--- Day changed Thu May 20 2010 00:14 -!- Phreedom [~quassel@109.254.6.63] has quit [Ping timeout: 248 seconds] 00:20 -!- shepazu [~schepers@76-253-3-102.lightspeed.sntcca.sbcglobal.net] has joined #hplusroadmap 01:08 < fenn> what do i do with $100 of amazon EC2? 01:09 < 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 01:10 < fenn> tomorrow meaning friday 01:10 < fenn> and more qs stuff at maker faire 01:11 < fenn> woah weird. i just googled "aether blog" because i wa thinking about setting up a blog, look what i get: http://aether.com/ 01:17 -!- randallagordon [~randallag@c-98-232-217-100.hsd1.or.comcast.net] has quit [Ping timeout: 240 seconds] 01:34 -!- clemux_ is now known as clemux 01:52 -!- randallagordon [~randallag@c-71-59-165-136.hsd1.or.comcast.net] has joined #hplusroadmap 02:20 -!- quantumkat [~kat@ip72-196-96-148.ga.at.cox.net] has quit [Ping timeout: 240 seconds] 02:22 -!- Alystair [Alystair@bas1-toronto10-1279556304.dsl.bell.ca] has quit [Ping timeout: 268 seconds] 02:25 -!- quantumkat [~kat@ip72-196-96-148.ga.at.cox.net] has joined #hplusroadmap 02:32 < 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? 02:33 < Utopiah> (wasn't kickstarter or capitalfactory) 03:20 -!- marainein [~marainein@220-253-153-170.VIC.netspace.net.au] has joined #hplusroadmap 05:07 -!- marainein [~marainein@220-253-153-170.VIC.netspace.net.au] has quit [Quit: Ex-Chat] 05:34 -!- jm|earth [~jm@p57B9E2BC.dip.t-dialin.net] has quit [Ping timeout: 260 seconds] 05:52 -!- quantumkat [~kat@ip72-196-96-148.ga.at.cox.net] has quit [Ping timeout: 265 seconds] 05:55 -!- quantumkat [~kat@ip72-196-96-148.ga.at.cox.net] has joined #hplusroadmap 06:34 -!- parolang [~user@8e4a01246100775874c4f448e9887093.oregonrd-wifi-1261.amplex.net] has joined #hplusroadmap 06:47 < kanzure> fenn: you could do rendering of reprap stuff in ec2, whole genome analysis 06:48 < kanzure> Utopiah: it had a 'p' and the word 'fund' in it i think 06:48 < kanzure> abundance fund? 06:51 < Utopiah> nop, plus I dont think you can count b and b as revert p 06:51 < Utopiah> b and d 07:01 -!- shepazu [~schepers@76-253-3-102.lightspeed.sntcca.sbcglobal.net] has quit [Quit: shepazu] 07:19 < 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) 08:44 -!- klafka [~klafka@cpe-66-66-5-254.rochester.res.rr.com] has joined #hplusroadmap 08:56 -!- wolfspraul [~wolfsprau@58.41.35.176] has joined #hplusroadmap 08:57 -!- wolfspraul [~wolfsprau@58.41.35.176] has quit [Client Quit] 09:01 -!- wolfspraul [~wolfsprau@58.41.35.176] has joined #hplusroadmap 09:27 -!- thesnark [enderkillb@dhcp-84-252.me.utexas.edu] has joined #hplusroadmap 09:28 < thesnark> hey all 09:32 < thesnark> damn, people must be at lunch 09:34 -!- thesnark [enderkillb@dhcp-84-252.me.utexas.edu] has quit [Quit: ""] 10:01 -!- Phreedom [~quassel@109.254.6.63] has joined #hplusroadmap 10:48 -!- nchaimov [nchaimov@c-71-237-208-209.hsd1.or.comcast.net] has quit [Ping timeout: 265 seconds] 10:49 -!- nchaimov [~cowtown@c-71-237-208-209.hsd1.or.comcast.net] has joined #hplusroadmap 10:53 -!- wolfspraul [~wolfsprau@58.41.35.176] has quit [Quit: leaving] 10:59 -!- wolfspraul [~wolfsprau@58.41.35.176] has joined #hplusroadmap 11:05 -!- shepazu [~schepers@client-235-129.events.shownets.net] has joined #hplusroadmap 11:14 -!- wolfspraul [~wolfsprau@58.41.35.176] has quit [Quit: leaving] 11:17 -!- shepazu [~schepers@client-235-129.events.shownets.net] has quit [Ping timeout: 248 seconds] 11:19 -!- shepazu [~schepers@client-235-129.events.shownets.net] has joined #hplusroadmap 11:31 -!- shepazu [~schepers@client-235-129.events.shownets.net] has quit [Quit: shepazu] 11:53 -!- lepton [~lepton@ma90736d0.tmodns.net] has joined #hplusroadmap 12:01 -!- lepton [~lepton@ma90736d0.tmodns.net] has quit [Remote host closed the connection] 12:01 -!- lepton [~lepton@ma90736d0.tmodns.net] has joined #hplusroadmap 12:04 < lepton> Paying for closed source software is making me really really unhappy this week 12:05 < 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" 12:09 -!- drewfer [~drewfer@67.58.77.138] has joined #hplusroadmap 12:10 < kanzure> hello drewfer 12:11 < 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> :) 12:12 < 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 12:49 < fenn> i've been playing with the cnc a lot lately: http://fennetic.net/irc/idler_brackets.jpg 12:51 < lepton> Nice 12:51 < lepton> what control software are you using? 13:06 < 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.. 13:07 < 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 13:08 < 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 13:09 < lepton> I suppose you could SSH into the host without vmware tools... 13:09 -!- ferrouswheel [~joel@121-98-81-17.bitstream.orcon.net.nz] has quit [Ping timeout: 245 seconds] 13:11 -!- ferrouswheel [~joel@121-98-81-17.bitstream.orcon.net.nz] has joined #hplusroadmap 13:13 -!- Incarnation [~lorem@66.51.248.231] has quit [] 13:17 -!- shepazu [~schepers@client-235-129.events.shownets.net] has joined #hplusroadmap 13:18 < fenn> lepton: mach 3 :( 13:18 < fenn> it's icky 13:24 < lepton> Why not EMC2? 13:37 < fenn> because it's already set up with mach 3 13:40 < 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 13:48 -!- shepazu [~schepers@client-235-129.events.shownets.net] has quit [Quit: shepazu] 13:57 -!- Redeemer [~lorddeeme@c-75-72-218-226.hsd1.mn.comcast.net] has joined #hplusroadmap 14:05 -!- shepazu [~schepers@client-235-129.events.shownets.net] has joined #hplusroadmap 14:13 -!- QuantumG [~qg@rtfm.insomnia.org] has quit [Remote host closed the connection] 14:13 -!- QuantumG [~qg@rtfm.insomnia.org] has joined #hplusroadmap 14:16 -!- QuantumG [~qg@rtfm.insomnia.org] has quit [Remote host closed the connection] 14:18 -!- QuantumG [~qg@rtfm.insomnia.org] has joined #hplusroadmap 14:18 < lepton> fenn: what are those brackets for? 14:40 -!- drazak [~drazak@ip-69-162-134-185.static.chi2.systeminplace.net] has joined #hplusroadmap 15:03 < fenn> idler pulleys for the mini mendel reprap 15:03 < fenn> the timing belt was rubbing against the x carriage with the original part 15:05 < fenn> http://fennetic.net/irc/mini_mendel.jpg 15:06 < fenn> it's still kinda sluggish 15:06 < fenn> next is electronics 15:06 < fenn> or should i try to do my homework instead 15:07 -!- zvader_ [~zvader@heckle.icmb.utexas.edu] has joined #hplusroadmap 15:08 -!- Netsplit *.net <-> *.split quits: zvader 15:20 -!- shepazu [~schepers@client-235-129.events.shownets.net] has quit [Quit: shepazu] 15:25 < kanzure> hi zvader_ 15:53 -!- shepazu [~schepers@client-235-129.events.shownets.net] has joined #hplusroadmap 16:11 -!- Phreedom [~quassel@109.254.6.63] has quit [Ping timeout: 276 seconds] 16:17 -!- Phreedom [~quassel@109.254.6.63] has joined #hplusroadmap 16:22 < QuantumG> http://www.youtube.com/watch?v=eoqBSNmYJYI 16:23 < QuantumG> fuckin' doomsayers are at it already. 16:23 < QuantumG> http://www.youtube.com/watch?v=qPE2CnThito 16:38 < lepton> People are silly 16:39 < 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) 16:40 < lepton> Spreading outward into the galaxy to diversify seems like the optimal way to address that issue 16:42 < 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 16:43 < 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" 16:45 < 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" 16:46 < 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 16:47 < 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 16:48 < lepton> :p 16:58 < 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 -!- jrayhawk_ is now known as jrayhawk 17:00 < 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 17:02 < 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 17:03 < 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. 17:06 < 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" 17:07 < 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. 17:10 < QuantumG> .. and no mention of the genome watermarking 17:10 < QuantumG> which is awesome 17:17 < lepton> oh? 17:18 < 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 17:23 < lepton> interesting 17:41 -!- Redeemer [~lorddeeme@c-75-72-218-226.hsd1.mn.comcast.net] has quit [Ping timeout: 240 seconds] 17:51 -!- shepazu [~schepers@client-235-129.events.shownets.net] has quit [Quit: shepazu] 18:22 -!- genehacker [~genehacke@pool-173-57-40-144.dllstx.fios.verizon.net] has joined #hplusroadmap 18:33 < fenn> fun fun fun http://fennetic.net/irc/IMG_0856.JPG http://fennetic.net/irc/IMG_0857.JPG 18:35 < QuantumG> DIY electron microscope? 18:35 < fenn> just a dissection scope, not even really what i consider a microscope 18:37 < QuantumG> ahh 18:41 < lepton> What's the image of (chip specifically) 18:42 -!- lepton [~lepton@ma90736d0.tmodns.net] has quit [Remote host closed the connection] 18:57 < genehacker> are those gold bonded wires? 18:59 < fenn> yes 18:59 < fenn> some prom chip from an old motherboard i think 19:20 < 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 19:36 < genehacker> oh blast doctorow is in austin today and I'm not 19:36 < genehacker> oops 19:36 < genehacker> oh well 19:37 < kanzure> meh 19:39 < genehacker> it's a book signing 19:39 < genehacker> not worth it 20:13 -!- genehacker [~genehacke@pool-173-57-40-144.dllstx.fios.verizon.net] has quit [Ping timeout: 248 seconds] 20:27 -!- JayDugger [~duggerj@pool-173-57-16-175.dllstx.fios.verizon.net] has joined #hplusroadmap 20:29 -!- JayDugger [~duggerj@pool-173-57-16-175.dllstx.fios.verizon.net] has quit [Read error: Connection reset by peer] 20:29 -!- Redeemer [~lorddeeme@c-75-72-218-226.hsd1.mn.comcast.net] has joined #hplusroadmap 20:35 -!- JayDugger [~duggerj@pool-173-57-16-175.dllstx.fios.verizon.net] has joined #hplusroadmap 20:46 -!- JayDugger [~duggerj@pool-173-57-16-175.dllstx.fios.verizon.net] has quit [Quit: Leaving.] 20:46 -!- neobii [~chatzilla@75-30-249-187.lightspeed.dllstx.sbcglobal.net] has joined #hplusroadmap 20:48 -!- ferric is now known as _why 20:49 -!- _why is now known as _how 20:50 < neobii> okay... where to start 20:50 < kanzure> :) 20:51 < 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? 20:52 < neobii> yeah I watched a video of someone programming something with netbeans 20:52 < neobii> the vetier lab or something 20:53 < neobii> any place with circuit diagrams? 20:54 -!- _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 20:55 < neobii> like teh gel boxes don't have circuit diagrams 20:56 < 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 20:57 < 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 20:58 < 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 21:02 < neobii> did anyone watch the shot glass dna extraction? 21:03 < 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 21:20 < neobii> nwonwoownownonwo talk to me! I must know everything! 21:39 -!- Overand is now known as Kenneth_ 21:39 -!- Kenneth_ is now known as Overand 21:46 -!- Redeemer [~lorddeeme@c-75-72-218-226.hsd1.mn.comcast.net] has quit [Ping timeout: 240 seconds] 21:59 -!- parolang [~user@8e4a01246100775874c4f448e9887093.oregonrd-wifi-1261.amplex.net] has quit [Remote host closed the connection] 22:35 < neobii> so any begining books out there? 22:51 < klafka> venter 22:51 < klafka> the venter thing isn't that as big a deal as the news is making it 22:53 < 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 22:54 < 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 22:55 < 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 22:56 < 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 22:57 < 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 22:58 < 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 22:59 < 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 23:00 < 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 23:01 < 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 23:02 < 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 23:04 < 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 23:05 < klafka> yeah extracting it isn't hard 23:05 < klafka> and you can even buy dna purification kits 23:06 < 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 23:07 < 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 23:09 < 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 23:10 < 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 23:11 < 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 -!- shepazu [~schepers@76-253-3-102.lightspeed.sntcca.sbcglobal.net] has joined #hplusroadmap 23:12 < klafka> http://www.polonator.org/ 23:12 -!- CIA-55 [cia@208.69.182.149] has quit [] 23:12 < 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 23:13 < 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? 23:14 < 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 23:15 < 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 23:16 < 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 23:17 < klafka> thanks we've mainly been doing a lot of stuff like http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000358 23:18 < neobii> yeah that's over my head 23:20 < 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 23:21 < 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 23:22 < neobii> I can never find a belt that matches that and a cog 23:23 < 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 23:24 < 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 23:25 < neobii> what I would be interested in is the abstraction of the dna sequence into a type of programming 23:26 < klafka> well the problem is it's really complicated 23:26 < neobii> yeah it's crazy 23:27 < 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? 23:28 < 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 23:29 < 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 23:30 < 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 23:31 < klafka> is that like your hackerspace? 23:31 -!- CIA-47 [cia@208.69.182.149] has joined #hplusroadmap 23:31 < fenn> yeah 23:32 < klafka> i've yet to actually go to our hackerspace here 23:32 < klafka> so busy 23:33 < 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 23:35 < 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 23:36 < 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 23:37 < 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? 23:38 < 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." 23:39 < 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 23:40 < 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 23:41 < 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 23:42 < 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 23:43 < 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 23:44 < 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? 23:45 < 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) 23:46 < fenn> should i start making life sized cardboard cutouts? 23:46 < kanzure> so they would be what, 23:46 < kanzure> 3 feet tall? 23:47 < 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 23:48 < 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 23:49 < 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 23:50 < 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 23:51 < 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 23:52 < 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 23:53 < 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 23:54 < 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 23:55 < 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 23:56 < 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 23:57 < 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 23:58 < 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 23:59 < 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