2012-07-23.log

--- Log opened Mon Jul 23 00:00:16 2012
* kanzure saw batman00:09
kanzure7zip is definitely not no default, shit00:09
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chidothe cover of the latest Nature issue is very h-plus-ish08:11
chidokanzure: how was batman?08:11
kanzureit was okay08:17
kanzurei think they ran out of money and fired the voice actor for bane for the last 25% of the movie08:19
delinquentmebut movies arent shot sequentially :D?08:20
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delinquentmeso kanzure why 7 zip?08:25
kanzuredon't use 7zip08:25
kanzurewho told you to use 7zip08:25
delinquentmeits actually substantially better than what the 1000 genomes gzip08:25
delinquentmeyou! lol08:26
kanzureok just don't use the .7z format08:26
kanzureuse something like bzip2 or some shit08:26
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delinquentme... these zip programs are taking a surprising amount of time..09:30
delinquentmekanzure, any reason why not the .7z format?09:30
kanzurehplusroadmap represeeeeent09:42
kanzurehttp://www.forbes.com/sites/andygreenberg/2012/07/23/hacker-will-expose-potential-security-flaw-in-more-than-four-million-hotel-room-keycard-locks/09:42
delinquentmeyou going?09:46
kanzurehuh?09:46
kanzureno i'm just saying, an hplusroadmap regular got in the news for an awesome thing.09:47
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delinquentmeohh ic ic10:01
AlonzoTG=P10:06
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delinquentmedude this is really cool10:07
delinquentmehttp://lgilchrist.com/how-we-got-50-women-to-our-hackathon/10:07
delinquentmeI totally love the way they've approached this .. and the icebreakers? someone is an amazing social hacker10:08
AdrianGthat must be first10:09
kanzureicebreakers aren't exactly novel?10:09
AdrianGwhat are the icebreakers they used10:12
delinquentmeso rock scissors paper is totally solid10:12
delinquentmeand also this thing called people find or something like that?10:12
delinquentmedude a social technology-engrained find someone excercise with a bunch of nerds?10:13
delinquentmelike im smiling just talking about it!10:13
delinquentmeso smart.10:13
AdrianGrock scissors paper?10:14
kanzuresomeone should make a "better way to visualize the github repos that you watch"10:15
delinquentmeyeah AdrianG10:15
AdrianGdelinquentme: what about them10:16
AdrianGi dont get u10:16
delinquentmedid you read the article?10:17
delinquentmeIts just brilliant that people get nerds and social interaction and came up with something thats cool for the girls too!10:17
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kanzureoh so now only guys can be nerds? are you sure you're thinking straight10:24
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delinquentmekanzure, nah not at all10:27
delinquentmebut like everyone likes it when the social introductions go smoothly10:27
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delinquentmesoo compression is a pretty intensive operation huh?10:33
kanzurehttp://peerproduction.net/issues/issue-2/ biohacking stuff.. but it's "journal of peer production" ugh10:36
kendokateach girls how to hack their ex's facebook10:38
kendokathen once they're hooked you can move on to biohacking10:38
delinquentmeHAHAHAHA10:40
kanzureis this what you think about maradydd?10:40
delinquentmekendoka, has some insight here...10:40
kanzureor chido?10:40
kanzuregeeze10:40
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delinquentmeif someone used rockets and SSDs for genomes10:44
delinquentmethat'd be pretty fast :D10:45
delinquentme"high bandwidth"10:45
delinquentmecould also use drones10:45
delinquentmebut punk kids might shoot those down10:45
* nsh notes proper bong-passing etiquette10:46
delinquentmelolol10:46
nshthe 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 information10:48
delinquentmensh, maybe we should just fab nanowires and use that10:48
nshgoogle tech talk: http://www.youtube.com/watch?v=sfyHdFo5GWE10:48
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delinquentmensh, but the signal : noise on that is substantial10:51
delinquentmelike I've got very simple questions10:51
delinquentmeI dont need to know the intricacies10:51
delinquentmejust need to know  " can we do simple shit to make genomes transfer faster ?"10:52
delinquentmenmz787, how was ohiopyle??10:52
nmz787ended up going to linn run state park10:52
nmz787near idlewild10:52
nshdelinquentme, why are you interested in this question in particular?10:53
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delinquentmeyeahhh! thats a cool place10:53
kanzuredelinquentme: ok so why is gzip not an answer?10:53
kanzuredelinquentme: have you even tried it?10:53
nshidlewild are an indie band from scottish western isles10:53
kanzureyashgaroth: hello10:53
yashgarothwhatup10:54
delinquentmekanzure, yeah i just did ... and i've got a little spreadsheet of the packaged sizes10:54
kanzuredelinquentme: ok. so what's the problem with that?10:54
delinquentmensh, Im really interested by the fact that backblaze has no genomics customers10:54
delinquentmeand stupid big data is an issue10:54
delinquentmewhy aren't they being utilized10:54
kanzurenot everyone knows about all products10:54
delinquentmethey're open source, they're backup and they're substantially cheaper than amazong10:54
kanzureare you just trying to get us to spend money10:55
nshthe teams who produce these data sets are often associated with large academic or commercial institutions with their own in-house storage solutions10:55
nshwhich isn't necessarily optimal, but is default10:55
kanzurefor a while google was offering to send free hard drives to academics10:56
ParahSailinjournal of peer production?10:56
kanzureand then people would load up their data and mail it back10:56
yashgarothillumina almost lost all their data in a flood a few years ago since they didn't backup10:56
kanzureneat.10:56
yashgaroththey do backups now, I hope10:56
ParahSailinthis company sometimes sends hard drives to clients as the delivery10:57
kanzurethis is because the cost of sequencing is still greater than the cost of data storage10:57
kanzureif you're spending $20k on a genome you might as well get it on a hard drive or two anyway10:58
delinquentmensh, exactly its the default way of doing it10:58
delinquentmethe default answer to my question is " No weve tried everything and its not that simple "10:59
delinquentmebut what if something is being overlooked in this data transfer problem?10:59
delinquentmeSURE thats an easy question to ask ... and utterly vacuous without a good answer10:59
delinquentmebut.. what if?10:59
kanzureit's not much of a problem.. transferring is still way faster than sequencing10:59
kanzureand OC148 is pretty fast11:00
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kanzurewell, i mean oc19211:00
kanzureooh they have oc768 now.11:02
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nsha good line of investigation would be: what is the nature of redundancy within genomic data which would lend it a particular genus of algorithmic compression11:06
nsh(sorry, started writing that line a good while ago and got distracted)11:06
delinquentmetrue and CpG islands would compress well11:06
kanzurewell, if he just wants fast transfer, then he should just use lookup tables and things like SNPs11:06
delinquentmeHMMM11:07
delinquentmekanzure, so you're saying look at the genome as the default sequence .. save for the differences?11:07
yashgarothwhat why would cpg islands compress well11:07
kanzureno, i'm saying just reference the existing remote packets instead of sending the entire genome11:08
delinquentmeyashgaroth, offhand? represent the whole sequence as a binary string?11:09
yashgarothno more so than any other dna sequence11:09
delinquentmeif you've got 10000 characters you're cutting down into 1 or 0 thats a substantial compression no?11:09
yashgarothit's not like they're cgcgcgcgcgcgcgcg everywhere, there's just more CGs than average11:09
delinquentmewell even at best the 2bit for ACTG is halved then no?11:09
delinquentmeIDK if you were here for my 00=A 10=C 01=T 11=G statement last night11:10
yashgarothno that's how I'd do it11:10
kanzuredelinquentme: 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 data11:10
kanzurebut often the problem is that this representation takes more space than the actual data11:10
ParahSailinmost of the heavy data is short reads11:10
kanzureso it's not really compression11:11
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delinquentmekanzure, im sorry you lost me11:11
ParahSailinassembled scaffolds take up comparatively little space11:11
yashgarothyeah, most data will be a short sequence (depending on the sequencing method) plus associated confidence levels for each bp11:11
delinquentmeParahSailin, this is true ... are the short reads stored often?11:11
kanzurewhy cant you just read up on existing algorithms so i don't have to teach you11:11
delinquentmekanzure, simplify11:12
ParahSailinusually clients want those as a deliverable11:12
delinquentmeParahSailin, yashgaroth do labs store the short reads for extended periods of time or just the consensus11:12
delinquentme?11:12
ParahSailinwell a sequencing company keeps those indefinitely11:13
delinquentmekanzure, you're talking signal processing and compression and like I cant pull out whats intelligible from the statement11:13
ParahSailindunno what labs do with them11:13
yashgarothdepends 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 sequences11:13
yashgaroththat was all fastq data btw11:15
delinquentmeis it a good practice to look to apply open research from academia to computation / processing problems11:16
delinquentmeas a way to find good business ventures?11:17
delinquentmeIDK. something I've been thinking about ... like how to generalize whats worth developing11:17
ParahSailinassembly based on reference11:17
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nmz787delinquentme: 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)11:19
nmz787with that you just saved 66% going from 10 bits to 311:20
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audyI keep all of my reads11:22
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audyI have them on 2 TB hard drives stacked in my office, backed up on another machine and also on Amazon S311:22
audyjust in case the lab explodes11:22
audyI wrote a web app to manage all of this11:23
audyI went to the genomic standards consortium meeting this year and one of the major topics was whether or not to store all of this data11:24
audyOne group proposed using lossy compression, another proposed throwing out the reads and just keeping the samples11:24
ParahSailinyou paid for it11:24
audybecause it's cheaper to re-sequence than to store11:24
nmz787compression could possibly be useful since there are transposons and other repeating elements11:25
audygzip works well. There's a new compression technique that uses assembly11:25
nmz787but it would have to be a bit smarter than binary compression that exists11:25
audycalled quip11:25
nmz787since some transposons are just flipped in orientation11:25
nmz787they could still be compressed with the same symbol, but need an extra bit to show their orientation11:26
audyyou could also convert ascii to a 2-bit format11:26
nmz787right11:26
nmz787you'd want to do that first11:26
ParahSailinreads have N11:26
delinquentmehttp://io9.com/5928274/the-universe-could-tear-itself-apart-sooner-than-anyone-believed11:27
audyParahSailin I mean post quality control11:27
audytrim the reads based on quality and throw out anything with an N11:27
delinquentmecarl had a panic attack =/11:27
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delinquentmebuddhist shit is not helping me cope with this.11:29
delinquentmebut by the same token doesnt this say that we've got 70% of the energy out there classified as 1 certain thing?11:29
delinquentmeIE if we dont know what it is .. its automatically "dark energy" and thus contributing to this "big rip"?11:30
yashgarothgod damnit do you want to talk about sequence storage or not11:30
audyI have 13 illumina runs on EC2, 50 gigs.11:31
audycosts about $5 per month11:31
ParahSailinstorage is maybe like the least pressing technological issue11:31
yashgarothor compression or whatever we're talking about11:32
kanzureyashgaroth: he's actually talking about business ventures -_-11:33
kanzureyashgaroth: it's hard to follow11:33
delinquentmeI'm kind of asking about the entire operation11:33
delinquentmeand audy has a point ... like $5/month isnt anything substantial11:33
delinquentmeand IDK if there are sequencing startups who need a cheap alternative11:34
delinquentmebut maybe large sequencing operations DO need long term storage?11:34
ParahSailinan illumina flowcell run costs what, $50k?11:35
ParahSailinstoring it is how many 2 TB hard drives?11:35
audyParahSailin 111:36
audyParahSailin uncompressed, including the actual images of the flowcell used to make the base calls11:36
* audy is talking about GAIIx, not hi-seq11:36
audydelinquentme you want to make a startup based around storing sequence data?11:36
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delinquentmeaudy, backblaze is a storage service which is really cheap ... moreso than amazon11:37
delinquentmeand I've just been wondering about a service based on this ... and the data transfers seem to be the bottleneck11:38
audydelinquentme can you cite a backblaze backup in a publication?11:38
delinquentmeumm well I asked them and they said they've got no genomics customers11:40
delinquentmeso maybe .. no?  But I havn't searched for a research paper with backblaze mentioned11:40
audyI think backblaze is for backing up your computer11:40
audylike timemachine but in the cloud11:40
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ParahSailinif you are looking for business venture, follow the plutocracy11:42
delinquentmeaudy, yeah it is11:42
delinquentmebut they're also wildly cheap backup11:42
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delinquentmeParahSailin, true ! but useful would be good too11:43
nmz787I might consider an evolution program for this bat http://www.filippidis.org/index/amazing/giant-bat.html11:43
delinquentmeunlike zynga11:43
nmz787dracula 2050... after a scientist spliced his own DNA with the bat's, a monster was born11:43
audyParahSailin what do you mean follow the plutocracy?11:46
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delinquentmefollow the $$$11:49
audygamified location-aware microcoupons?11:50
kanzureno that's what klafka is doing11:51
yashgarothcloud...blogging?11:51
delinquentmeaudy, hahah <311:51
delinquentmeyesss the cynics11:51
nmz787delinquentme: so what area /do/ you live in, if not pgh?11:53
nmz787i assumed you were some college dude slumming it up in Oakland11:53
delinquentmenah im like east of PGH11:53
delinquentmebut that could change shortly11:54
delinquentmeIDK11:54
ParahSailinaudy: pick an industry closest to the counterfeiters11:54
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ParahSailinsilicon valley and wall st are the top choices11:54
nmz787delinquentme: like, east pittsbugh, north versailles, forest hills?11:55
nmz787what neighborhood11:55
delinquentmegreensburg =]11:55
delinquentmeits close to the westmoreland mall lol11:56
* delinquentme feels like such a suburbanite11:56
kanzureit's called.. west more land?11:56
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nmz787ahh11:57
nmz787kanzure: yeah, i figure moreland was west of philly and DC and NYC back in the early days11:58
nmz787so then you had to have a west-moreland11:58
nmz787lol11:58
nmz787its actually a county name too11:58
nmz787westmoreland county11:58
kanzurewestmorelandbetterthanthisshittyland11:58
audyParahSailin pharma11:58
delinquentmelol12:04
nmz787kanzure: I drove past that westmoreland mall a few days ago and was thinking of the origns of the name :P12:04
delinquentmesucks I keep missing you12:04
delinquentmetheres a really awesome outdoor air bar here too12:04
delinquentmegreat place to chill and concept :D12:05
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nshconcept is not a verb12:10
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nsh.wik General Westmoreland12:10
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_Westmoreland12:10
nshthough the name had vintage before the general12:11
audyI like to concept in the concept den12:11
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,_Pennsylvania12:14
nmz787wayy before 'nam12:14
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nsh.wik Westmorland cumbria13:08
hplunny"Search for 'Westmorland cumbria' in existing articles." - http://en.wikipedia.org/wiki/Westmorland_cumbria13:08
nsh.wik Westmorland13:08
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/Westmorland13:08
nshway before 'merka13:08
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kanzureobscurite: have you met nate or carl yet? they should be in your area i think.13:34
obscuritekanzure, I don't believe so13:35
kanzurehrmm https://github.com/mitsuhiko/flask-pastebin13:37
delinquentmeobscurite, howdy!13:43
delinquentmePitt?13:43
delinquentmebrb!13:46
obscuritedelinquentme -- I'm a new york city boy, but work for U.Pitt yeah.13:46
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kanzureoh derr14:13
kanzurenmz787: are you still in pittsburgh?14:13
kanzureyou should go find jordan miller (jmil) and obscurite14:14
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nmz787kanzure: no back in NYC14:20
kanzuredoh14:21
kanzurenmz787: well have you met perry metzger yet? he was recently porting nanoengineer to osx and he's in nyc14:21
kanzureby recently i mean four days ago ish14:21
nmz787no14:22
nmz787is he in here ever?14:22
kanzurehe hasn't been in here for a year14:23
nmz787ahh14:23
kanzurelast was in here july 14th 201114:23
nmz787jmil is at uPenn14:23
nmz787that's closer to philly14:24
nmz787about 5 hours or so from pittsburgh14:24
kanzureoops14:24
kanzureokay, then you probably wouldn't have run into him14:24
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nmz787kanzure: if this is right, perry seems to also be in philly, not NYC... as it says he in pursuit of PhD at uPenn16:44
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kanzureoh maybe he has moved16:48
kanzurethat is lame.16:48
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eudoxiahe was in NYC for HOPE a couple days ago16:58
eudoxiaI think16:58
kanzureour distributed stalking skills are rusty17:03
eudoxiaI'm working on it17:03
eudoxiaI started keeping a stalking/internet-detectiving log17:03
kanzureoh great we can compare notes17:05
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delinquentmehow do mailing lists work17:10
delinquentmeim getting what I think is a consensus list and I want to start my own topic17:10
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kanzuredelinquentme: well, there's mailman, pipermail, and some other older things17:19
kanzurebut sometimes when people say "mailing list" they just mean "a list of email addresses that i paste into a carbon copy field"17:19
kanzureor they mean "my spam/marketing campaign"17:19
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delinquentmehow is it that commercial production of algae in mass is an issue?17:27
yashgarothin what sense17:28
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delinquentmehttp://www.openalgae.com/solutions/17:30
delinquentmeit might be that im looking at marketing materials17:31
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delinquentmebut carbon negative might be part of that too17:31
delinquentme ( im not making a statement on global warming )  I've just been wandering the internet17:31
yashgarothit's only carbon-negative until someone combusts the oil they extract17:34
delinquentmethis is very true17:36
yashgarothanyway generally there's a number of issues with algae production but please don't tell me you want to get into algae farming now17:37
delinquentmeyashgaroth, do you have an academic background?17:38
yashgarothI went to school yes17:38
delinquentmemaster?17:38
delinquentmemasters*?17:38
yashgarothno fuck that17:39
delinquentmehmm17:39
delinquentmewell you're not totally lost17:39
delinquentmecuriosity is a good thing17:39
delinquentmeas is breadth and width of knowledge17:39
* nsh chuckles17:39
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yashgarothpretty sure those mean the same thing17:40
delinquentmeahhh eff17:40
delinquentmefml17:40
nshseppuku would be appropriate17:41
delinquentme=/17:44
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nmz787delinquentme: generally algae unmodified isn't great for investment/business in today's economy18:17
nmz787delinquentme: is costs a lot to crack them open (lyse), when they could be continuously (actively) pumping it out18:17
kanzuregrrr why is sqlalchemy hosted on svn18:17
delinquentmeah so part of the operation is to get the cell to excrete it instead of sequester it?18:18
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delinquentmeSCHMEH im gonna watch some nova18:19
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nmz787delinquentme: 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 strains18:22
nmz787but i'm less interested in that18:23
delinquentmeoh yeah the cool shit is engineering the organism18:24
delinquentmenormal engineering we've done :D18:24
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kendokaAmyris and LS9 are biofuel companies to watch for18:44
kendokamodified cyanobacteria can apparently excrete hydrocarbon fuels directly18:45
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delinquentmehttp://www.sacbee.com/2012/07/22/v-print/4648415/2-uc-davis-neurosurgeons-accused.html18:56
delinquentmeneurosurgeons created brain infections in patients with brain tumors18:56
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kendokabeats having mind control implants put in you19:07
kendokagoogle robert naeslund19:07
kendokahey kanzure19:07
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kendokai mean if you've got glioblastoma you're already dead19:09
kendokausually anyway19:10
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kendokamight as well experiment19:10
kanzurekendoka: hi.19:10
kendokado you have that nature protocols paper by Tyler et al?19:11
kanzureyes19:11
kendokais it on your fserve?19:12
kanzurehttp://diyhpl.us/~bryan/papers2/neuro/ultrasound/Ultrasonic%20neuromodulation%20by%20brain%20stimulation%20with%20transcranial%20ultrasound%20-%20Nature%20Protocols%20-%202011.pdf19:12
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kendokacool saved me 30 bucks19:14
kendokahaven't heard any updates from his lab since he got that DARPA grant19:15
kanzurekendoka: there are some other papers in that folder19:15
kanzureoh i guess no 2012 papers19:15
kendokaguess there's some strings attached19:16
kendokaNat'l Security etc19:16
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delinquentmewhat inputs on a form would have hidden "sid" values20:57
delinquentmeanyone know what these are?20:58
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nmz787delinquentme: i've used hidden values before to store metadata21:05
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kanzuredelinquentme: sometimes it's just the web developer fucking with you.21:09
kanzurejust pass the value along with the form.21:09
delinquentmeyeah i think thats what it is21:09
delinquentmesome kind of verification21:09
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delinquentmenmz787, yeah POS metadata :D21:11
delinquentmeat least in this application21:11
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delinquentmeand a tfset:240 in a form data?21:37
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delinquentmeSo if im in chrome and I profile the network traffic on a login21:45
delinquentmeand ensure that all the fields which are contained within a form submit are represented in the automated submission21:47
delinquentmeit SHOULDDDD work21:47
delinquentmebut its nawt21:47
delinquentmehmmm21:47
kanzurecookies21:47
kanzureuser agent21:48
kanzuresometimes the order matters.21:48
kanzurecontent-type is sometimes the form-urlencoded one21:48
delinquentmeohhh22:01
delinquentmesoo it looks like the cookies has the SID listed22:02
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