminkainenreplication of published papers generally fucking sucks17:20
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fennbecause it's expensive and has no reward17:21
Lemminkainenbut online we can share enough about our experiments to collaboratively build upon them and get that replication hit17:21
fennwhen collaborating online you HAVE to replicate, unless you have a really good telepresence setup17:21
Lemminkainenexactly17:21
Lemminkainenacademic researchers right now are in competition to publish first instead of collaborating17:22
fennso, by doing things online we've multiplied the cost of the experiment by N collaborators, while reducing the cost of overhead (?)17:23
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LemminkainenI view that as cheaper than having shitty irreproducible experiments leading to incremental experiments not working at all17:23
fennbut better replicability17:23
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Lemminkainenfenn this discussion is thus far interesting but I must afk for an hour to purchase supplies; thank you for your attention17:24
fennwhat i have seen happening in reality, for example with the reprap nozzle design experiments of nophead, is that people have different equipment and can't justify the cost of standardizing (or just don't want to)17:25
fennor can't agree on what should be standard17:26
fennchrist, in 2013 people are still asking if kerning should be applied to chemical structures17:29
fenn(the answer is yes, by the way)17:31
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fennoh, you have to type "go" after every command in mdb-sql17:34
fenngreat, so i can get data out of TheMerckIndex.mdb17:35
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Lemminkainenfenn all those grievances aside, remember that you alone are more powerful than a German kingdom just 5 generations ago17:59
fenni have no power ladders :(18:01
delinquentmeeconomic, technological, and with information access18:01
delinquentmealso you guys would be upset with me if my hypothesis was " try a bunch of shit ... see what happens "18:01
delinquentmebut I lold18:02
fennif anyone cares, apt-get install mdb-tools; for i in `mdb-tables -1 TheMerckIndex.mdb`; do mdb-export TheMerckIndex.mdb $i > $i.csv ; do18:02
fenns/; do/; done/18:02
Lemminkainendelinquentme go ahead and try a bunch of shit, just remember to include negative controls or you aren't measuring anything18:02
Lemminkainentrying is better than talking about trying, in general18:03
delinquentmetrue!18:03
fennhow is it possible that csv is more efficient than mdb format18:03
delinquentmeLemminkainen, let me buy you  a beer18:03
delinquentmeor get you drunk.18:03
delinquentmeyour choice .18:03
LemminkainenI need to refactor this Android app tonight, otherwise I'd take you up on that18:03
delinquentmefenn, csv is pretty lightweight no? You're talking "comma separated values" right?18:03
fennright18:04
delinquentmeLemminkainen, women in coffee event18:04
delinquentme<< is here ... didn't plan it this way18:04
delinquentmeI swear these things happen around me18:04
Lemminkainen"women in coffee"18:04
delinquentmenono srsly. thats the event name.18:04
Lemminkainenthey would probably do well to iterate beyond that name18:04
fennis it a giant vat of coffee with scantily clad ladies doing formation swimming?18:05
delinquentme^advertising!18:05
delinquentmeLemminkainen, are you in mountain view or up here in oakland?18:05
LemminkainenI'm at Hackistan18:05
delinquentmelol18:05
delinquentmeTIL.18:05
delinquentmesooooo I was gonna wait till monday to email this prof...18:06
delinquentmeI wonder if I'll get lucky w a response tonight18:06
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fennthe internet seems to think that's 3276 logan street18:08
Lemminkainenfuck that's online?18:10
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fennbetter get to work on that missile defense project18:11
Lemminkainenit's on Foursquare, of course18:11
LemminkainenI blame #nerdtracker18:11
Lemminkainenany ideas on how to reduce the cost of attending FutureMED?18:27
cpopellwho's hosting it?18:27
LemminkainenSingularity University18:28
@kanzuretime for flight18:28
cpopellHmm.18:28
cpopellI know a couple SU people but none well enough I could pull strings.18:28
cpopellBleargh.18:28
Lemminkainen$10k for Dre and I to attend is a bit much to justify right now when we'd rather spend that on reagents18:28
cpopellGotta bug my Raytheon contact Monday18:28
@kanzurewhat do you need from them18:28
cpopellkanzure: me?18:29
@kanzurethey are boring but i have at lesst 3 blackmails18:29
@kanzurei mean strings18:29
LemminkainenI need greatly reduced prices to attend FutureMED because otherwise I cannot go18:29
cpopelloh, singularity university18:29
@kanzureoh kust show up18:29
@kanzurethey wont kick you out18:30
LemminkainenI may do exactly that18:30
cpopellSo I found the best place to recruit clients18:30
cpopellI can't afford them mostly yet18:30
cpopellbut I found them18:30
Lemminkainenand then I can spend cash on boutique polymers instead18:30
Lemminkainendo tell cpopell you cocktease you18:30
cpopellIntelligence community meetups18:31
cpopellespecially ones that are trying to be 'cutting edge'18:31
LemminkainenO_____18:31
Lemminkainen          o18:31
Lemminkainenthe other eye fell off18:31
Lemminkainenbahahahahahhah18:31
cpopellYeah, I had better luck with people approaching me there than I've had in months18:32
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Lemminkainenyou need a bigger winch18:35
cpopellWell18:36
cpopellMonday is hopefully next step with Hungarian dudes18:36
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@kanzureokay back in austin23:08
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