2013-02-07.log

--- Log opened Thu Feb 07 00:00:53 2013
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@kanzurepdfparanoia discussion stuff:00:36
@kanzurehttps://groups.google.com/forum/?fromgroups=#!topic/diybio/o6irBNeCmrE00:36
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gnushahttps://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f89963c9 Bryan Bishop: list of modification projects01:29
@kanzure"Hacked microbes introduced into oral microbiome to fight cavities"01:30
@kanzure"Skin lighteningGENESLC24ASmulti billion $/year industry in Asia."01:30
@kanzure"Straight hairGENEP2RY5 (?)grow straight hair. Multi billion $/year industry in US"01:31
@kanzurehis orgasmotron is dumb, you have to target the pedundal nerves not the spine -_-01:32
@kanzure"Baby, this is a gene therapy that causes semen to sweeten like hot syrup. A gene mod to the Cowper’s gland that makes your semen contain a ton more fructose than normal. Perhaps also add other minor flavorings to round out the taste."01:33
@kanzureeh.01:38
superkuhWhat are you quoting from?01:39
@kanzurethe thing i added to diyhpluswiki.git01:39
@kanzureit's from rich lee01:39
@kanzurehttp://diyhpl.us/wiki/genetic-modifications.csv01:41
superkuhI don't think targeting the dorsal spinal nerve bundles is dumb. That's where stewart mallory (or however his name is spelled) did it with direct electrical stimulation in exploratory surgery for correcting chronic pain.01:42
@kanzurechido has a few friends who are doing nerve stimulation for similar purposes, maybe she will drop a link to what their project actually is01:42
@kanzurei don't see how the chronic pain is the same; is there any experimental evidence that this nerve bundle is the right one? i don't even know where the pedundal nerve loops back to.01:45
superkuhsacral.01:45
superkuhAnd yes.01:45
superkuhI used to have the articles.01:46
superkuhIt was during exploratory surgery for electrical stimulation to correct chronic pain that the effect was found.01:47
superkuhThat's the only relation.01:47
@kanzure"It originates in Onuf's nucleus in the sacral region of the spinal cord, and travels in the S2-S4 nerves of the sacral plexus."01:47
@kanzureah.01:47
superkuhFor male rats.01:47
superkuh?01:48
@kanzurejust quoting wikipedia http://en.wikipedia.org/wiki/Pudendal_nerve01:48
superkuh"Stuart Meloy"01:48
superkuhpaperbot: http://www.nature.com/scientificamerican/journal/v300/n5/full/scientificamerican0509-22.html01:50
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Turn%20It%20Up%2C%20Dear.pdf01:50
superkuhEh, nevermind. Not very useful.01:51
@kanzurewhy is there a picture of a anthropomorphic microcontroller smoking a cigarette in a nature publication01:52
superkuhBetween T9 and T10.01:52
@kanzuresciam publication. oh that explains it.01:52
superkuhNot in the sacral like the pudenal nerves.01:52
superkuhhttp://www.google.com/patents/US2010022285801:54
gnushahttps://secure.diyhpl.us/cgit/paperbot/commit/?id=0ef3debc Bryan Bishop: prevent a catastrophic error in paper retrieval01:56
gnushapaperbot: reload papers01:56
paperbotgnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-02-07 09:56:15)01:56
superkuhUnfortunately TMS of the spine is very variable with coil shape and placement due to the funky shape and changes in dielectric constant of the spine bone messing up the induced electrical field.01:56
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archelssuperkuh: but TMS is magnetic induction. How does the permittivity come into play?01:58
superkuhI don't know. That is what I read long ago. Thinking of it know I supposed it just makes the current paths from the induced field all twisted and inhomogeneous.02:00
superkuhs/know/now/02:00
superkuhI am certain I read multiple papers about the failure of spinal magnetic stimulation with both pancake and butterfly coils.02:00
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superkuhIt's not that the electrical field is not induced. Just that the current density is unpredictable.02:02
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archelsright. H-field induces E-field, then E-field induces currents02:08
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nmz787http://www.google.com/patents/US791029202:42
nmz787"The present invention provides a lithographic process "...." The invention also discloses a reciprocating microengine (10) comprising a cylinder (14), piston (12) and crankshaft made by the process."02:42
nmz787the drawings SUCKASS though02:43
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ielofenn, hi03:47
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ManaLordbiohacking... hacking out the kidneys of people and selling them? is that what's going on in here?09:39
chris_99i hope not09:40
ManaLordwell, it's in the greeting-message...09:41
chris_99heh so it is09:41
ManaLordbut I'm more interested in the dimensions available for healthy people: like nootropics...09:42
chris_99mm, i think theres some people into that09:43
ManaLordhmmm, I see, so what else, implanted android phones?09:44
ManaLordat least that's probably where a lot of tech for biohacking will come out of...09:45
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@kanzurehttps://www.techdirt.com/articles/20130204/12241621879/eu-commission-wants-more-copyright-licensing-not-creative-commons-fair-use.shtml10:47
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@kanzurehttp://www.nature.com/news/researchers-opt-to-limit-uses-of-open-access-publications-1.1238410:47
@kanzurehttp://blog.okfn.org/2013/01/08/consequences-risks-and-side-effects-of-the-license-module-non-commercial-use-only-2/10:47
@kanzurefor whatever reason, i sent the pdfparanoia announcement to a group of librarians11:04
@kanzureand now they are quoting me silly regulations11:04
@kanzure"The IEEE Academic license says we cannot " remove, obscure or modify in any way copyright notices, other notices or disclaimers that appear on Articles or eBooks or in the Licensed Products.""11:04
@kanzure"I am guessing that this and other language in the license would be interpreted that modification to PDFs would not be acceptable. The IEEE license is pretty common of many of our licenses."11:04
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@kanzurewell, then don't use it sillyhead11:04
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@kanzurepaperbot: http://www.sciencedirect.com/science/article/pii/S193459091200644312:18
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Loss%20of%20Dickkopf-1%20Restores%20Neurogenesis%20in%20Old%20Age%20and%20Counteracts%20Cognitive%20Decline.txt12:18
@kanzurepaperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=274143&_user=1694017&_pii=S1934590912006443&_check=y&_origin=article&_zone=toolbar&_coverDate=2013--07&view=c&originContentFamily=serial&wchp=dGLbVlB-zSkWA&pid=1-s2.0-S1934590912006443-main.pdf&_valck=1&md5=c189654c6fd0d18dcecf6a2b280ef36b&ie=/sdarticle.pdf12:18
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/2aaf9554321254c97c3e42030a102efd.txt12:18
@kanzurebah12:18
ParahSailinhttp://www.eurekagenomics.com is hiring12:18
@kanzurewhat do they want to hire12:19
ParahSailina guy who can program12:19
@kanzureremote?12:19
ParahSailinsend resume in to vyfofanov@eurekagenomics.com12:20
ParahSailinfrom time to time, people have worked remotely here12:20
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@kanzurethat's encouraging12:21
@kanzureokay, email sent.12:21
ParahSailinour indian guy spent a month over there last year, working remotely, and he had done that before when he had visa issues12:23
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ParahSailinbtw, eg is definitely looking for a guy to help out with web dev12:31
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ParahSailinour sysadmin/webdev is pretty swamped at the moment12:32
@kanzuresame person?12:33
ParahSailinwell, its a small place12:34
ParahSailinit's down to 5 people in this office as of today12:34
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@kanzure"The Dewey Decimal Classification (DDC), or Dewey Decimal System, is a proprietary library classification system created by Melvil Dewey in 1876.[1] It has been revised and expanded through 23 major editions, the latest issued in 2011.[2]"12:48
@kanzureso how is dewey decimal still in copyright? the older editions should be out of copyright.12:48
@kanzurewow, ipython is much more active than i thought it would be13:00
@kanzurehttps://github.com/ipython/ipython/issues13:00
@kanzure463 open issues, 2431 closed issues13:00
@kanzurehttps://github.com/ipython/ipython/issues/128613:03
@kanzurehttps://github.com/ipython/ipython/issues/248613:03
@kanzurethese issues are the worst. when i reverse search in ipython sometimes it executes a line i don't want.13:03
@kanzureis .mailmap a git feature? https://github.com/ipython/ipython/blob/master/.mailmap13:09
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QasaurHey13:20
@kanzureQasaur: hello13:26
Qasaurso13:27
QasaurI just recently started looking into DIYBio13:27
Qasaurand it seems awesome!13:27
QasaurHow do I get started?13:27
@kanzurehttp://diyhpl.us/wiki/diybio/faq13:27
Qasaurthanks kaz13:27
Qasaurkanzure*13:27
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@kanzureuh.13:28
ThomasEgii wonder what that qasaur guy will put in his report about the potetial threat from DIYBio communities and how we should all be put on some terror watchlist13:47
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ParahSailinkanzure: lol, you really started your email with "Yo"?14:19
nmz787ThomasEgi: why do you think he's writing something?14:24
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@kanzureParahSailin: totes.14:27
@kanzureParahSailin: you have to keep it real14:27
@kanzureParahSailin: i'm really bad at culture14:28
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nmz787ParahSailin: is your real name viacheslav?14:31
@kanzureno14:31
ParahSailinnah, that's my supervisor14:34
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@kanzurewell, hopefully this will fix ipython's terrible ctrl-c handling:15:18
@kanzurehttps://github.com/ipython/ipython/pull/289515:18
chris_99i've just been playing about with lua, tis a pretty cool little language15:18
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streetykanzure: for ipython notebooks do you know of any way to upload files from the web interface?15:41
@kanzurewhat web interface15:41
streetythe web interface when you use a ipython notebook15:44
@kanzuredidn't know that's a thing15:44
@kanzurei just use ipython15:44
streetyfair enough, it's touted as a way to save your 'experiment', it's worth giving a try15:47
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streetyI think the expectation is you have shell access as well so can just move files in that way. I'm considering using it as a teaching aid (spin up an EC2 instance for each student and point them at the web interface) but being unable to move files in easily may kill the idea15:48
@kanzureexperiments?15:49
streetyexperiments/prototypes/learning-new-commands anything you might want to go back to and understand exactly what you did15:53
streetyyou can save a session - perhaps key point I don't think I mentioned15:53
@kanzureipython in the shell can also save sessions with %save15:54
nmz787kanzure: a few weeks ago i asked you about the online notebook feature too15:55
nmz787kanzure: the web interface looks like a wiki, but can run python code that you type in15:56
streetyI had not realised that15:56
nmz787kanzure: i bet there are major security issues :P15:56
nmz787seems like there would be anyway15:56
streetyyou essentially have shell access so security issues are certainly not far away15:57
streetythat's why I was considering ec2 instances rather than my personal server - I can burn them to the ground after the tutorial15:57
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juri_if you have a virtualization capable server, this sounds like good KVM teritory.16:08
juri_I've written something that, while difficult to set up, allows me to install a VM with a single command, start it with a different command, and destroy it with a third command. if you're doing that a lot, it might be worth the time investment.16:09
juri_</shameless_plug>16:10
nmz787kanzure: i'm not sure what this site is, but i can see the dir listings, and this is some kind of title page that lists the pdfs in that dir http://144.206.159.178/ft/885/92512/1608523.pdf16:16
nmz787kanzure: seems like each dir doesn't include that index page16:17
@kanzurenmz787: it's Kurchatov Institute of Atomic Energy16:17
nmz787kanzure: Subject Index of Volume 38 http://144.206.159.178/ft/885/52362/919164.pdf16:18
nmz787kanzure: there's tons of stuff http://144.206.159.178/ft/16:19
streetyjuri_: my personal server is already a VM. VMs inside VMs isn't a direction I want to go in. sounds interesting though (I was actually planning to take a look at vagrant this weekend)16:21
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juri_streety: my software is https://gitorious.org/createvm . If you have a thing for autoinstalls, shell scripting (its almost entirely shell scripts, and uses a shell script based autoinstaller), and debian, you'll wonder why you did without it.16:22
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nmz787kanzure: the search even works16:22
streetyjuri_: thanks, I'll have a play with it this weekend16:24
@kanzurenmz787: no, that error message is not helpful because the details are disabled in their configuration file16:26
@kanzurehttp://www.securityartwork.es/2013/02/07/the-result-of-pinging-all-the-internet-ip-addresses/?lang=en16:33
nmz787kanzure: seems you can't use the search on the pdf filename, I was hoping it would allow easy metadata retrieval since their search gives that16:33
@kanzuredo any of you windows users feel like trying my ipython fix?16:38
@kanzurehttps://github.com/ipython/ipython/pull/289516:38
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jrayhawkI though that simple management thing was what libvirt was for?17:44
@kanzurehm?17:45
@kanzureoh, management of virtual machines17:45
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klafkaman i love vim17:55
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juri_jrayhawk: i didn't like the approach: despite the name, it is very monolythic in design.18:03
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juri_I've looked at making XML files that are compatible with libvirt, but the xml parser they use freaks when it comes into contact with entities that tlibvirt does not know how to handle.18:04
juri_I also pulled off a cheat libvirt isn't compatible with: i use screen to manage the physical consoles of the VMs.18:05
juri_i dunno. i just feel my aproach is more 'unixy'. i use a lot of different tools shell scripted together, instead of trying to do it all with a graphical app.18:05
@kanzure"Bio, Tech and Beyond lab" is that really what yashgaroth is naming it?18:06
juri_arno-iptables-firewall for the firewalling.. isc DHCPD and bind.. screen.. tintin++.. and FAI for doing the installs.18:06
@kanzurewhy is kevin lustig (assaydepot.com) listed as an organizer of that yashgaroth's lab?18:07
@kanzure-that18:07
juri_my software just being wrapper/management scripts, it isn't even running, right now... but i have ~20 VMs running.18:07
jrayhawkhttp://www.omgwallhack.org/home/jrayhawk/src/sandbox.sh might be interesting to you18:13
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@kanzure"At this point, we managed to dump over there: Packard microarray scanner, inverted microscope/CCD camera, Roche LightCycler real time PCR machine, Buchi Rotovap, Speed Vac,"18:14
@kanzure"slide based PCR machine, 4 different lasers (650nm, 532nm, 600nm, 488nm), Photomulitplier tube (working), hudson control plate crane robot arm, VandP replicator pins, scales, refrigerator with fluorophores"18:14
@kanzureposted on http://www.meetup.com/DIYbio-San-Diego/events/103092922/18:14
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gnushahttps://secure.diyhpl.us/cgit/paperbot/commit/?id=b6977593 Bryan Bishop: set pdfparanoia as a dependency19:08
gnushapaperbot: reload papers19:08
gnushaquack19:10
gnushaq\nuack19:10
gnusha-e qnuack19:10
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gnushamoo19:19
gnusha/names19:19
archboxhi gnusha19:20
jrayhawklet me know if you actually succeed in doing anything interesting with that socket interface19:22
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JayDuggerThis is where I order the 3d printed kidneys for my automatic rifle, right?19:49
jrayhawkonly if you're using them to shoot and then perform surgery on your glow-in-the-dark cat19:54
jrayhawkwith magnetic implants19:54
JayDuggerGreat!19:56
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juri_give me time... ;)20:19
juri_i THINK i have a good plan for 3d printing aluminium.20:20
ThomasEgijuri_, if it works, i'll hire you to print a couple of things :)20:20
juri_I'm pretty sure i have a good plan.20:20
juri_i blew a huge hole in it today, but repaired the hole in the plan. ;)20:21
ThomasEgiprinting copper or brass would be convenient too20:21
juri_one step at a time. ;)20:22
ThomasEgiwell. as i said. if you can make it work. i'd hire you to print a few microphone cases20:22
ThomasEgigiven you don't get oxid layers in. as i need high conductivity20:23
juri_this will be an oxygen-free environment.20:24
ThomasEgigood good.20:25
ThomasEgiwhat's your targeted resolution/precision?20:25
juri_a little bit better than a standard rostock.20:25
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juri_hi everybody! ;)20:27
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jrayhawkfreenode is the best20:30
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kanzurefreenode is equal to or greater than the best20:33
kanzureso the ipython devs are arguing with me that because the bug is due to python/readline refusing to implement more api hooks, they wont fix their bug.20:34
kanzuremeanwhile, using ctrl-c in ipython leads to disastrous consequences of re-running code while the input line looks blank.20:34
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klafkaoh?20:55
ThomasEgijuri_, what did you decide for ? vaccuum chamber?21:00
juri_thomas: yep.21:13
juri_http://www.reprap.org/wiki/Fusionreprap21:13
ThomasEgiwhat do you plan to use as container to keep the vacuum up?21:13
juri_pressure canners.21:14
kanzuresmall children21:15
juri_the souls of my enemies.21:16
kanzurei approve this message21:16
ThomasEgia pressure canner like used to prepare food?21:17
juri_Yes.21:17
juri_only the heaviest duty version they make.21:17
ThomasEgiarent they designed to withstand a lot of pressure from inside?21:17
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ThomasEgiinstead of pressure from outside??21:17
juri_they're just cast aluminum. so far as i know, there is no 'directionality' to the ability of the container to contain force. in fact, i think pressure from outside will be better taken care of, by the round shape. compressive force, instead of explosive force.21:18
ThomasEgiusualy it's just the other way round21:19
yashgarothkanzure I didn't name the lab, btw uploading pictures of it now21:19
ThomasEgias metal is very good with tension forces21:19
ThomasEgibut doesn't do much good if you add pressure.21:19
ThomasEgiso even if a container can easily withstand 10bar inside pressure. it still could implode with just half a bar pressure from outside21:20
juri_I've seen people using the little ones for pulling the air out of modeling mixtures.21:20
ThomasEgii just wanted to raise that concern.21:20
juri_noted.21:20
juri_and thanks.21:20
ThomasEgithe bigger the container. the more risky to use in low pressure21:20
juri_yea, i know. i'll start small.21:20
ThomasEgii highly recommend some dry runs. maybe even by sinking that pot into a lake. and see how deep it goes befor imploding21:21
ThomasEgiso you know the safety factor at least.21:21
juri_just in case. i'll be doing all of this in a old rack.21:22
juri_so that shrapnel has a lower chance of hiting anyone.21:22
ThomasEgigood good.21:22
ThomasEgiwell an imploding metal container isnt really prone to shrapnelling21:22
juri_good to know.21:22
ThomasEgireminds be of that video of a liquid-container train-trailer  thingy21:23
ThomasEgiwhich they removed air from. and let the crowd guess at what pressure itd implode21:23
ThomasEgihttp://www.youtube.com/watch?v=Zz95_VvTxZM21:24
juri_oyea. seen it. ;)21:24
ThomasEgithey are usualy made for 10bar inner pressure21:24
yashgarothok my terrible photos are up http://imgur.com/a/zGWGR21:24
ThomasEgiand at bout 0.7 it went fupp21:24
ThomasEgipingpongtable.. nice.21:25
yashgaroth*free* pingpong table21:25
ThomasEgiyou should get a stable stand for your camera tho21:25
yashgarothyeah I was a little drunk21:25
yashgaroththe other photos gave me motion sickness so I didn't upload them, but we had about 40 people there21:26
yashgarothsome guy brought 2 repraps, a pcr machine, a microarray reader, a real-time pcr machine, and a bunch of other electronic crap that I don't even know what it's for21:27
yashgaroththey were chilling beer in a centrifuge for some reason21:28
juri_fun.21:28
yashgarothanyway it's much larger than those photos, but again, motion blur sickness21:28
kanzurei don't see any free weights21:31
yashgarothjojack is saving those for himself21:32
kanzurei hope that's tile and not carpeting21:32
yashgarothsweet absorbent mold-harboring carpet, yeah21:32
kanzurewonderful21:32
yashgaroththat's priority one, covering or replacing it21:32
yashgarothoh and http://biotechnbeyond.com/ is the website since I may as well plug that21:35
cpopellyash.21:36
cpopellare we going drinking thursday21:36
cpopellbefore we drive up friday21:36
kanzurethe n is weird21:36
yashgarothwhere at, vista? if I can stay up there for the night then sure21:36
kanzurewould you guys prefer to use blackhatbio.com? i still have it.21:36
yashgarothyeah it's kinda dumb, like biotech 'n' beyond, darn tootin'21:36
kanzurepfft jojack in a lab coat.21:36
yashgarothwith a tube of green21:37
kanzurewho... who made this site.21:37
kanzure:(21:37
kanzure"designed by Richard Sportsman"21:37
kanzurenever hire this man for web design21:37
yashgarothyeah ,him21:37
kanzureand it's wordpress?? hah.21:38
yashgarothhis family does wine testing, I don't know where he got his web dev skills21:38
yashgarothbut he was the free-est option21:38
kanzureyou guys could've asked me..21:38
yashgarothluckily chido's logo is there making it look good21:38
yashgarothI'll pitch you to jojack21:38
cpopellyashgaroth: yeah, might be best. my dad's a curmudgeonly old fuck though21:39
yashgarothhaha21:39
yashgarothwell we'll be drinking up in LA presumably?21:40
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kanzurelibcurl pop3 buffer overflow vulnerability http://blog.volema.com/curl-rce.html#.URSbGfZA7CA22:33
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--- Log closed Fri Feb 08 00:00:54 2013

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