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| fenn | what do i do with $100 of amazon EC2? | 01:08 |
|---|---|---|
| fenn | it came with the machine learning class; amazon will be coming to see what we did with it | 01:09 |
| fenn | and apparently I'm talking at google tomorrow about reprap | 01:09 |
| fenn | small informal thing i hope | 01:09 |
| fenn | tomorrow meaning friday | 01:10 |
| fenn | and more qs stuff at maker faire | 01:10 |
| fenn | woah weird. i just googled "aether blog" because i wa thinking about setting up a blog, look what i get: http://aether.com/ | 01:11 |
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| Utopiah | there was a link posted few weeks ago here regarding a "chain of social entrepreneurs" , it was a kind of seed funding a la YCombinator but focusing on society improving projects and re-injecting capitals in the following projects, rings any bell? | 02:32 |
| Utopiah | (wasn't kickstarter or capitalfactory) | 02:33 |
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| kanzure | fenn: you could do rendering of reprap stuff in ec2, whole genome analysis | 06:47 |
| kanzure | Utopiah: it had a 'p' and the word 'fund' in it i think | 06:48 |
| kanzure | abundance fund? | 06:48 |
| Utopiah | nop, plus I dont think you can count b and b as revert p | 06:51 |
| Utopiah | b and d | 06:51 |
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| kanzure | cool just got off the phone with someone who knows don and doug at 80/20 | 07:19 |
| kanzure | (don and doug are the father-son pair running the company) | 07:19 |
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| thesnark | hey all | 09:28 |
| thesnark | damn, people must be at lunch | 09:32 |
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| lepton | Paying for closed source software is making me really really unhappy this week | 12:04 |
| lepton | Because it's unstable and causing us more trouble than it's solving | 12:05 |
| lepton | and their locked down IP issues are making the problems a lot more difficult to solve (on our end and theirs) | 12:05 |
| lepton | "/rant" | 12:05 |
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| kanzure | hello drewfer | 12:10 |
| drewfer | hiya | 12:11 |
| kanzure | lepton: i still haven't fixed pythonocc installation instructions :x | 12:11 |
| kanzure | but now that i think about it, i think i have time to do it now | 12:11 |
| kanzure | i just need to go find some lunch real quick | 12:11 |
| lepton | :) | 12:11 |
| drewfer | I'm just stumbling through the synthetic biology seminars, etc. and found a link to this chat group from diybio.org | 12:12 |
| lepton | Don't worry, I've been too busy with crappy closed software so far this week to work on awesome open software | 12:12 |
| lepton | I still greatly apprecaite you're help, though | 12:12 |
| lepton | and once the CNC is running again I'll have more time to sit around and babysit it / develop in PythonOCC | 12:12 |
| fenn | i've been playing with the cnc a lot lately: http://fennetic.net/irc/idler_brackets.jpg | 12:49 |
| lepton | Nice | 12:51 |
| lepton | what control software are you using? | 12:51 |
| kanzure | blah it's been too long since i've used vmware | 13:06 |
| kanzure | how do i do the shared hard drive thing, again? | 13:06 |
| kanzure | i really don't want to have to download opencascade stuff that i already have archives for locally.. | 13:06 |
| kanzure | i remember doing it at one point, but for some reason a lot of my search results are telling me it's impossible | 13:07 |
| kanzure | O_o | 13:07 |
| lepton | Which VMWare are you using? | 13:07 |
| lepton | Vmware Server/Player OS-X/Linux | 13:07 |
| kanzure | vmware workstation 6.5.2 | 13:07 |
| kanzure | running on linux | 13:07 |
| lepton | perfect, just like me | 13:08 |
| lepton | Do you have vmware tools installed in the guest? | 13:08 |
| kanzure | yes | 13:08 |
| kanzure | hm, actually i do not | 13:08 |
| kanzure | it's stuck at "Installing VMware Tools.." | 13:08 |
| lepton | Go into "edit virtual machine settings", under options there's "shared folders" | 13:08 |
| kanzure | *... | 13:08 |
| lepton | that should be all you need | 13:08 |
| kanzure | ah | 13:08 |
| lepton | Yeah, you need vmware tools for it to work | 13:08 |
| lepton | I suppose you could SSH into the host without vmware tools... | 13:09 |
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| fenn | lepton: mach 3 :( | 13:18 |
| fenn | it's icky | 13:18 |
| lepton | Why not EMC2? | 13:24 |
| fenn | because it's already set up with mach 3 | 13:37 |
| lepton | Gotcha | 13:40 |
| lepton | That's why we're not running EMC2, as well | 13:40 |
| lepton | though I talk about switching all the time | 13:40 |
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| lepton | fenn: what are those brackets for? | 14:18 |
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| fenn | idler pulleys for the mini mendel reprap | 15:03 |
| fenn | the timing belt was rubbing against the x carriage with the original part | 15:03 |
| fenn | http://fennetic.net/irc/mini_mendel.jpg | 15:05 |
| fenn | it's still kinda sluggish | 15:06 |
| fenn | next is electronics | 15:06 |
| fenn | or should i try to do my homework instead | 15:06 |
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| kanzure | hi zvader_ | 15:25 |
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| QuantumG | http://www.youtube.com/watch?v=eoqBSNmYJYI | 16:22 |
| QuantumG | fuckin' doomsayers are at it already. | 16:23 |
| QuantumG | http://www.youtube.com/watch?v=qPE2CnThito | 16:23 |
| lepton | People are silly | 16:38 |
| lepton | Though I do agree with the general sentiment that the more advanced this civilization becomes, the higher the risk / disruption there is to old paradigms (both human and ecological) | 16:39 |
| lepton | Spreading outward into the galaxy to diversify seems like the optimal way to address that issue | 16:40 |
| QuantumG | there's an overall anti-progress attitude in modern society that saddens me | 16:42 |
| kanzure | lepton: btw QuantumG is a troll .. sometimes. be careful :) | 16:42 |
| QuantumG | kanzure: you injure me | 16:42 |
| kanzure | i just feel the rant coming | 16:43 |
| kanzure | sorry | 16:43 |
| QuantumG | watch that last video kanzure | 16:43 |
| QuantumG | they even manage to get Venter saying that this "new" technology needs to be "strictly controlled" | 16:43 |
| kanzure | hm | 16:45 |
| kanzure | oh, venter's latest news stuff | 16:45 |
| lepton | I concur that there is a prevalent anti-process attitude | 16:45 |
| lepton | There's also a prevalence of the opinion that expansion into space is bad because "humans are a disease and ruin everything" | 16:45 |
| lepton | which saddens me, as well | 16:46 |
| kanzure | lepton: there was a scifi book that once explored that line of thought | 16:46 |
| kanzure | so, what happens if humans are a cancer? | 16:46 |
| QuantumG | yeah, there's a whole generation that have been brought up believing that they are bad bad bad just for being alive. | 16:46 |
| kanzure | wait, don't listen to me. i'm not into this right now. :P /me goes back to code | 16:46 |
| lepton | It seems important to be positive and optimitic about the potential of sentient life, and not get too caught up in the specifics of this place in this society right NOW | 16:46 |
| kanzure | sure | 16:47 |
| lepton | right NOW isn't nearly a big enough sample size to make general statements about humanity | 16:47 |
| lepton | but yeah, I should focus on toolpaths | 16:47 |
| lepton | :p | 16:48 |
| jrayhawk_ | I believe human beings are inefficient and will eventually be supplanted, be it either by an overwhelmingly more effective machine intelligence or a more efficient biological paradigm. The awkward question is "are people right to fear the end of their species?" | 16:58 |
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| jrayhawk | I don't think it's fair to call that fear "silly" any more than it is to call people with strong convictions "crazy". | 17:00 |
| lepton | hmm | 17:00 |
| lepton | I agree on all points | 17:00 |
| lepton | I think the future is too unknown/variable to anticipate exactly how things will go, for example, if contemporary humanity does give way to something(s) more advanced, it doesn't necessarily have to be a harsh step or catalysm | 17:02 |
| lepton | There are many very positive potential scenarios from a traditional human perspective | 17:03 |
| QuantumG | yeah, they reason why I said "new" technology is because what Venter's done is interesting and amazing, but it's not actually all that relevant to what the doomsayers are saying. The ability to sequence a long enough DNA strand to encompass a minimal genome. It's great science, but it's not something you need to make bioweapons. | 17:03 |
| lepton | true. It seems like the reporting on it is pretty sensationalist, both in the "we're technological gods and make life from scratch," "we're playing god and the world is in great danger" | 17:06 |
| lepton | rather than "cool, a successful demonstration of a genetics technique" | 17:06 |
| QuantumG | not to mention that they're talking about the genome transplant as being new... when it's not, they did that a year ago. | 17:07 |
| QuantumG | .. and no mention of the genome watermarking | 17:10 |
| QuantumG | which is awesome | 17:10 |
| lepton | oh? | 17:17 |
| QuantumG | yeah, they have a published standard somewhere and they're putting together a serial number database and encouraging (future) researchers to watermark all DNA they write. | 17:18 |
| QuantumG | he talks about it in http://www.youtube.com/watch?v=tcazafdJmPE | 17:18 |
| lepton | interesting | 17:23 |
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| fenn | fun fun fun http://fennetic.net/irc/IMG_0856.JPG http://fennetic.net/irc/IMG_0857.JPG | 18:33 |
| QuantumG | DIY electron microscope? | 18:35 |
| fenn | just a dissection scope, not even really what i consider a microscope | 18:35 |
| QuantumG | ahh | 18:37 |
| lepton | What's the image of (chip specifically) | 18:41 |
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| genehacker | are those gold bonded wires? | 18:57 |
| fenn | yes | 18:59 |
| fenn | some prom chip from an old motherboard i think | 18:59 |
| genehacker | hmmm... I'm going to need to do some reestimates on the profitability of ewaste gold extraction | 19:20 |
| genehacker | I thought microchips contained less gold than that | 19:20 |
| genehacker | oh blast doctorow is in austin today and I'm not | 19:36 |
| genehacker | oops | 19:36 |
| genehacker | oh well | 19:36 |
| kanzure | meh | 19:37 |
| genehacker | it's a book signing | 19:39 |
| genehacker | not worth it | 19:39 |
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| neobii | okay... where to start | 20:50 |
| kanzure | :) | 20:50 |
| neobii | is there like an online syllabus to start with diy? | 20:51 |
| kanzure | http://openwetware.org/wiki/DIYbio/FAQ | 20:51 |
| kanzure | might be helpful? | 20:51 |
| neobii | yeah I watched a video of someone programming something with netbeans | 20:52 |
| neobii | the vetier lab or something | 20:52 |
| neobii | any place with circuit diagrams? | 20:53 |
| -!- _how is now known as ferric | 20:54 | |
| kanzure | circuit diagrams for what? electronics? regulation networks? | 20:54 |
| neobii | I think I'll read these things | 20:54 |
| neobii | like teh gel boxes don't have circuit diagrams | 20:55 |
| neobii | have you read the boook sequence analysis in a nutshell? | 20:56 |
| kanzure | no | 20:56 |
| kanzure | (also i might be falling asleep) | 20:56 |
| neobii | haha | 20:56 |
| neobii | okay | 20:57 |
| QuantumG | http://oreilly.com/catalog/9780596004941 | 20:57 |
| neobii | it will give me time to look all this stuff over | 20:57 |
| neobii | and barrage soem lucky man with questions | 20:57 |
| QuantumG | Released: January 2003 | 20:57 |
| neobii | oo | 20:57 |
| neobii | 2003 gross | 20:57 |
| QuantumG | wow, I wonder if they've updated it | 20:57 |
| neobii | I wouldn't read a webdesign book from that long ago | 20:58 |
| QuantumG | they need an update for that book at least every 2 years | 20:58 |
| neobii | yeah | 20:58 |
| neobii | oriely always lists what edition the book is | 20:58 |
| neobii | if it doesn't say 2nd edition | 20:58 |
| neobii | then it's trash | 20:58 |
| neobii | did anyone watch the shot glass dna extraction? | 21:02 |
| neobii | is it just a basic non-polar organic extraction? | 21:03 |
| neobii | and they are using isopropl gross | 21:03 |
| neobii | they'd be much better off using petroleum ether or hexane | 21:03 |
| neobii | nwonwoownownonwo talk to me! I must know everything! | 21:20 |
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| neobii | so any begining books out there? | 22:35 |
| klafka | venter | 22:51 |
| klafka | the venter thing isn't that as big a deal as the news is making it | 22:51 |
| neobii | yeah seems like | 22:53 |
| neobii | okay | 22:53 |
| neobii | so what do gel box's do? | 22:53 |
| neobii | d you know | 22:53 |
| klafka | um well they filter particulate based on size | 22:53 |
| klafka | you load the wells with whatever, apply current and since you have a positive and negative end, the whatever in the wells that is negatively charged is gonna be attracted to the other end and move | 22:54 |
| klafka | how fast it moves is dependent on how big it is | 22:54 |
| neobii | so the proteins are usually the biggest? | 22:55 |
| klafka | well typically you put DNA in it | 22:55 |
| klafka | or proteins | 22:55 |
| klafka | not mixed together | 22:55 |
| neobii | yeah what does it do to the dna? | 22:56 |
| neobii | is it a tool for sequencing it? | 22:56 |
| klafka | sometimes | 22:56 |
| klafka | not so much anymore | 22:56 |
| neobii | so what does it do to the dna? | 22:57 |
| klafka | http://en.wikipedia.org/wiki/Northern_blot | 22:57 |
| klafka | it separates it out into different sizes | 22:57 |
| neobii | yeah but the gel box is used because it's diy? | 22:58 |
| klafka | i guess people in DIY bio use them because they are cheap | 22:58 |
| klafka | you can use it for genetic engineering | 22:58 |
| klafka | for like splicing plasmids and shit | 22:58 |
| klafka | iirc | 22:58 |
| neobii | yeah I haven't connected connected the dots on that | 22:59 |
| neobii | I have an arduino and I've done some projects with that | 22:59 |
| neobii | but I'm just now getting into diybio | 22:59 |
| klafka | http://www.infoplease.com/cig/biology/fundamentals-genetic-engineering.html | 23:00 |
| klafka | i haven't done that stuff in a long time | 23:00 |
| neobii | yeah I have a cloud that I can process a genome with | 23:00 |
| klafka | lol | 23:01 |
| neobii | if it requires a lot of computational power | 23:01 |
| neobii | but | 23:01 |
| neobii | I don't know where to start | 23:01 |
| klafka | to do genome sequencing you need a modern sequencing technology | 23:01 |
| neobii | or even if I can process a genome | 23:01 |
| klafka | you can totally process a genome if you have the raw data | 23:01 |
| neobii | or even if that is in the diy realm | 23:01 |
| klafka | sort of | 23:01 |
| klafka | it's in the "i really know whta i'm doing and have lots of money" diy realm | 23:02 |
| neobii | hahah | 23:02 |
| neobii | well I mean what if someone used a botnet to process genome sequences | 23:02 |
| klafka | sequencing a genome is not a trivial task, to do it in a decent amount of time you want to use a NGS machine like a 454, SOLiD, or illumina | 23:02 |
| klafka | + you have to purify and amplify the genomic material | 23:04 |
| klafka | then once you have back the raw reads from the NGS machine you can assemble it against a ref genome | 23:04 |
| neobii | I was looking at some of the dna extractions | 23:04 |
| klafka | which is where you'd need a big cloud | 23:04 |
| neobii | it looked like a simple organic extraction | 23:04 |
| klafka | yeah extracting it isn't hard | 23:05 |
| klafka | and you can even buy dna purification kits | 23:05 |
| klafka | i mean you can send your DNA off to some of these companies that do whole genome sequencing and they just ship you back the unassembled genome contigs | 23:06 |
| neobii | have you ever seen how much the 454 | 23:06 |
| neobii | well I want to try to sequence stuff like carrots | 23:06 |
| neobii | or strawberries | 23:06 |
| klafka | how much a 454 costs? | 23:06 |
| klafka | cool | 23:06 |
| klafka | then you won't have a reference genome nad you have to do what is called de novo assembly | 23:06 |
| klafka | that requires a much higher level of coverage | 23:06 |
| klafka | and with given NGS technology is much harder | 23:07 |
| klafka | although i think the new pac bio machine will change things a lot | 23:07 |
| klafka | basically to sequence an organism that has never been sequenced costs a LOT of money and requires quite a bit of expertise and i'd say it's out of the range of the hobbyist currently | 23:09 |
| klafka | although i hope that will change soon | 23:09 |
| neobii | dang | 23:09 |
| neobii | haha | 23:09 |
| klafka | well "soon" in the next 20 years | 23:09 |
| klafka | the cost of sequencing is decreasing something like by a magnitude of 10 fold every year | 23:09 |
| neobii | nice | 23:09 |
| neobii | so what exactly do you do in the diybio then haha | 23:10 |
| klafka | idk | 23:10 |
| klafka | probably umm do some simple genetic engineerig | 23:10 |
| klafka | engineering | 23:10 |
| klafka | i don't do DIY bio frankly | 23:10 |
| neobii | yeah maybe it's a topic that people want to exist so badly that it does | 23:11 |
| klafka | it's important | 23:11 |
| klafka | but it's not at the level people want it to be | 23:11 |
| klafka | there is trying to be a sort of open source next gen sequencer | 23:11 |
| klafka | it'd be cool if they could have a DIY sequencer | 23:11 |
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| klafka | http://www.polonator.org/ | 23:12 |
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| neobii | yeah it's like just gimmie a circuit diagram | 23:12 |
| neobii | and the mouser electronics part numbers | 23:12 |
| neobii | and I can make one haha | 23:12 |
| klafka | oh this has open protocols | 23:13 |
| klafka | but not open design specs | 23:13 |
| klafka | when we can 3d print like useful things | 23:13 |
| klafka | that's when things willreally start to happen | 23:13 |
| klafka | imo | 23:13 |
| klafka | also wheen we can print circuit boards at home | 23:13 |
| neobii | yeah | 23:13 |
| neobii | go look at copper etching | 23:13 |
| neobii | have you ever done a circuit like that? | 23:13 |
| klafka | no | 23:14 |
| klafka | i've never done anything with circuits | 23:14 |
| neobii | aha | 23:14 |
| * klafka is a computational biologist | 23:14 | |
| neobii | what exactly is that? | 23:14 |
| QuantumG | klafka: what sort of stuff do you do? | 23:14 |
| klafka | i model biological systems computationally, or analyze biological data, or a combination of the two | 23:14 |
| klafka | QuantumG, I mainly work in network reconstruction via graphical models | 23:15 |
| QuantumG | cool. Have you published anything? | 23:15 |
| klafka | but i also do like area specific stuff, i am doing like some analysis for this lab working on presbycusis | 23:15 |
| klafka | not yet :( this is my first year as a grad student, my advisor and I came up w/ a cool idea that is hopefully publishable, but he taught the two classes i took this quarter,, killed both of our abilities to do much research | 23:16 |
| neobii | http://www.bcae1.com/circuitboardetch.htm | 23:16 |
| QuantumG | well, good luck with it | 23:16 |
| klafka | thanks we've mainly been doing a lot of stuff like http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000358 | 23:17 |
| neobii | yeah that's over my head | 23:18 |
| neobii | are you using python? | 23:20 |
| klafka | actually yes | 23:20 |
| klafka | heh | 23:20 |
| neobii | yeah that's what I Thought | 23:20 |
| klafka | python with some C | 23:20 |
| neobii | I know you can program with python in maya | 23:20 |
| neobii | maybe in autocad to | 23:21 |
| neobii | o | 23:21 |
| klafka | although matlab has really upped their game so my advisor si thinking of maybe writing code in clojure and then running it from matlab | 23:21 |
| neobii | yeah 3d printing is going to be really usefull | 23:21 |
| klafka | someday | 23:21 |
| neobii | whenever I get a motor from the store | 23:21 |
| neobii | I can never find a belt that matches that and a cog | 23:22 |
| klafka | idk when 3d printing can do like nano level resolution or micro level resolution w/ heterogenous sources | 23:23 |
| neobii | so you are talking about printing dna | 23:23 |
| klafka | no just whatever | 23:23 |
| neobii | print the higgs boson? | 23:24 |
| klafka | no i'm thinking more like you can print complex machinery | 23:24 |
| klafka | w/ circuitry | 23:24 |
| klafka | and chips | 23:24 |
| neobii | what I would be interested in is the abstraction of the dna sequence into a type of programming | 23:25 |
| klafka | well the problem is it's really complicated | 23:26 |
| neobii | yeah it's crazy | 23:26 |
| klafka | like there is this thing called the central dogma right, parts of dna code for mRNA which code for protein | 23:27 |
| klafka | proteins are the things that generally do shit | 23:27 |
| neobii | yeah teh amino acids correct? | 23:27 |
| klafka | but the thing is there are numerous mRNA that alter how other pieces of DNA work, there are pieces of DNA that physically interact with other pieces of DNA and change how they make proteins, there are other parts of DNA surrounding the genes that depending on what proteins or other things bind to it effect how other genes | 23:28 |
| fenn | meep | 23:29 |
| klafka | basically you have the basic linear pathway of dna -> protein, but you also have mRNA -> DNA, protein -> DNA, DNA -> DNA | 23:29 |
| klafka | the field of synthetic biology is specifically trying to abstract DNA sequencing into a form of programming, stuff like biobricks | 23:29 |
| klafka | http://bbf.openwetware.org/ | 23:29 |
| neobii | yeah I read abotu biobricks | 23:29 |
| fenn | chris anderson is giving a presentation on clotho (bioCAD) on the 29th(?) | 23:30 |
| fenn | should i go? | 23:30 |
| klafka | idk i've never heard of it | 23:30 |
| fenn | eh it's at the dojo, i'll probably be there anyway :P | 23:30 |
| klafka | is that like your hackerspace? | 23:31 |
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| fenn | yeah | 23:31 |
| klafka | i've yet to actually go to our hackerspace here | 23:32 |
| klafka | so busy | 23:32 |
| fenn | apparently anselm levskaya used to work with chris anderson | 23:33 |
| klafka | who is that? | 23:33 |
| fenn | my potential housemate | 23:33 |
| fenn | my world is imploding :\ | 23:33 |
| klafka | um cool | 23:33 |
| fenn | i was like "oh, chris anderson? didnt he write a wired article about skdb and stuff?" "no not that one, the other chris anderson" | 23:35 |
| fenn | then he turns up in my email a few days later | 23:35 |
| fenn | klafka you know much about "cloud computing"? | 23:36 |
| kanzure | you could end up with worse housemates than anselm | 23:36 |
| * kanzure is doing "cloud computing" now :/ | 23:36 | |
| fenn | yeah he's great | 23:36 |
| klafka | i know a bit | 23:36 |
| kanzure | google app engine, amazon aws ec2, and everything :/ | 23:36 |
| fenn | woo | 23:36 |
| kanzure | i'm such a whore | 23:36 |
| klafka | what's the biggest ec2 instance you've made? | 23:36 |
| fenn | ok so what do you do with free compute time? | 23:36 |
| klafka | er # of computers? | 23:36 |
| kanzure | fenn: what? | 23:36 |
| kanzure | klafka: right now, 0 :) | 23:36 |
| klafka | give them to me | 23:36 |
| fenn | i'm trying to figure out what to do with this, should probably be focusing on, you know, stuff that matters | 23:37 |
| kanzure | "do with this" this=? | 23:37 |
| klafka | how'd you get free compute time? amazon grant | 23:37 |
| fenn | free $100 of ec2 | 23:37 |
| kanzure | klafka: not free | 23:37 |
| kanzure | oh, for fenn | 23:37 |
| kanzure | fenn: maybe the whole genome analysis stuff from melanie swan and raymond mccauley? | 23:37 |
| kanzure | the ec2 whole genome stuff. | 23:37 |
| fenn | amazon gave coupons to everyone in the hacker dojo machine learning class | 23:37 |
| klafka | aah | 23:37 |
| klafka | kanzure what's that? | 23:37 |
| kanzure | http://diygenomics.org/ | 23:38 |
| kanzure | hm wait | 23:38 |
| kanzure | bowtie | 23:38 |
| kanzure | and crossbow | 23:38 |
| kanzure | http://bowtie-bio.sourceforge.net/crossbow/index.shtml | 23:38 |
| kanzure | "Crossbow is a scalable software pipeline for whole genome resequencing analysis. It combines Bowtie, an ultrafast and memory efficient short read aligner, and SoapSNP, an accurate genotyper, within Hadoop to distribute and accelerate the computation with many nodes." | 23:38 |
| kanzure | "The pipeline can accurately analyze over 35x coverage of a human genome in one day on a 10-node local cluster, or in 3 hours for about $100 using a 40-node, 320-core cluster rented from Amazon's EC2 utility computing service. " | 23:39 |
| fenn | it's hard to think of neat stuff to do when you have no data to work with | 23:39 |
| kanzure | if you need a genome, i have a few | 23:39 |
| fenn | for this to be relevant i'd need like 1000 genomes | 23:39 |
| klafka | if you do you should submit them to pubmed | 23:39 |
| kanzure | these are private ;) | 23:39 |
| fenn | how many human genomes have been sequenced? | 23:39 |
| klafka | pfft private data sucks | 23:39 |
| klafka | a lot | 23:39 |
| kanzure | depends on which coverage | 23:39 |
| kanzure | klafka: i agree | 23:39 |
| kanzure | *what coverage | 23:39 |
| klafka | lol yeah | 23:39 |
| kanzure | one of the weirdest things lately for me is this concept of privacy | 23:39 |
| fenn | i dont care about 100% coverage | 23:39 |
| fenn | privacy is bullshit | 23:39 |
| kanzure | like, why in the fuck do all you fucks want me to sign so many DNAs | 23:40 |
| kanzure | NDAs | 23:40 |
| klafka | NDA | 23:40 |
| klafka | heh | 23:40 |
| fenn | secrecy != privacy | 23:40 |
| fenn | they're both stupid though | 23:40 |
| kanzure | heh | 23:40 |
| kanzure | so am i aloud to tell you about capital factory, or not? | 23:40 |
| * kanzure doesn't know | 23:40 | |
| kanzure | but i probably will anyway | 23:40 |
| fenn | ask foriveness, not permission | 23:40 |
| neobii | are you against both secrecy and privacy? | 23:40 |
| fenn | yes | 23:40 |
| kanzure | um, i just don't understand it half the time | 23:40 |
| kanzure | it doesn't tend to make sense | 23:41 |
| neobii | how do you feel about facebook? | 23:41 |
| neobii | or google monitoring private wifi stuff | 23:41 |
| klafka | mark zuckerberg is an asshole | 23:41 |
| fenn | kanzure: it's probably an evolved mechanism of some sort | 23:41 |
| kanzure | fenn: my lack of understanding? | 23:41 |
| fenn | neobii: facebook is on my shit list because their data is not open | 23:41 |
| kanzure | oh please | 23:42 |
| klafka | see what i don't like is how people give up their data to these people but then they sell it | 23:42 |
| fenn | kanzure: the feeling of privacy in general | 23:42 |
| neobii | what do you mean? | 23:42 |
| kanzure | everyone loves hating facebook this week | 23:42 |
| klafka | like i feel that way about 23andme | 23:42 |
| klafka | i've hated facebook before hating it was cool | 23:42 |
| kanzure | let me guess, yet another diaspora lover | 23:42 |
| klafka | um no | 23:42 |
| neobii | you can grab alot of data through the fbql | 23:42 |
| klafka | god that's such a hype factory | 23:42 |
| kanzure | i can't believe they raised $170k without any fucking code | 23:42 |
| neobii | or whatever it is | 23:42 |
| kanzure | neobii: yes but you have to comply with their privacy policies and other things like that | 23:42 |
| klafka | kanzure, it's coz they got that nyt article | 23:42 |
| kanzure | fenn got a nytm article, why doesn't he have six digits yet? | 23:43 |
| klafka | did he? | 23:43 |
| kanzure | sort of. | 23:43 |
| klafka | link? | 23:43 |
| neobii | yeah | 23:43 |
| neobii | recently | 23:43 |
| klafka | sorry nyt article on how you're gonna kill facebook | 23:43 |
| neobii | they said | 23:43 |
| kanzure | http://www.nytimes.com/2010/05/02/magazine/02self-measurement-t.html | 23:43 |
| neobii | that you were able to store data from facebook | 23:43 |
| neobii | it was ilke 2 weeks ago | 23:43 |
| kanzure | people have been banned for scraping data from facebook | 23:43 |
| fenn | well, i did get a fancy job interview out of it, but they decided not to hire because i didnt know java. hard to say whether that was good or bad | 23:43 |
| neobii | it was because people were having problems deleting stuff from the cache after 1 day | 23:44 |
| klafka | also kanzure about crossbow, i think that clovr uses that in their pipeline | 23:44 |
| kanzure | clovr=? | 23:44 |
| neobii | that was the original policy | 23:44 |
| klafka | http://clovr.igs.umaryland.edu/ | 23:44 |
| klafka | fenn bizarre | 23:44 |
| kanzure | fenn: an interview? that's all? | 23:44 |
| fenn | and lunch :P | 23:45 |
| fenn | seriously i dont know how to monetize 3 lines of media exposure | 23:45 |
| fenn | 'buy my book!' | 23:45 |
| klafka | 'BUY MY BOOK!' | 23:45 |
| fenn | you're hired, mister | 23:45 |
| klafka | (like the critic) | 23:45 |
| fenn | should i start making life sized cardboard cutouts? | 23:46 |
| kanzure | so they would be what, | 23:46 |
| kanzure | 3 feet tall? | 23:46 |
| kanzure | i talked with these guys yesterday: http://chaoticmoon.com/ | 23:47 |
| kanzure | still not sure what they, uh, do.. | 23:47 |
| fenn | explanation, for generation Z: http://www.youtube.com/watch?v=aDTwO0TlwOU | 23:47 |
| klafka | also i mainly mention clovr kanzure because orbitz works on it | 23:47 |
| klafka | ooh crafted with awesomeness | 23:47 |
| neobii | it looks like they just make mobile phone apps | 23:48 |
| kanzure | sort of | 23:48 |
| neobii | probably with cocoa | 23:48 |
| kanzure | they take YOUR app, and then "make it better" | 23:48 |
| kanzure | meh | 23:48 |
| klafka | yeah | 23:48 |
| klafka | their website sucks | 23:48 |
| kanzure | i was also talking with these guys yesterday: http://8020.vizseek.com/ | 23:48 |
| kanzure | terrible website too | 23:48 |
| neobii | ohhhh | 23:49 |
| neobii | chaotic moon | 23:49 |
| neobii | are interaction designers | 23:49 |
| kanzure | wtf does that mean | 23:49 |
| klafka | they design interfaces basically | 23:49 |
| neobii | yeah | 23:49 |
| kanzure | meh | 23:50 |
| klafka | one of my advisors does a lot of that stuff | 23:50 |
| neobii | it's an emerging field | 23:50 |
| klafka | she works w/ eyetracking hardware | 23:50 |
| neobii | I'm a web app developer | 23:50 |
| kanzure | neobii: i'm sorry | 23:50 |
| neobii | and you'd be suprised how essential it is | 23:50 |
| neobii | and how oever looked it is | 23:50 |
| fenn | i think we would survive without web apps | 23:50 |
| klafka | works on stuff like using eye tracking hardware to create next gen interfaces | 23:50 |
| kanzure | let me guess, you're going to push rails on me next | 23:50 |
| neobii | nah | 23:50 |
| klafka | LOL | 23:50 |
| kanzure | let's hear it | 23:50 |
| kanzure | oh, then maybe it's nosql | 23:50 |
| neobii | haha | 23:50 |
| neobii | cassandra!!!!!!!! | 23:51 |
| klafka | wha'ts nosql? | 23:51 |
| * kanzure sighs | 23:51 | |
| neobii | haha | 23:51 |
| neobii | I know | 23:51 |
| klafka | oh | 23:51 |
| neobii | don't feel like splicing accoc arrays? | 23:51 |
| fenn | hm i'm all out of buzzwords tonight | 23:51 |
| neobii | bigtable | 23:51 |
| kanzure | graph database! mongodb! couchdb! memcache! | 23:51 |
| neobii | haha | 23:51 |
| kanzure | directededge! | 23:51 |
| klafka | heh couchdb | 23:51 |
| neobii | I like to do new media stuff with the web design | 23:51 |
| kanzure | json! haml! yaml! | 23:52 |
| neobii | I'm setting up a red5 server | 23:52 |
| kanzure | what the fuck | 23:52 |
| klafka | it seems like most biological data is sort of setup like nosql | 23:52 |
| klafka | setups | 23:52 |
| kanzure | i played around with red5 a few days ago. meh. | 23:52 |
| neobii | haha yeah I noticed that the bio brick wasn't in json but in xml | 23:52 |
| kanzure | sbml is also in xml :/ | 23:52 |
| klafka | sbml is xml | 23:52 |
| klafka | :P | 23:52 |
| kanzure | well, yes. | 23:52 |
| klafka | also MiNiML | 23:52 |
| neobii | yeah well | 23:52 |
| neobii | I have some ideas for some hobby electronics | 23:52 |
| neobii | like a highfive machine | 23:52 |
| neobii | using a flexiforce pressure sensor | 23:53 |
| neobii | arduino | 23:53 |
| kanzure | maybe it will help me solve the one hand clapping problem | 23:53 |
| neobii | w/ flash | 23:53 |
| klafka | haha | 23:53 |
| neobii | that will connect to an rtmp server | 23:53 |
| neobii | where you can high five people online | 23:53 |
| kanzure | why rtmp? i thought you said you do web development | 23:53 |
| neobii | haha rtmp as an open socket server is much better than using sockets through php | 23:54 |
| neobii | for flash | 23:54 |
| neobii | I eman | 23:54 |
| klafka | it's like a new take on the old fufme device | 23:54 |
| neobii | red5 is an open socket server | 23:54 |
| klafka | except w/ high fives | 23:54 |
| fenn | you could build two of them and hook it up to The Clapper (tm) | 23:54 |
| kanzure | if i had ops, i'd kickban you for mentioning php | 23:54 |
| neobii | haha | 23:54 |
| neobii | now you are going to push python on me right? | 23:54 |
| kanzure | probably | 23:54 |
| neobii | python on rails | 23:54 |
| klafka | django | 23:54 |
| neobii | hehe | 23:54 |
| klafka | or perhaps that other thing | 23:54 |
| neobii | jquery? | 23:55 |
| kanzure | web.py, django, cherrypy, pyjs, pydesktop, pypy | 23:55 |
| neobii | joomla | 23:55 |
| klafka | pylons | 23:55 |
| kanzure | joomla is php | 23:55 |
| neobii | yeah I know | 23:55 |
| kanzure | you fail | 23:55 |
| neobii | cms | 23:55 |
| fenn | didnt you write web.py? are you just grepping your logs now? | 23:55 |
| klafka | pypy is a python compiler kanzure | 23:55 |
| kanzure | klafka: do'h | 23:55 |
| kanzure | fenn: no, aaron swartz (rss dude) did web.py | 23:55 |
| kanzure | web.py is the name of a python web framework | 23:55 |
| neobii | joomla is scalable within a cloud | 23:56 |
| klafka | it's like the successor to unladen swallow | 23:56 |
| neobii | http://www.cloudaccess.net/ | 23:56 |
| kanzure | web.py is also the pathetic name of the file i wrote and committed to skdb | 23:56 |
| klafka | heh | 23:56 |
| kanzure | skdb.git i mean | 23:56 |
| fenn | well it's a stupid name for a project too | 23:56 |
| kanzure | agreed | 23:56 |
| fenn | program.py | 23:56 |
| kanzure | namespace conflicts galore | 23:56 |
| kanzure | test.py | 23:56 |
| fenn | pycam | 23:56 |
| klafka | kanzure, i think that should be a good goal for DIYers | 23:57 |
| kanzure | that's no buzzword | 23:57 |
| kanzure | klafka: ? | 23:57 |
| fenn | to maximize namespace conflicts? | 23:57 |
| klafka | to develop an open design NGS sequencer based off the polonator protocols that can be largely built via a 3d printer | 23:57 |
| kanzure | too bad polonator isn't open source | 23:57 |
| kanzure | it claims it is, but that's shit | 23:57 |
| klafka | no it's not | 23:57 |
| klafka | but it's protocols are | 23:57 |
| klafka | so you could use them to build an OS design | 23:58 |
| kanzure | i'll pay you to do it | 23:58 |
| klafka | that's what i'm suggesting | 23:58 |
| klafka | i'd help but i h ave no um engineering expertise | 23:58 |
| klafka | :P | 23:58 |
| kanzure | nobody else does either | 23:58 |
| kanzure | not even the "engineers" | 23:58 |
| klafka | true | 23:58 |
| fenn | i have expertise galore | 23:59 |
| kanzure | yes but i offer you money and you just move further away | 23:59 |
| fenn | isnt polonator just an inkjet? | 23:59 |
| klafka | but i think when either sequencers become cheap enough that we can buy them easily or we can implememt the protocols in a machine we can build easy enough | 23:59 |
| klafka | fenn i have nfc | 23:59 |
| kanzure | as far as i can tell, polonator is just vaporware | 23:59 |
| fenn | kanzure i hope you realize you aren't exactly a reliable source of funding | 23:59 |
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