--- Log opened Mon Jul 23 00:00:16 2012
00:09  * kanzure saw batman
00:09 < kanzure> 7zip is definitely not no default, shit
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08:11 < chido> the cover of the latest Nature issue is very h-plus-ish
08:11 < chido> kanzure: how was batman?
08:17 < kanzure> it was okay
08:19 < kanzure> i think they ran out of money and fired the voice actor for bane for the last 25% of the movie
08:20 < delinquentme> but movies arent shot sequentially :D?
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08:25 < delinquentme> so kanzure why 7 zip?
08:25 < kanzure> don't use 7zip
08:25 < kanzure> who told you to use 7zip
08:25 < delinquentme> its actually substantially better than what the 1000 genomes gzip
08:26 < delinquentme> you! lol
08:26 < kanzure> ok just don't use the .7z format
08:26 < kanzure> use something like bzip2 or some shit
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09:30 < delinquentme> ... these zip programs are taking a surprising amount of time..
09:30 < delinquentme> kanzure, any reason why not the .7z format?
09:42 < kanzure> hplusroadmap represeeeeent
09:42 < kanzure> http://www.forbes.com/sites/andygreenberg/2012/07/23/hacker-will-expose-potential-security-flaw-in-more-than-four-million-hotel-room-keycard-locks/
09:46 < delinquentme> you going?
09:46 < kanzure> huh?
09:47 < kanzure> no i'm just saying, an hplusroadmap regular got in the news for an awesome thing.
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10:01 < delinquentme> ohh ic ic
10:06 < AlonzoTG> =P
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10:07 < delinquentme> dude this is really cool
10:07 < delinquentme> http://lgilchrist.com/how-we-got-50-women-to-our-hackathon/
10:08 < delinquentme> I totally love the way they've approached this .. and the icebreakers? someone is an amazing social hacker
10:09 < AdrianG> that must be first
10:09 < kanzure> icebreakers aren't exactly novel?
10:12 < AdrianG> what are the icebreakers they used
10:12 < delinquentme> so rock scissors paper is totally solid
10:12 < delinquentme> and also this thing called people find or something like that?
10:13 < delinquentme> dude a social technology-engrained find someone excercise with a bunch of nerds?
10:13 < delinquentme> like im smiling just talking about it!
10:13 < delinquentme> so smart.
10:14 < AdrianG> rock scissors paper?
10:15 < kanzure> someone should make a "better way to visualize the github repos that you watch"
10:15 < delinquentme> yeah AdrianG
10:16 < AdrianG> delinquentme: what about them
10:16 < AdrianG> i dont get u
10:17 < delinquentme> did you read the article?
10:17 < delinquentme> Its just brilliant that people get nerds and social interaction and came up with something thats cool for the girls too!
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10:24 < kanzure> oh so now only guys can be nerds? are you sure you're thinking straight
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10:27 < delinquentme> kanzure, nah not at all
10:27 < delinquentme> but like everyone likes it when the social introductions go smoothly
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10:33 < delinquentme> soo compression is a pretty intensive operation huh?
10:36 < kanzure> http://peerproduction.net/issues/issue-2/ biohacking stuff.. but it's "journal of peer production" ugh
10:38 < kendoka> teach girls how to hack their ex's facebook
10:38 < kendoka> then once they're hooked you can move on to biohacking
10:40 < delinquentme> HAHAHAHA
10:40 < kanzure> is this what you think about maradydd?
10:40 < delinquentme> kendoka, has some insight here...
10:40 < kanzure> or chido?
10:40 < kanzure> geeze
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10:44 < delinquentme> if someone used rockets and SSDs for genomes
10:45 < delinquentme> that'd be pretty fast :D
10:45 < delinquentme> "high bandwidth"
10:45 < delinquentme> could also use drones
10:45 < delinquentme> but punk kids might shoot those down
10:46  * nsh notes proper bong-passing etiquette
10:46 < delinquentme> lolol
10:48 < nsh> the data processing systems involved with the large hadron collider are worth investigating, if you're interested in how scientists deal with mind-numbing amounts of information
10:48 < delinquentme> nsh, maybe we should just fab nanowires and use that
10:48 < nsh> google tech talk: http://www.youtube.com/watch?v=sfyHdFo5GWE
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10:51 < delinquentme> nsh, but the signal : noise on that is substantial
10:51 < delinquentme> like I've got very simple questions
10:51 < delinquentme> I dont need to know the intricacies
10:52 < delinquentme> just need to know  " can we do simple shit to make genomes transfer faster ?"
10:52 < delinquentme> nmz787, how was ohiopyle??
10:52 < nmz787> ended up going to linn run state park
10:52 < nmz787> near idlewild
10:53 < nsh> delinquentme, why are you interested in this question in particular?
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10:53 < delinquentme> yeahhh! thats a cool place
10:53 < kanzure> delinquentme: ok so why is gzip not an answer?
10:53 < kanzure> delinquentme: have you even tried it?
10:53 < nsh> idlewild are an indie band from scottish western isles
10:53 < kanzure> yashgaroth: hello
10:54 < yashgaroth> whatup
10:54 < delinquentme> kanzure, yeah i just did ... and i've got a little spreadsheet of the packaged sizes
10:54 < kanzure> delinquentme: ok. so what's the problem with that?
10:54 < delinquentme> nsh, Im really interested by the fact that backblaze has no genomics customers
10:54 < delinquentme> and stupid big data is an issue
10:54 < delinquentme> why aren't they being utilized
10:54 < kanzure> not everyone knows about all products
10:54 < delinquentme> they're open source, they're backup and they're substantially cheaper than amazong
10:55 < kanzure> are you just trying to get us to spend money
10:55 < nsh> the teams who produce these data sets are often associated with large academic or commercial institutions with their own in-house storage solutions
10:55 < nsh> which isn't necessarily optimal, but is default
10:56 < kanzure> for a while google was offering to send free hard drives to academics
10:56 < ParahSailin> journal of peer production?
10:56 < kanzure> and then people would load up their data and mail it back
10:56 < yashgaroth> illumina almost lost all their data in a flood a few years ago since they didn't backup
10:56 < kanzure> neat.
10:56 < yashgaroth> they do backups now, I hope
10:57 < ParahSailin> this company sometimes sends hard drives to clients as the delivery
10:57 < kanzure> this is because the cost of sequencing is still greater than the cost of data storage
10:58 < kanzure> if you're spending $20k on a genome you might as well get it on a hard drive or two anyway
10:58 < delinquentme> nsh, exactly its the default way of doing it
10:59 < delinquentme> the default answer to my question is " No weve tried everything and its not that simple "
10:59 < delinquentme> but what if something is being overlooked in this data transfer problem?
10:59 < delinquentme> SURE thats an easy question to ask ... and utterly vacuous without a good answer
10:59 < delinquentme> but.. what if?
10:59 < kanzure> it's not much of a problem.. transferring is still way faster than sequencing
11:00 < kanzure> and OC148 is pretty fast
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11:00 < kanzure> well, i mean oc192
11:02 < kanzure> ooh they have oc768 now.
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11:06 < nsh> a good line of investigation would be: what is the nature of redundancy within genomic data which would lend it a particular genus of algorithmic compression
11:06 < nsh> (sorry, started writing that line a good while ago and got distracted)
11:06 < delinquentme> true and CpG islands would compress well
11:06 < kanzure> well, if he just wants fast transfer, then he should just use lookup tables and things like SNPs
11:07 < delinquentme> HMMM
11:07 < delinquentme> kanzure, so you're saying look at the genome as the default sequence .. save for the differences?
11:07 < yashgaroth> what why would cpg islands compress well
11:08 < kanzure> no, i'm saying just reference the existing remote packets instead of sending the entire genome
11:09 < delinquentme> yashgaroth, offhand? represent the whole sequence as a binary string?
11:09 < yashgaroth> no more so than any other dna sequence
11:09 < delinquentme> if you've got 10000 characters you're cutting down into 1 or 0 thats a substantial compression no?
11:09 < yashgaroth> it's not like they're cgcgcgcgcgcgcgcg everywhere, there's just more CGs than average
11:09 < delinquentme> well even at best the 2bit for ACTG is halved then no?
11:10 < delinquentme> IDK if you were here for my 00=A 10=C 01=T 11=G statement last night
11:10 < yashgaroth> no that's how I'd do it
11:10 < kanzure> delinquentme: so there are other situations where you do a polynomial expansion with a ew hundred thousand terms, and the coefficients and values to things like sine/cosine determine the placement of data
11:10 < kanzure> but often the problem is that this representation takes more space than the actual data
11:10 < ParahSailin> most of the heavy data is short reads
11:11 < kanzure> so it's not really compression
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11:11 < delinquentme> kanzure, im sorry you lost me
11:11 < ParahSailin> assembled scaffolds take up comparatively little space
11:11 < yashgaroth> yeah, most data will be a short sequence (depending on the sequencing method) plus associated confidence levels for each bp
11:11 < delinquentme> ParahSailin, this is true ... are the short reads stored often?
11:11 < kanzure> why cant you just read up on existing algorithms so i don't have to teach you
11:12 < delinquentme> kanzure, simplify
11:12 < ParahSailin> usually clients want those as a deliverable
11:12 < delinquentme> ParahSailin, yashgaroth do labs store the short reads for extended periods of time or just the consensus
11:12 < delinquentme> ?
11:13 < ParahSailin> well a sequencing company keeps those indefinitely
11:13 < delinquentme> kanzure, you're talking signal processing and compression and like I cant pull out whats intelligible from the statement
11:13 < ParahSailin> dunno what labs do with them
11:13 < yashgaroth> depends on the lab...we got a library next-gen sequenced and delivered by hard drive, but in the end we just did a heatmap of enriched sequences
11:15 < yashgaroth> that was all fastq data btw
11:16 < delinquentme> is it a good practice to look to apply open research from academia to computation / processing problems
11:17 < delinquentme> as a way to find good business ventures?
11:17 < delinquentme> IDK. something I've been thinking about ... like how to generalize whats worth developing
11:17 < ParahSailin> assembly based on reference
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11:19 < nmz787> delinquentme: old time compression was just look for a pattern that's common, then remove all those patterns and put in a placeholder that's really short... so the pattern could be 10 bits long, but the placeholder might only be 2 or 3 bits long (as long as the placeholder is unique in that it didn't exist in the dataset before)
11:20 < nmz787> with that you just saved 66% going from 10 bits to 3
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11:22 < audy> I keep all of my reads
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11:22 < audy> I have them on 2 TB hard drives stacked in my office, backed up on another machine and also on Amazon S3
11:22 < audy> just in case the lab explodes
11:23 < audy> I wrote a web app to manage all of this
11:24 < audy> I went to the genomic standards consortium meeting this year and one of the major topics was whether or not to store all of this data
11:24 < audy> One group proposed using lossy compression, another proposed throwing out the reads and just keeping the samples
11:24 < ParahSailin> you paid for it
11:24 < audy> because it's cheaper to re-sequence than to store
11:25 < nmz787> compression could possibly be useful since there are transposons and other repeating elements
11:25 < audy> gzip works well. There's a new compression technique that uses assembly
11:25 < nmz787> but it would have to be a bit smarter than binary compression that exists
11:25 < audy> called quip
11:25 < nmz787> since some transposons are just flipped in orientation
11:26 < nmz787> they could still be compressed with the same symbol, but need an extra bit to show their orientation
11:26 < audy> you could also convert ascii to a 2-bit format
11:26 < nmz787> right
11:26 < nmz787> you'd want to do that first
11:26 < ParahSailin> reads have N
11:27 < delinquentme> http://io9.com/5928274/the-universe-could-tear-itself-apart-sooner-than-anyone-believed
11:27 < audy> ParahSailin I mean post quality control
11:27 < audy> trim the reads based on quality and throw out anything with an N
11:27 < delinquentme> carl had a panic attack =/
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11:29 < delinquentme> buddhist shit is not helping me cope with this.
11:29 < delinquentme> but by the same token doesnt this say that we've got 70% of the energy out there classified as 1 certain thing?
11:30 < delinquentme> IE if we dont know what it is .. its automatically "dark energy" and thus contributing to this "big rip"?
11:30 < yashgaroth> god damnit do you want to talk about sequence storage or not
11:31 < audy> I have 13 illumina runs on EC2, 50 gigs.
11:31 < audy> costs about $5 per month
11:31 < ParahSailin> storage is maybe like the least pressing technological issue
11:32 < yashgaroth> or compression or whatever we're talking about
11:33 < kanzure> yashgaroth: he's actually talking about business ventures -_-
11:33 < kanzure> yashgaroth: it's hard to follow
11:33 < delinquentme> I'm kind of asking about the entire operation
11:33 < delinquentme> and audy has a point ... like $5/month isnt anything substantial
11:34 < delinquentme> and IDK if there are sequencing startups who need a cheap alternative
11:34 < delinquentme> but maybe large sequencing operations DO need long term storage?
11:35 < ParahSailin> an illumina flowcell run costs what, $50k?
11:35 < ParahSailin> storing it is how many 2 TB hard drives?
11:36 < audy> ParahSailin 1
11:36 < audy> ParahSailin uncompressed, including the actual images of the flowcell used to make the base calls
11:36  * audy is talking about GAIIx, not hi-seq
11:36 < audy> delinquentme you want to make a startup based around storing sequence data?
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11:37 < delinquentme> audy, backblaze is a storage service which is really cheap ... moreso than amazon
11:38 < delinquentme> and I've just been wondering about a service based on this ... and the data transfers seem to be the bottleneck
11:38 < audy> delinquentme can you cite a backblaze backup in a publication?
11:40 < delinquentme> umm well I asked them and they said they've got no genomics customers
11:40 < delinquentme> so maybe .. no?  But I havn't searched for a research paper with backblaze mentioned
11:40 < audy> I think backblaze is for backing up your computer
11:40 < audy> like timemachine but in the cloud
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11:42 < ParahSailin> if you are looking for business venture, follow the plutocracy
11:42 < delinquentme> audy, yeah it is
11:42 < delinquentme> but they're also wildly cheap backup
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11:43 < delinquentme> ParahSailin, true ! but useful would be good too
11:43 < nmz787> I might consider an evolution program for this bat http://www.filippidis.org/index/amazing/giant-bat.html
11:43 < delinquentme> unlike zynga
11:43 < nmz787> dracula 2050... after a scientist spliced his own DNA with the bat's, a monster was born
11:46 < audy> ParahSailin what do you mean follow the plutocracy?
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11:49 < delinquentme> follow the $$$
11:50 < audy> gamified location-aware microcoupons?
11:51 < kanzure> no that's what klafka is doing
11:51 < yashgaroth> cloud...blogging?
11:51 < delinquentme> audy, hahah <3
11:51 < delinquentme> yesss the cynics
11:53 < nmz787> delinquentme: so what area /do/ you live in, if not pgh?
11:53 < nmz787> i assumed you were some college dude slumming it up in Oakland
11:53 < delinquentme> nah im like east of PGH
11:54 < delinquentme> but that could change shortly
11:54 < delinquentme> IDK
11:54 < ParahSailin> audy: pick an industry closest to the counterfeiters
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11:54 < ParahSailin> silicon valley and wall st are the top choices
11:55 < nmz787> delinquentme: like, east pittsbugh, north versailles, forest hills?
11:55 < nmz787> what neighborhood
11:55 < delinquentme> greensburg =]
11:56 < delinquentme> its close to the westmoreland mall lol
11:56  * delinquentme feels like such a suburbanite
11:56 < kanzure> it's called.. west more land?
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11:57 < nmz787> ahh
11:58 < nmz787> kanzure: yeah, i figure moreland was west of philly and DC and NYC back in the early days
11:58 < nmz787> so then you had to have a west-moreland
11:58 < nmz787> lol
11:58 < nmz787> its actually a county name too
11:58 < nmz787> westmoreland county
11:58 < kanzure> westmorelandbetterthanthisshittyland
11:58 < audy> ParahSailin pharma
12:04 < delinquentme> lol
12:04 < nmz787> kanzure: I drove past that westmoreland mall a few days ago and was thinking of the origns of the name :P
12:04 < delinquentme> sucks I keep missing you
12:04 < delinquentme> theres a really awesome outdoor air bar here too
12:05 < delinquentme> great place to chill and concept :D
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12:10 < nsh> concept is not a verb
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12:10 < nsh> .wik General Westmoreland
12:10 < hplunny> "William Childs Westmoreland (March 26, 1914 – July 18, 2005) was a United States Army General, who commanded US military operations in the Vietnam War at its peak (1964–68), during the Tet Offensive." - http://en.wikipedia.org/wiki/General_Westmoreland
12:11 < nsh> though the name had vintage before the general
12:11 < audy> I like to concept in the concept den
12:14 < nmz787> .wik "Westmoreland County is a county located in the U.S. state of Pennsylvania. It was founded on February 26, 1773,"
12:14 < hplunny> "Westmoreland County is a county located in the U.S. state of Pennsylvania." - http://en.wikipedia.org/wiki/Westmoreland_County,_Pennsylvania
12:14 < nmz787> wayy before 'nam
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13:08 < nsh> .wik Westmorland cumbria
13:08 < hplunny> "Search for 'Westmorland cumbria' in existing articles." - http://en.wikipedia.org/wiki/Westmorland_cumbria
13:08 < nsh> .wik Westmorland
13:08 < hplunny> "Westmorland ( /ˈwɛstmərlənd/; formerly also spelt Westmoreland[3]|; even older spellings are Westmerland and Westmereland) is an area of North West England and one of the 39 historic counties of England." - http://en.wikipedia.org/wiki/Westmorland
13:08 < nsh> way before 'merka
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13:34 < kanzure> obscurite: have you met nate or carl yet? they should be in your area i think.
13:35 < obscurite> kanzure, I don't believe so
13:37 < kanzure> hrmm https://github.com/mitsuhiko/flask-pastebin
13:43 < delinquentme> obscurite, howdy!
13:43 < delinquentme> Pitt?
13:46 < delinquentme> brb!
13:46 < obscurite> delinquentme -- I'm a new york city boy, but work for U.Pitt yeah.
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14:13 < kanzure> oh derr
14:13 < kanzure> nmz787: are you still in pittsburgh?
14:14 < kanzure> you should go find jordan miller (jmil) and obscurite
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14:20 < nmz787> kanzure: no back in NYC
14:21 < kanzure> doh
14:21 < kanzure> nmz787: well have you met perry metzger yet? he was recently porting nanoengineer to osx and he's in nyc
14:21 < kanzure> by recently i mean four days ago ish
14:22 < nmz787> no
14:22 < nmz787> is he in here ever?
14:23 < kanzure> he hasn't been in here for a year
14:23 < nmz787> ahh
14:23 < kanzure> last was in here july 14th 2011
14:23 < nmz787> jmil is at uPenn
14:24 < nmz787> that's closer to philly
14:24 < nmz787> about 5 hours or so from pittsburgh
14:24 < kanzure> oops
14:24 < kanzure> okay, then you probably wouldn't have run into him
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16:44 < nmz787> kanzure: if this is right, perry seems to also be in philly, not NYC... as it says he in pursuit of PhD at uPenn
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16:48 < kanzure> oh maybe he has moved
16:48 < kanzure> that is lame.
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16:58 < eudoxia> he was in NYC for HOPE a couple days ago
16:58 < eudoxia> I think
17:03 < kanzure> our distributed stalking skills are rusty
17:03 < eudoxia> I'm working on it
17:03 < eudoxia> I started keeping a stalking/internet-detectiving log
17:05 < kanzure> oh great we can compare notes
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17:10 < delinquentme> how do mailing lists work
17:10 < delinquentme> im getting what I think is a consensus list and I want to start my own topic
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17:19 < kanzure> delinquentme: well, there's mailman, pipermail, and some other older things
17:19 < kanzure> but sometimes when people say "mailing list" they just mean "a list of email addresses that i paste into a carbon copy field"
17:19 < kanzure> or they mean "my spam/marketing campaign"
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17:27 < delinquentme> how is it that commercial production of algae in mass is an issue?
17:28 < yashgaroth> in what sense
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17:30 < delinquentme> http://www.openalgae.com/solutions/
17:31 < delinquentme> it might be that im looking at marketing materials
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17:31 < delinquentme> but carbon negative might be part of that too
17:31 < delinquentme>  ( im not making a statement on global warming )  I've just been wandering the internet
17:34 < yashgaroth> it's only carbon-negative until someone combusts the oil they extract
17:36 < delinquentme> this is very true
17:37 < yashgaroth> anyway generally there's a number of issues with algae production but please don't tell me you want to get into algae farming now
17:38 < delinquentme> yashgaroth, do you have an academic background?
17:38 < yashgaroth> I went to school yes
17:38 < delinquentme> master?
17:38 < delinquentme> masters*?
17:39 < yashgaroth> no fuck that
17:39 < delinquentme> hmm
17:39 < delinquentme> well you're not totally lost
17:39 < delinquentme> curiosity is a good thing
17:39 < delinquentme> as is breadth and width of knowledge
17:39  * nsh chuckles
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17:40 < yashgaroth> pretty sure those mean the same thing
17:40 < delinquentme> ahhh eff
17:40 < delinquentme> fml
17:41 < nsh> seppuku would be appropriate
17:44 < delinquentme> =/
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18:17 < nmz787> delinquentme: generally algae unmodified isn't great for investment/business in today's economy
18:17 < nmz787> delinquentme: is costs a lot to crack them open (lyse), when they could be continuously (actively) pumping it out
18:17 < kanzure> grrr why is sqlalchemy hosted on svn
18:18 < delinquentme> ah so part of the operation is to get the cell to excrete it instead of sequester it?
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18:19 < delinquentme> SCHMEH im gonna watch some nova
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18:22 < nmz787> delinquentme: that is the goal of current research (that I think is interesting)... there are a lot of people working on scaling up grow ponds, and what types of ponds are best for certain strains
18:23 < nmz787> but i'm less interested in that
18:24 < delinquentme> oh yeah the cool shit is engineering the organism
18:24 < delinquentme> normal engineering we've done :D
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18:44 < kendoka> Amyris and LS9 are biofuel companies to watch for
18:45 < kendoka> modified cyanobacteria can apparently excrete hydrocarbon fuels directly
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18:56 < delinquentme> http://www.sacbee.com/2012/07/22/v-print/4648415/2-uc-davis-neurosurgeons-accused.html
18:56 < delinquentme> neurosurgeons created brain infections in patients with brain tumors
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19:07 < kendoka> beats having mind control implants put in you
19:07 < kendoka> google robert naeslund
19:07 < kendoka> hey kanzure
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19:09 < kendoka> i mean if you've got glioblastoma you're already dead
19:10 < kendoka> usually anyway
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19:10 < kendoka> might as well experiment
19:10 < kanzure> kendoka: hi.
19:11 < kendoka> do you have that nature protocols paper by Tyler et al?
19:11 < kanzure> yes
19:12 < kendoka> is it on your fserve?
19:12 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/ultrasound/Ultrasonic%20neuromodulation%20by%20brain%20stimulation%20with%20transcranial%20ultrasound%20-%20Nature%20Protocols%20-%202011.pdf
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19:14 < kendoka> cool saved me 30 bucks
19:15 < kendoka> haven't heard any updates from his lab since he got that DARPA grant
19:15 < kanzure> kendoka: there are some other papers in that folder
19:15 < kanzure> oh i guess no 2012 papers
19:16 < kendoka> guess there's some strings attached
19:16 < kendoka> Nat'l Security etc
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20:57 < delinquentme> what inputs on a form would have hidden "sid" values
20:58 < delinquentme> anyone know what these are?
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21:05 < nmz787> delinquentme: i've used hidden values before to store metadata
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21:09 < kanzure> delinquentme: sometimes it's just the web developer fucking with you.
21:09 < kanzure> just pass the value along with the form.
21:09 < delinquentme> yeah i think thats what it is
21:09 < delinquentme> some kind of verification
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21:11 < delinquentme> nmz787, yeah POS metadata :D
21:11 < delinquentme> at least in this application
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21:37 < delinquentme> and a tfset:240 in a form data?
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21:45 < delinquentme> So if im in chrome and I profile the network traffic on a login
21:47 < delinquentme> and ensure that all the fields which are contained within a form submit are represented in the automated submission
21:47 < delinquentme> it SHOULDDDD work
21:47 < delinquentme> but its nawt
21:47 < delinquentme> hmmm
21:47 < kanzure> cookies
21:48 < kanzure> user agent
21:48 < kanzure> sometimes the order matters.
21:48 < kanzure> content-type is sometimes the form-urlencoded one
22:01 < delinquentme> ohhh
22:02 < delinquentme> soo it looks like the cookies has the SID listed
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--- Log closed Tue Jul 24 00:00:17 2012