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strangewarp | Belatedly... there has been some transhumanist sentiment in small slices of the furry community over the years. At its best, it was entirely self-aware and creative, and led to lovely inspired storytelling in places like Puzzlebox (my username is an homage to part of that place), which sadly has fallen off the internet largely un-archived.. | 00:23 |
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sylph_mako | http://en.wikifur.com/wiki/Puzzlebox_MUCK | 00:43 |
sylph_mako | strangewarp smells like someone I know. I'm pretty sure they're not him. We'll see. | 00:43 |
strangewarp | I'm not. I'm just a guy who arrived to the party late, and already burned out. : | 00:46 |
strangewarp | :P | 00:46 |
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strangewarp | To clarify: I stumbled over that MUCK's wiki (now offline) in 2008 or so, at about the same time I was reading through the posts on OvercomingBias that would spark LessWrong (I know, I know, I've come to dislike their lack of actionable engineering or coherent plans for such), and the two served as representations of conflicting impulses while I was waking up intellectually. | 01:03 |
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JayDugger | Good morning, everyone. | 01:39 |
Mariu | hey, JayDugger | 01:40 |
Mariu | how's it going ? | 01:40 |
JayDugger | All well enough. | 01:40 |
JayDugger | No real progress on projects of interest here, but otherwise life goes well. | 01:41 |
Mariu | Cool, nice to hear that. | 01:41 |
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Lucas_ | http://www.youtube.com/watch?v=qx72xt0utm4 | 11:48 |
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delinquentme | OMG MISSED YEW AW | 13:32 |
delinquentme | <3 | 13:32 |
sylph_mako | ..? | 13:39 |
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ybit | hi delinquentme, sylph_mako | 15:24 |
ybit | hope everyone here is doing well, been awhile since i've talked with anyone | 15:25 |
sylph_mako | I just hung up a yule bow ^ ^ | 15:25 |
sylph_mako | I wish a joyous yuletide festival from to you all. | 15:26 |
ybit | gracias y back to you | 15:26 |
delinquentme | ^_^ | 15:27 |
* ybit ^5s delinquentme | 15:27 | |
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sylph_mako | Wait a second. Yule is a winter celebration. | 15:40 |
sylph_mako | I live in the southern hemisphere. | 15:40 |
sylph_mako | It's summer. | 15:40 |
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delinquentme | sylph_mako, (christmas_tree)^-1 | 15:57 |
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mrtrousers | Hello | 18:11 |
mrtrousers | Is there a diy way to sequence genome? | 18:11 |
kanzure | how diy do you want to do it | 18:14 |
kanzure | you can buy a dna sequencing machine | 18:14 |
kanzure | or you can build your own dna sequencing machine | 18:14 |
kanzure | or you can manually write down fluorescent colors as you see them pass by under a microscope.. | 18:14 |
klafka1 | lol | 18:19 |
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mrtrousers | So to lets say.. To sequence your own genome you either pay to get it done or buy a sequencer machine? | 18:34 |
kanzure | well, it depends on how much coverage you want | 18:34 |
kanzure | to a certain extent it's more efficient to just use 23andme and get a number of snps and apply that against a knonw-good genome | 18:35 |
kanzure | but! getting your own dna sequencer opens up a lot of other possible projects | 18:35 |
mrtrousers | What is 23andme? How much are sequencers running for? Any open source project on it? | 18:36 |
kanzure | there's at least one open source sequencer but i think its material cost is 20k | 18:36 |
kanzure | working, used dna sequencers from 10 years ago go for maybe 12-15k | 18:37 |
kanzure | new dna sequencers will cost 50k-1200k | 18:37 |
klafka1 | 50k would be pretty cheap | 18:38 |
klafka1 | what would that be? | 18:38 |
kanzure | i am making shit up | 18:38 |
klafka1 | oh | 18:38 |
klafka1 | lmao | 18:38 |
kanzure | i know that some "top of the line" models go for 700k | 18:38 |
klafka1 | yeah | 18:38 |
klafka1 | exactly | 18:38 |
kanzure | but i'm pretty sure there's some <100k models | 18:38 |
mrtrousers | Out of my budget.. Theres got to be a cheaper way to do it.. | 18:38 |
klafka1 | the church one is like 150k~ | 18:38 |
klafka1 | mrtrousers you can pay someone | 18:38 |
klafka1 | what is it like 10k? | 18:38 |
kanzure | mrtrousers: you can just send in samples to someone | 18:38 |
klafka1 | or so | 18:38 |
klafka1 | still | 18:38 |
mrtrousers | Yup.. | 18:38 |
kanzure | i haven't seen an order form for pgp | 18:38 |
kanzure | does it actually exist yet? | 18:39 |
klafka1 | no idea | 18:39 |
klafka1 | that's what i've heard | 18:39 |
kanzure | i know they have sequenced some people, but they could have just outsourced that to knome or something | 18:39 |
kanzure | when are you going to be in sf? | 18:39 |
klafka1 | kanzure no i'm talking about their machines | 18:39 |
klafka1 | tomorrow | 18:39 |
kanzure | ok i'm in sf tomorrow | 18:39 |
kanzure | what time? | 18:39 |
klafka1 | polonator | 18:40 |
klafka1 | umm i think i get in around 5pm | 18:40 |
kanzure | ah i'll be gone before then | 18:40 |
klafka1 | ah | 18:40 |
kanzure | you have a place to stay? | 18:40 |
klafka1 | the company is putting me up at a hotel | 18:40 |
mrtrousers | By the way.. Going around the world sequencing diferent organism genomes could be made into a job? | 18:40 |
kanzure | you can take my place at langton labs (where fenn sleeps) | 18:40 |
klafka1 | oh can i stay tehre for a few months? | 18:41 |
klafka1 | :P | 18:41 |
kanzure | mrtrousers: sure... check out beijing genomics institute | 18:41 |
kanzure | klafka1: yeah, i think they have some rooms open for rent | 18:41 |
klafka1 | oooooh | 18:41 |
klafka1 | really? | 18:41 |
klafka1 | fenn_ get in here | 18:41 |
kanzure | pretty chill place too | 18:41 |
klafka1 | tell me about your magic land | 18:41 |
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kanzure | fenn is currently ignoring irc i think | 18:41 |
klafka1 | i wanna stay some place cheap and hopefully near caltrain if i get this job | 18:41 |
kanzure | this is near bart- look it up on google maps ("langton labs") | 18:42 |
klafka1 | for like a month or two then get an apt and have the gf move out | 18:42 |
kanzure | are they in sf? | 18:42 |
mrtrousers | kanzure: interesting.. | 18:42 |
klafka1 | menlo park | 18:42 |
kanzure | ah lame.. langton might not be best then | 18:42 |
klafka1 | if it's cheap it'll work | 18:43 |
klafka1 | maybe | 18:43 |
kanzure | yeah i'll pester fenn to get online in a bit | 18:43 |
kanzure | try pm'ing him.. | 18:43 |
klafka1 | ok | 18:43 |
klafka1 | sweet | 18:44 |
mrtrousers | kanzure: So lets say one sequences the genome for diferent organisms.. How do you monetize it? | 18:44 |
klafka1 | all kinds of ways | 18:44 |
kanzure | uhh are you broke | 18:44 |
klafka1 | me? | 18:44 |
kanzure | no | 18:44 |
klafka1 | oh | 18:44 |
klafka1 | heh | 18:44 |
klafka1 | mrtrousers you don't make money so much from the sequencing | 18:45 |
kanzure | it's just a little unusual or someone to have to monetize a genome | 18:45 |
kanzure | *for someone to have to monetize a genome | 18:45 |
klafka1 | typically places that sequence are either gov/grant funded or they do consulting work or they do lab work for hire | 18:45 |
klafka1 | e.g. they have a big ass sequencing lab and other people pay them to sequence shit for them | 18:45 |
mrtrousers | You travel the world seguencing rare genomes and monetizing so you can keep doing it.. | 18:45 |
mrtrousers | Im broke too | 18:46 |
klafka1 | well | 18:46 |
klafka1 | if you're craig venter | 18:46 |
klafka1 | and own a company | 18:46 |
klafka1 | and are rich | 18:46 |
klafka1 | then you can do that | 18:46 |
mrtrousers | Did Craig Venter hit something interesting on that sailing expedition? | 18:47 |
kanzure | he published a few papers | 18:48 |
kanzure | and usually you pay a bucketload to publish a paper (unfortunately) | 18:48 |
klafka1 | yeah | 18:49 |
klafka1 | like 3-4k | 18:49 |
kanzure | klafka1: my last paper was 2k per coauthor | 18:49 |
kanzure | there were 11 coauthors | 18:49 |
klafka1 | wtf | 18:49 |
mrtrousers | People pay to publish a paper? Really? | 18:49 |
klafka1 | kanzure it's usually a per page cost i thought | 18:49 |
kanzure | mrtrousers: it's all kinds of fucked up | 18:49 |
kanzure | klafka1: yeah there was that too | 18:49 |
klafka1 | kanzure it's preferable to the alternative | 18:49 |
klafka1 | honestly | 18:49 |
klafka1 | the current alternative | 18:49 |
kanzure | this was the "open access fee" | 18:49 |
klafka1 | i maintain it's still preferable to the alternative currently | 18:50 |
mrtrousers | Is there a database of currently sequenced organisms, people, etc.. ? | 18:52 |
klafka1 | sure | 18:52 |
klafka1 | check out pubmed.com | 18:52 |
klafka1 | fucking flac | 18:52 |
kanzure | mrtrousers: yes you can download genomes via ftp on ncbi | 18:52 |
mrtrousers | cool | 18:53 |
mrtrousers | What do you think of biobricks? Do you work with the registry of standarized parts? | 18:53 |
kanzure | biobricks is a nice concept but there's lots of edge cases that you run into | 18:54 |
kanzure | plus, i don't think they are mailing biobrick books to non-institutions at the moment | 18:54 |
klafka1 | i haven't looked into synthetic biology | 18:54 |
klafka1 | however i think that there are going to be lots of emergent phenomenon and epiphenomenon that occur when you try and combine a lot of them | 18:54 |
mrtrousers | ... | 18:55 |
kanzure | like "taking a random metabolic network from one organism and into another organism" might have conflicting proteomes and shit | 18:55 |
mrtrousers | So when you combine the parts to make more complex devices.. It wont work? | 18:55 |
klafka1 | yes | 18:55 |
kanzure | or "other shit breaks" | 18:55 |
klafka1 | yeah that's slightly more accurate | 18:55 |
kanzure | and then you're debugging for three or four years.. | 18:55 |
klafka1 | the things may do what you want, but they may do OTHER shit that you have no idea about | 18:56 |
mrtrousers | Im trying to design a biosensor from existin devices.. | 18:56 |
kanzure | go for it | 18:56 |
klafka1 | mrtrousers you have to remember that biological 'programming' isn't like regular programming, the program is also data is also physical | 18:56 |
kanzure | what are ou sensing? | 18:56 |
kanzure | *you | 18:56 |
mrtrousers | Id like to sens air quality and pollutants from oil, gas, chemicals would trigger a change of colour or phosphorescent light.. I think e. choli chassis.. | 18:57 |
kanzure | sounds like you should just express some surface protein or other object that can bind to air pollutants non-selectively | 18:58 |
kanzure | the problem with non-selectively.. | 18:58 |
mrtrousers | is.. | 18:59 |
kanzure | uh? it's non-selective and thus useless if anything can set it off | 18:59 |
mrtrousers | Anything that is a pollutant? | 19:00 |
mrtrousers | Well anyway, I need to work on it.. | 19:01 |
mrtrousers | Klafka1: you have to remember that biological 'programming' isn't like regular programming, the program is also data is also physical.. Id like to hear more on that.. | 19:02 |
kanzure | no not just "anything that is a pollutant" more like... anything anything | 19:03 |
klafka1 | well your 'program' ends up being DNA which has actual physical properties and DNA can interact with DNA in various physical ways in addition to containing the basic 'atcg' information | 19:03 |
kanzure | klafka1: i think protein-protein interactions are more relevant here | 19:04 |
klafka1 | further mRNAs interact with each other, they compete competitively for polymerase translation | 19:04 |
kanzure | right | 19:04 |
klafka1 | er | 19:04 |
klafka1 | transcription | 19:04 |
klafka1 | adn ribosomal translation | 19:04 |
klafka1 | and THEN the protein end-products are physical things that can interact in emergent phenomena | 19:04 |
klafka1 | which is the big thing i think kanzure and I agree on | 19:04 |
kanzure | or other things can happen like.. pH changing drastically and killing your cell | 19:05 |
klafka1 | yeah | 19:05 |
kanzure | some of this can be modelled and predicted ahead of time i think, | 19:05 |
kanzure | like "Oh, i'm modifying the ph stability stuff, hur dur" | 19:05 |
kanzure | but anything else is a guessing game | 19:06 |
kanzure | more probabilistic | 19:06 |
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klafka1 | yeah | 19:06 |
klafka1 | basically things aren't impossible but they are fucking hard and they have the ability to really go off the wall | 19:06 |
mrtrousers | You guys are hobyists or biology academics? | 19:07 |
klafka1 | i'm no longer in academia but i was involved in comp bio @ in academia | 19:07 |
kanzure | i'm just a tortoise | 19:07 |
kanzure | i'm not even human | 19:07 |
eudoxia | Is there such a thing as an open manufacturing wiki? | 19:10 |
mrtrousers | There is open cource ecology..They do open hardware.. | 19:10 |
kanzure | eudoxia: no, but there's appropedia, gvcs stuff on openfarmtech.org, old hplusroadmap wiki stuf.. | 19:10 |
eudoxia | Oh I know that one, I was just wondering something more broad, though it would be 90% OSE | 19:11 |
kanzure | there's also wikipedia | 19:11 |
mrtrousers | Can I make silly questions? | 19:14 |
kanzure | silly questions are the best kind.. | 19:14 |
klafka1 | sure | 19:14 |
mrtrousers | If in a species every organism has a slightly diferent genome.. How do we decide which genome is the average or the one that defines the specie? | 19:15 |
kanzure | statistics | 19:15 |
kanzure | most members of a population have the same genome and just have different alleles | 19:15 |
mrtrousers | So when they sample bees, they dont just do one, they do lots.. | 19:16 |
klafka1 | eh it's more like typically they try and take a 'normal' member of a species | 19:17 |
klafka1 | and sequence it's genome | 19:17 |
kanzure | eudoxia: feel free to talk in here.. | 19:18 |
kanzure | instead of separately.. | 19:18 |
klafka1 | you have to understand that genome sequencing itself is a very probabilistic thing as well, each base pair is determined typically with some margin of error | 19:18 |
klafka1 | 99% of a species genome is the same and it's a set of SNPs that separate individuals | 19:18 |
kanzure | and then there's all sorts of parts of the genome that are too highly repetitive to sequence with any certainty [with current techniques] | 19:19 |
klafka1 | yep | 19:19 |
mrtrousers | Iv seen when sequencing they break the dna into lots of strands to read it.. How do they piece it in the right order afterwards? | 19:20 |
ybit | fenn_: do you think the ml-class was worth your time? | 19:20 |
kanzure | ybit: i just saw him walk in.. klafka has dibbs on him first | 19:20 |
kanzure | let me pester him | 19:20 |
klafka1 | mrtrousers by looking at overlap | 19:21 |
klafka1 | it's a fairly classic substring reconstruction problem | 19:21 |
mrtrousers | Ok | 19:22 |
klafka1 | for de novo sequencing there are two ways of doing it, either they create longer strands using sanger sequencing then using NGS to do 'shotgun sequencing' | 19:22 |
klafka1 | or um you can do denovo sequencing with just NGS but it requires very very high coverage | 19:22 |
mrtrousers | Do you think laptops will incorporate labonachips to run experiments in the near future? | 19:23 |
eudoxia | that would be a mildly expensive adon | 19:24 |
eudoxia | addon* | 19:24 |
klafka1 | er um | 19:24 |
klafka1 | why would a laptop have a lab on a chip? | 19:24 |
kanzure | fenn is currently ignoring the interwebs | 19:25 |
mrtrousers | Dont know yet.. | 19:25 |
eudoxia | while we're at it, we could also add a scanning probe and an electron microscope | 19:25 |
mrtrousers | So you could run experiments on the fly, read genomes, etc.. | 19:25 |
kanzure | direct dna sequencing with electron microscopy is another technique, although not ready for commercial use | 19:25 |
mrtrousers | Or.. Would there be a day where you code something on a computer and something is grown on a petri? | 19:26 |
klafka1 | kanzure who is doing that? | 19:26 |
eudoxia | I wonder if you could sequence DNA with an atomic force microscope... | 19:26 |
kanzure | mrtrousers: why? do you need that | 19:26 |
kanzure | klafka1: halcyon molecular | 19:26 |
klafka1 | mrtrousers this is slightly beyond near future | 19:26 |
kanzure | eudoxia: yeah.. you can | 19:26 |
klafka1 | more like 5+ years at least | 19:26 |
kanzure | http://diyhpl.us/~bryan/papers2/DNA/ | 19:27 |
klafka1 | man kanzure i boought pacbio stock | 19:27 |
kanzure | http://diyhpl.us/~bryan/papers2/AFM/ | 19:27 |
klafka1 | i hope they aren't tanking lately | 19:27 |
kanzure | pacbio will probably end up on top | 19:27 |
klafka1 | i think they had a rough patch | 19:27 |
klafka1 | but they have solid tech | 19:27 |
klafka1 | don't you agree? | 19:27 |
klafka1 | wow halcyon hasn't had an update since Nov 2010 | 19:27 |
klafka1 | that's not good at all | 19:28 |
kanzure | they aren't a website company | 19:28 |
kanzure | kim jong is dead | 19:28 |
kanzure | everybody hide under your desk! | 19:28 |
klafka1 | well i guess they are still around | 19:29 |
klafka1 | they are hiring a help desk admin | 19:29 |
klafka1 | kanzure just growing startups usually have regular news blurbs, are hiring, have jobs posted on their sites, etc... | 19:29 |
klafka1 | but anyway they are still doing well? | 19:30 |
klafka1 | are they sort of flying under the radar atm while they dev? | 19:30 |
kanzure | uhrm | 19:30 |
kanzure | it's a long story | 19:30 |
klafka1 | ah | 19:30 |
klafka1 | oh | 19:30 |
kanzure | and i just got done ranting/complaining about them yesterday, so it will be a few days until i care enough to complain again | 19:30 |
klafka1 | ok | 19:31 |
klafka1 | well when you do let me know | 19:31 |
klafka1 | i want to know their story | 19:31 |
kanzure | okie dokie | 19:31 |
klafka1 | since i intimately care about the state of sequencing tech | 19:31 |
klafka1 | so let's just remember http://kimjongillookingatthings.tumblr.com/ | 19:33 |
kanzure | oh man that's great | 19:34 |
kanzure | ☑ Kim Jong Il ☑ Khaddafi ☑ Osama Bin Laden ☑ Saddam Hussein ☐ Internet Explorer | 19:34 |
mrtrousers | funny | 19:35 |
* ybit pokes fenn_ | 19:42 | |
kanzure | ybit: try calling him | 19:42 |
* ybit calls fenn_ | 19:43 | |
kanzure | ybit: see pm | 19:43 |
ybit | see pm | 19:43 |
ybit | *eeeevil* | 19:44 |
ybit | kanzure: can you just hit him with a wadded sheet of paper and tell him that's from me and that he should answer my question? | 19:46 |
kanzure | no | 19:46 |
kanzure | he's behind a door | 19:46 |
foucist | ah, you are sharing the same geolocation | 19:49 |
foucist | that explains some pecularities of this channel | 19:49 |
ybit | not all of them | 19:49 |
kanzure | foucist: most of the time, no | 19:50 |
kanzure | but the last week, yes | 19:50 |
ybit | i still don't understand why kanzure tells fenn_ to roll over sometimes | 19:50 |
kanzure | roll over? | 19:50 |
ybit | bad joke? | 19:50 |
kanzure | "bend over" would be funnier | 19:50 |
ybit | i would explain the picture in my head, but i'd rather that image not be there | 19:51 |
ybit | http://www.r-tutor.com/ | 19:52 |
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klafka1 | lol | 19:52 |
klafka1 | foucist it's hard to explain the pecularities of the channel | 19:52 |
klafka1 | ybit this seems interesting | 19:52 |
ybit | klafka1: the images do | 19:52 |
klafka1 | also why are the images like crazy | 19:53 |
ybit | they make you think there's going to be some amazing visuals | 19:53 |
ybit | my question too | 19:53 |
klafka1 | i've never seen an ANOVA graph look so cool | 19:53 |
klafka1 | i was curious to see GPU SVM with R though | 19:53 |
klafka1 | anyway | 19:53 |
klafka1 | shower | 19:53 |
klafka1 | bbiaf | 19:53 |
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foucist | what does "X has experience in mobile app, but he mostly does native app development." mean to you | 20:04 |
foucist | native app dev = iOS ? | 20:04 |
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ybit | yeah, sounds like objective-c or java | 20:08 |
ybit | not mobile site development | 20:08 |
kanzure | foucist: it means he's bad at english | 20:10 |
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ybit | https://plus.google.com/108772200278976934119/posts/2xXxs3nMPaU | 20:31 |
kanzure | you are obligated to explain obfuscated links | 20:31 |
kanzure | unless the context is obvious | 20:31 |
ybit | new biotech badge | 20:32 |
ybit | from adafruit | 20:32 |
klafka1 | that's cool | 20:39 |
klafka1 | that reminds me that i just bought http://www.spacetribe.com/shop/images/JK54_M30A_XL.jpg | 20:42 |
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foucist | what's the alternatives to phonegap? | 21:05 |
ybit | maybe alternativeto.net knows | 21:05 |
kanzure | foucist: there is no alternative | 21:08 |
kanzure | keep using it | 21:08 |
kanzure | but there's also appcelerator/titanium or whatever | 21:08 |
kanzure | foucist: if you use phonegap i can help you out bunches | 21:08 |
kanzure | foucist: what are you up to | 21:09 |
kanzure | POKEMON DIDN'T EVOLVE, GOD MADE POKEMON, DONT BELIEVE THE LIBERAL ATHEIST LIES! | 21:22 |
kanzure | http://i.imgur.com/eXGKy.jpg | 21:22 |
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joshcryer | req: Observing the Multiexciton State in Singlet Fission and Ensuing Ultrafast Multielectron Transfer | 21:25 |
foucist | kanzure: i was just at startup weekend bangkok and my team won | 21:29 |
foucist | we get to do the asian ycombinator bootcamp in singapore | 21:29 |
foucist | ycombinator-like | 21:29 |
foucist | the biz idea is to let people chat with others that are also watching the same TV show they are | 21:31 |
foucist | original name was TVeeter (TV twitter) | 21:31 |
foucist | kanzure: anyways basically need to do a mobile app with twitter integration.. made good progress with jquery mobile/rails during the weekend but time to start looking at doing a proper job of it | 21:32 |
foucist | do you think phonegap is suitable for a twitter mobile app? | 21:32 |
kanzure | uh.. sure | 21:58 |
kanzure | yeah i don't see a problem doing that | 21:58 |
kanzure | foucist: you should meet up with http://www.justin-klein.com/ | 22:01 |
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ybit | #webdev #android #ios www.curl.com | 23:13 |
ybit | http://opalang.org/ | 23:16 |
ybit | #note-to-self | 23:16 |
* ybit throws a paper airplane at fenn_ and calls it a night | 23:18 | |
ybit | was wondering if the ml-class was worth it, just in case you didn't see | 23:19 |
ybit | bye now | 23:19 |
kanzure | ybit: he says "i don't know because i didn't do it but generally no i don't think it's worth it" | 23:36 |
kanzure | "tell him to just read the book" | 23:36 |
kanzure | "or better yet just read the lecture notes and look at the wikipedia articles" | 23:37 |
kanzure | "i mean ml is just statistics" | 23:37 |
kanzure | "statistics is boring" | 23:37 |
kanzure | "but it's useful so pffrtt" | 23:37 |
kanzure | i can't type the sound he made | 23:37 |
kanzure | "like statistics with optimization" | 23:37 |
Utopiah | ybit: you can get opinions from people who did it on #ml-class | 23:40 |
--- Log closed Mon Dec 19 00:00:35 2011 |
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