--- Log opened Thu Aug 30 00:00:11 2012
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01:13 <@kanzure> http://diyhpl.us/~bryan/papers2/Swartz,%20Aaron%20Indictment.pdf
01:13 <@kanzure> so i hadn't read this, but it appears that he was using mailinator :P
01:15 <@kanzure> "gary host" "ghost"
01:16 < brownies> kanzure: and Grace Host!
01:16 < brownies> hahah
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01:17 <@kanzure> "keepgrabbing.py"
01:18 <@kanzure> lolz "“Keepgrabbing2.py” had distinct similarities to “keepgrabbing.py.”"
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01:21 <@kanzure> it's funny because my secret identity is "john testing" (johntesting@mailinator.com) of "john testing solutions, ltd."
01:21 <@kanzure> but ghost makes more sense i guess
01:24 < brownies> did they subpoena Mailinator?
01:24 <@kanzure> no
01:24 <@kanzure> or, i don't think so
01:24 <@kanzure> they probably just saw that he was using those email addresses
01:25 <@kanzure> mailinator has to receive a tremendous amount of email.. no way they are keeping any of it
01:26 < brownies> yeah but they probably keep server logs right?
01:26 < brownies> i.e. it's not what you use if you're actually serious about privacy
01:26 <@kanzure> oh sure, i just use mailinator when i don't care
01:29 < brownies> yeah, same.
01:29 <@kanzure> why are you awake
01:29 <@kanzure> aren't you supposed to be writing paranoid deletion stuff?
01:29 < brownies> bleh
01:29 < brownies> spent like an hour chasing a heisenbug ... now i'm eating dinner and procrastinating
01:30 < brownies> i've been super unproductive lately. i should just block all the timewasters.
01:30 < brownies> why are YOU awake? isn't it like 4am for you?
01:30 <@kanzure> i mistimed some amphetamine intake because i'm an idiot
01:31 < brownies> solid reason
01:33 < archels> kanzure: pm
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01:44 <@kanzure> archels: counter pm
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04:58 < archels> http://www.nature.com/news/calorie-restriction-falters-in-the-long-run-1.11297
04:58 < archels> well, fuck.
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05:27 < chris_99> http://www.wired.co.uk/news/archive/2012-07/25/mit-algorithm
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06:12 < foucist> chris_99: yeah someone pasted that in #startups, my comment was that it seems like a trivial development, but i didn't look at the paper
06:13 < chris_99> i want to know what kind of camera they used and it's fps rate
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06:17 < chris_99> 'processes 640 × 480 videos at
06:17 < chris_99> 45 frames per second'
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10:04 < kanzure> sokushinbutsu: hi
10:05 < sokushinbutsu> hey
10:05 < sokushinbutsu> have we talked on irc before?
10:05 < sokushinbutsu> i normally hang out in #reddit-nootropics
10:07 < kanzure> no, we've never talked.
10:14 < delinquentme> sokushinbutsu, kanzure is into noots
10:16 < kanzure> "pen Source Ecology is currently recruiting two key members to our team: a Master Prototyper and a Machine Designer. This is part of our work on the Global Village Construction Set (GVCS)."
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10:39 < delinquentme> THIS
10:39 < delinquentme> http://medgadget.com/2012/08/stanford-cooling-glove-more-dope-than-steroids-video.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+Medgadget+%28Medgadget%29&utm_content=FaceBook
10:39 < delinquentme> from 180 pullups >> 620  over 6 weeks
10:39 < delinquentme> with COOLING.
10:39 < delinquentme> kanzure, lets make these.
10:40 < chris_99b> what do they use, peltier?
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10:40 < chris_99b> oh haha
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10:43 < chris_99b> that reminds me of Zoolander
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10:52 < kanzure> nmz787: hi
10:53 < delinquentme> chris_99, the glove?
10:53 < chris_99b> yeah
10:55 < nmz787> hi
11:06 < nmz787> I posted that Eulerian Video Magnification link to a ciocurious discussion about a month ago
11:06 < nmz787> but I think the organism has a shell
11:06 < nmz787> so it may not have shown any noticable patterns
11:07 < delinquentme> dude
11:07 < delinquentme> this s NUTS
11:07 < delinquentme> kanzure, start weight lifting :D
11:07 < delinquentme> its good for longevity
11:07 < delinquentme> nmz787, http://medgadget.com/2012/08/stanford-cooling-glove-more-dope-than-steroids-video.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+Medgadget+%28Medgadget%29&utm_content=FaceBook
11:07 < delinquentme> simple glove for heat exchange boosts performance ... substantially
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11:18 < chris_99b> so what benefits does this glove give
11:18 < chris_99b> i doubt you'd notice much difference unless you're already an elite athlete?
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11:20 < chris_99b> what do you mean about the Eulerian video thing, they're using it to show peoples pulses
11:20 < chris_99b> from what i can tell nmz787
11:20 < nmz787> yeah
11:21 < nmz787> but it magnifies certain parameters
11:21 < chris_99b> yeah like the colour
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11:21 < nmz787> this guy wanted some kind of feedback to tell if his mollusks or something were living OK
11:21 < nmz787> to test different growth additives and components
11:21 < nmz787> I think the code is all on MITs site
11:22 < nmz787> but I think the organisms have shells
11:22 < nmz787> so dunno if you'd be able to really magnify much of any phenomena
11:22 < chris_99b> ah right, so someone wants to use that MIT stuff with a shelled creature
11:22 < nmz787> maybe an imaging spectrometer could... hmm
11:22 < nmz787> that's not a bad thought
11:23 < nmz787> well I suggested it
11:23 < nmz787> to the guy
11:23 < chris_99b> or how about a FLIR
11:23 < nmz787> who was asking "how might I tell my thing is not dying, before it dies/is past point of no return"
11:23 < delinquentme> chris_99, its a glove which increases vasodilation through a small vacuum and then acts as a heat exchanger
11:23 < nmz787> maybe FLIR would tell something, but I'm not sure
11:24 < delinquentme> so like this could be built with 2 small pumps
11:24 < chris_99b> yeah i read a bit about the vacuum delinquentme so it says it prevents muscle fatigue
11:24 < delinquentme> one for the air and another for the water circulation
11:24 < chris_99b> but surely you'd have to be pretty decent to get to the point it helps
11:24 < delinquentme> no
11:25 < nmz787> delinquentme: i havent read yet... but you could just go swimming
11:25 < nmz787> derp
11:25 < chris_99b> hehe
11:25 < nmz787> heat derp exchanger derp all around
11:25 < delinquentme> nmz787, true but you're not doing massive weight bearing while swimming
11:25 < nmz787> :P
11:25 < nmz787> why not
11:25 < chris_99b> yeah just weight lift in the pool
11:25 < chris_99b> hehe
11:26 < delinquentme> you could but no one that I know of has stuck weights in a pool
11:26 < delinquentme> im trying to figure out what specifically induces the performance benefit
11:26 < nmz787> there http://www.youtube.com/watch?v=F8DMs4ovKcY
11:26 < delinquentme> "acute needs at peak exertion for heat dissipation "
11:26 < nmz787> so many "weight lifting underwater"
11:26 < nmz787> this http://www.youtube.com/watch?v=g5WOAdzlpGs
11:26 < kanzure> nmz787: so tom's post to diybio is a little unusual
11:27 < kanzure> it sounds like operon was trying to do yeast cloning to figure out whether or not the gene was being expressed?
11:27 < kanzure> and they didn't realize that it was just a promoter?
11:27 < chris_99b> read this bit delinquentme ''In 2009, it was discovered that muscle pyruvate kinase, or MPK, an enzyme that muscles need in order to generate chemical energy, was highly temperature- sensitive. At normal body temperature, the enzyme is active – but as temperatures rise, some of the enzyme begins to deform into the inactive state. By the time muscle temperatures near 104 degrees Fahrenheit, MPK activity completely shuts down.''
11:27 < kanzure> gah i mean operon-the-company not operon-the-thing
11:28 < delinquentme> HMMM!
11:28 < delinquentme> chris_99, was that on the website?
11:28 < chris_99b> yes
11:28 < chris_99b> http://news.stanford.edu/news/2012/august/cooling-glove-research-082912.html
11:28 < chris_99b> oh it's a different website
11:28 < chris_99b> but yeah
11:30 < kanzure> nmz787: "It is possible the presence of folding motifs or the GC rich portion interfered with the correct assembly of the gene (we were unable to obtain a clone with the correct gene sequence)"
11:30 < kanzure> "a clone" here refers to what?
11:30 < chris_99b> delinquentme, so i say we build a suit that does this ;)
11:31 < delinquentme> chris_99, you nailed it with whatever you googled
11:31 < nmz787> kanzure: just read
11:31 < delinquentme> im looking at the patents atm
11:31 < delinquentme> the balance needs to be struck where the vacuum is just sufficient to overcome the vessel constriction that happens with cooling
11:31 < nmz787> kanzure: it's because they aren't doing single molecule sequencing I think
11:31 < delinquentme> vasoconstriction oddly enough :D
11:32 < nmz787> and because they aren't doing single molecule synthesis
11:32 < kanzure> what are they doing, then?
11:32 < nmz787> same old same old
11:32 < nmz787> all current gen can't handle that kind of stuff
11:32 < kanzure> so when they say "cloning" they mean some PCR reaction, not yeast cloning stuff?
11:32 < nmz787> or rather, handles it poorly
11:32 < chris_99b> delinquentme, do you even have to have a vacuum
11:32 < delinquentme> chris_99, yeah its probably quite influential
11:32 < delinquentme> think about your hands in the cold
11:32 < nmz787> cloning is a not specific to a organism
11:33 < delinquentme> its WAS an adaptive mechanism to constrict when it gets cold ...
11:33 < kanzure> nmz787: i think i have a misunderstanding about when the word 'cloning' can be used :)
11:33 < nmz787> they don't use cloning
11:33 < nmz787> they say clone
11:33 < kanzure> hmm.
11:33 < nmz787> the reactions are all bulk
11:33 < kanzure> ok
11:34 < nmz787> then they bulk put them in bulk vectors
11:34 < chris_99b> i think you could just whack a peltier on them, delinquentme ?
11:34 < nmz787> then do a bulk electroporation
11:34 < kanzure> wait what? why are they using vectors at all??
11:34 < nmz787> and dilute to spread the cells out far enough so only 1 cell will form a colony... rather than two close cells growing into the same visually detectable colony
11:34 < kanzure> is this to increase the yield of the construct?
11:34 < nmz787> then the pick that colony, and PCR the vector, and sequence
11:34 < nmz787> and then find a good clone
11:35 < nmz787> that is identical to what text file you sent them
11:35 < nmz787> rather than checking the text file at the synthesis level
11:35 < kanzure> so for some reason i assumed they would just synthesize -> pcr -> sequence
11:36 < nmz787> no, it would likely get lost... or PCR is more erroneous than in vivo amplification
11:36 < nmz787> plus they're not using microfluidics
11:36 < nmz787> if they were, sure on board PCR could work
11:36 < nmz787> but they're still just doing bulk synthesis
11:36 < nmz787> of 20-200 mers
11:36 < kanzure> i think yashgaroth is a proponent of doing the colony picking for dna synthesis, he's mentioned it once or twice
11:36 < kanzure> in some positive fashion
11:37 < nmz787> so the PCR would be heterogenous in data
11:37 < kanzure> maybe there's some "dna repair" and "dna maintenance" benefits that you get out of the cells
11:37 < nmz787> yes
11:37 < nmz787> or you get a better polymerase that is slower
11:37 < nmz787> but has error correction
11:37 < nmz787> but its not perfect
11:38 < nmz787> but nano/microfluidics solves a lot of this time
11:38 < kanzure> well, i blame failure of memory for me not identify their method as using-cells-as-reactors-for-dna-synthesis
11:38 < kanzure> *identifying
11:38 < nmz787> that is why clone was there
11:38 < nmz787> "we were unable to obtain a clone with the correct gene sequence"
11:39 < delinquentme> chris_99, MAYBE.
11:39 < delinquentme> chris_99, but I think the function here is the net thermal capacity
11:40 < delinquentme> do peltiers have that kind of total thermal capacity?
11:40 < delinquentme> My guess is they'd be substantially less...
11:40 < chris_99b> you can cool stuff pretty damn cold with them, to below freezing
11:41 < nmz787> just weightlift under a waterfall
11:41 < nmz787> geez
11:41 < nmz787> and use a water chiller
11:41 < chris_99b> heh or that
11:43 < delinquentme> dunk nuts on the lower half of squats?
11:46 < delinquentme> chris_99, do you have pelts laying around?
11:46 < chris_99b> yes
11:46 < chris_99b> i've got ones that require a car battery to run ;)
11:47 < chris_99b> (400W ones)
11:47 < delinquentme> Hmmm
11:47 < nmz787> delinquentme: why not just lift in front of a big ass A/C
11:47 < delinquentme> so you apply electricity and it gets cold ... why dont people use these in AC units?
11:47 < nmz787> or install A/Cs from multiple directions
11:48 < delinquentme> nmz787, you no read article.
11:48 < nmz787> because they're not efficient
11:48 < nmz787> reading now
11:49 < delinquentme> nmz787, heat exchange through most parts of the body is hindered by body fat, muscle etc
11:49 < chris_99b> you need to cool the hell out of the hot side delinquentme
11:49 < delinquentme> and heat exchange in the hands is hindered by vasoconstriction
11:49 < delinquentme> so you need to fight that
11:49 < delinquentme> chris_99, the wikipedia article says it can heat or cool
11:49 < chris_99b> it can
11:50 < chris_99b> it has a hot and cold side
11:50 < delinquentme> I guess a plugin version would be interesting
11:51 < gnusha> diyhpluswiki.git: fa4f3cb add a contact for egyptian diybio
11:51 < delinquentme> chris_99, soooo how about a reading from those that you have
11:51 < delinquentme> like whats the temp difference between the cool side and ambient
11:52 < delinquentme> ALSO water / coolant would easily wrap around hands ...
11:52 < delinquentme> are these peltiers stiff?
11:52 < chris_99b> i know that you can easily get from 25C on one side or less to < 0 on the cold side
11:52 < chris_99b> and yes they are stiff
11:53 < delinquentme> id bet the best cooling spot would be the back of the hand
11:53 < delinquentme> greatest vessel diameter + little to no body fat / muscle
11:53 < delinquentme> BTW these sell for 3K a pop on their website :D
11:54 < delinquentme> and they *do* have patents
11:54 < chris_99b> link to the patent?
11:54 < nmz787> ok
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11:55 < nmz787> still seems like my mom who swims as primary excercise is covered
11:55 < nmz787> but pretty cool
11:56 < nmz787> could just have a weight room next to a swimming pool.... do a set, do a lap
11:56 < delinquentme> http://www.google.com/patents?id=qdytAAAAEBAJ&pg=PA46&lpg=PA46&dq=avacore&source=bl&ots=jFAC4kNxwc&sig=3Gcv61jjElePDIEnT2ExMEZtEUI&hl=en&sa=X&ei=lbA_UNe9H8Xv6wGe74GwBg&ved=0CDUQ6AEwAQ#v=onepage&q=avacore&f=false
11:56 < delinquentme> http://www.google.com/patents?id=-h0FAgAAEBAJ&pg=PA28&lpg=PA28&dq=avacore&source=bl&ots=nDenJPih_d&sig=xXvcYpkr08-1enfMCH2sbyAGA0M&hl=en&sa=X&ei=lbA_UNe9H8Xv6wGe74GwBg&ved=0CDgQ6AEwAg#v=onepage&q=avacore&f=false
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11:56 < delinquentme> nmz787, its the heat transfer
11:56 < chris_99b> say you could cool yourself while running though nmz787
11:56 < chris_99b> that could be interesting
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11:56 < delinquentme> you dont get heat transfer into your core as quickly swimming laps
11:57 < nmz787> i've never been overheated in water
11:57 < delinquentme> specifically because you're cooling exteriors which leads to decreased blood flow in those areas
11:57 < delinquentme> the function here is to drop the core temperature
11:57 < nmz787> i feel like the body would be smarter than that, aren't those blood vessels controlled by the neuro system?
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11:57 < delinquentme> no
11:57 < nmz787> no?
11:58 < delinquentme> the body is designed to constrict blood flow to spots that are cold
11:58 < kanzure> jrayhawk: is there a way to get the ikiwiki toc plugin to give semantic anchor names instead of stuff like "index17h1"?
11:58 < delinquentme> why do you think your hands get cold in winter if you're a white male
11:58 < nmz787> "more convenient than, say, full-body submersion in ice water"
11:58 < nmz787> telling me if you don't like swimming, buy our product
11:58 < delinquentme> but again if the function here... is to NOT decrease muscle temp ( external )
11:58 < nmz787> my hands are always warmer than my dark girl
11:58 < nmz787> in the winter
11:59 < nmz787> it doesn't say don't decrease muscle temp
11:59 < delinquentme> IDK my hands get cold in the winter .. it was adaptive
11:59 < kanzure> "weightlifting under a waterfall" sounds bad ass, let's do that
11:59 < delinquentme> it saved thermal energy and diverted it to the core
11:59 < nmz787> your hands get cold because of heat transfer to the cold air
11:59 < delinquentme> and because of the process known as vasoconstriction
12:00 < delinquentme> blood is shunted
12:00 < nmz787> and because your blood vessels close up so your core temp doesnt drop
12:00 < delinquentme> ^^^^^^^^^^
12:00 < nmz787> but i don't think that's the same when the rest of your body is hot
12:00 < delinquentme> thats the process that the vacuum fights
12:00 < delinquentme> but as you cool your hands
12:00 < delinquentme> its a localized function
12:00 < nmz787> i don't think the vacuum does much, that seems like it could be explained by pressure physics
12:00 < delinquentme> you want to retain the blood flow capacity
12:01 < nmz787> it would enable blood to enter, just as much as it would hinder it leaving
12:02 < nmz787> still seems like you would not overheat if you just worked out in a pond
12:02 < nmz787> just get rubber coated weights
12:02 < delinquentme> nmz787,
12:02 < nmz787> put all your stuff in the pool
12:02 < delinquentme> I think your solutions are silly.
12:02 < nmz787> sure, but it would work
12:02 < delinquentme> I like super gloves
12:02 < delinquentme> and they're also cheaper than pools
12:02 < nmz787> if you are into running, well, i think thats silly, much worse than swimming on the knees
12:03 < nmz787> but you could prob just take a mold of your hand
12:03 < nmz787> make a negative, make it a little bigger, cast some metal around that, and there's your vacuum glove
12:04 < nmz787> or 3D scanner your hand
12:04 < gnusha> laser_etcher.git: 6bb5233 buncha optics links,
12:04 < gnusha> laser_etcher.git: 9c5e333 Merge branch 'master' of diyhpl.us:/srv/git/laser_etcher
12:04 < delinquentme> nmz787, im totally about swimming.
12:04 < delinquentme> but for weight lifting and the like ... swimming will cut and tone
12:05 < delinquentme> swimming wont build mass
12:05 < delinquentme> you need all of these things
12:05 < nmz787> right, which is why i said put the weights in the water
12:05 < nmz787> that /will/ work
12:05 < kanzure> nmz787: what is "CD-ROM MECHANICS__COEN 180.htm"
12:05 < nmz787> a file
12:05 < EnLilaSko-> lol nmz787
12:05 < delinquentme> but can we agree that these hand held jobs ... even at 3k a piece ... are cheaper than pools
12:05 < delinquentme> like I think you're just trying to mess with me nmz787
12:05 < delinquentme> *pushes into pool*
12:05 < nmz787> I dont see it here http://diyhpl.us/laser_etcher/
12:06 < nmz787> no
12:06 < kanzure> ikiwiki doesn't handle files with spaces :P
12:06 < nmz787> i think a pool could be found for free on craigslist
12:06 < nmz787> grr
12:06 < nmz787> why isnt it here http://diyhpl.us/laser_etcher/CD-ROM%20MECHANICS__COEN%20180.htm
12:06 < kanzure> nmz787: but you can find it here: http://diyhpl.us/cgit/laser_etcher/tree/
12:06 < kanzure> like i said, it's because ikiwiki doesn't do spaces
12:07 < ThomasEgi> anyone ever tried to build a laser-etcher based on the same principle as a drum-scanner, just in reverse?
12:07 < kanzure> in filenames.
12:07 < nmz787> ThomasEgi: interesting idea
12:07 < ThomasEgi> at least for scanning they get insane high resolutions. and the mechanics are comparebly simple
12:07 < nmz787> ThomasEgi: does the drum have a very good roundness and flatness profile?
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12:09 < gnusha> laser_etcher.git: 4fdc18b removed spaces
12:10 < kanzure> nmz787: according to git, you deleted all the files
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12:10 < kanzure> i mean, the files that you added
12:10 < ThomasEgi> nmz787, i meant just the overall principle. you can get very precise drums off the shelf.
12:10 < ThomasEgi> maybe something like a spinning table would make more sense here
12:11 < gnusha> laser_etcher.git: 54a2153 removed another space
12:11 < ThomasEgi> the whole point would be to avoid stacking 2 linear axis
12:11 < nmz787> http://diyhpl.us/laser_etcher/CD-ROM_MECHANICS__COEN_180.htm
12:11 < nmz787> there it is
12:11 < nmz787> ThomasEgi: how about getting the PDMS onto the drum
12:12 < ThomasEgi> hey i am no expert :D i was just throwing the idea into the room
12:12 < nmz787> if you added it wet, it would stretch after peeling off on one side (tension)
12:12 < nmz787> opposite would occur if you placed flat dry PDMS on a the drum
12:12 < nmz787> yeah interesting
12:12 < kanzure> "Have you heard of Cycript? It's an open source JavaScript-ObjC bridge, maintained by Jay Freeman, the creator of Cydia. It currently supports this interactive console functionality (with tabbed autocomplete!), by injecting into a specified process."
12:13 < nmz787> maybe you could just have drum microfluidics
12:13 < ThomasEgi> as i said. maybe having it on a flat disk that spins, like a cdrom, would work too.
12:13 < kanzure> saurik strikes again
12:13 < kanzure> http://cycript.org/
12:13 < ThomasEgi> nmz787, might work too.
12:13 < nmz787> ThomasEgi: I've thought of that, I even have some MATLAB/Octave code that's supposed to turn an image into a CD-ROM ISO for burning
12:14 < nmz787> but i don't remember messing with it too much after it didn't immediately work
12:14 < nmz787> but I want to avoid a pulsed writing system
12:14 < nmz787> rather, I want as few on/off cycles as possible
12:14 < ThomasEgi> why?
12:14 < ThomasEgi> that's just electronics.
12:15 < nmz787> I feel like pulsing would make jagged channels
12:15 < nmz787> well the laser is CW otherwise
12:15 < nmz787> constant wave
12:15 < ThomasEgi> hm. it's not a diode-laser?
12:15 < nmz787> it is
12:16 < nmz787> but its CW
12:16 < ThomasEgi> that's odd.
12:16 < ThomasEgi> how many watts?
12:16 < nmz787> output is max 800mW I believe
12:16 < nmz787> in 405nm
12:16 < ThomasEgi> uhm.
12:16 < ThomasEgi> that.. should be totaly within pulseable limits
12:16 < nmz787> prob about 4 W at the power supply
12:16 < nmz787> yeah, but I dont want pulses
12:16 < nmz787> I want CW
12:17 < nmz787> to avoid jagged channel edges
12:17 < ThomasEgi> what you want, is to avoid jagged channel edges, not to aloid pulsed lasers
12:17 < ThomasEgi> appropriately handeled i see no problem there.
12:18 < nmz787> what's the advantage of pulsing?
12:18 < ThomasEgi> you could use continous motion for the mechanics
12:18 < ThomasEgi> less vibrations, easier to handle.
12:18 < nmz787> you mean DC motors?
12:19 < nmz787> instead of steppers?
12:19 < ThomasEgi> i'd recommend 3phase motors for maximum smoothness
12:19 < ThomasEgi> but if you would go with a drum like setup
12:19 < nmz787> hmm, I've heard the inertia will keep things smooth between steps
12:19 < ThomasEgi> you can have the drum spin pretty fast and just meassure it's rpm. and moving the laser on a signle axis.
12:19 < ThomasEgi> and the pulsing does the rest
12:20 < TheEmpath> Can the thermodynamic arrow of time be definitively established pre-ignition of the Big Bang?
12:21 < ThomasEgi> nmz787, i mean.. drumscanners are known to scan more than 10000ppi
12:21 < ThomasEgi> try getting that with another mechanical setup.
12:22 < ThomasEgi> bbl. need to go out  shopping for some food.
12:22 < nmz787> hmm
12:22 < nmz787> me too
12:22 < nmz787> ttyl
12:25 < jrayhawk> Re: ikiwiki toc anchors: no, ikiwiki has a poor relationship with anchors in general
12:26 < jrayhawk> it'd be nice if headers generated at least 'id' attributes if not full anchors
12:27 < jrayhawk> re: spaces in filename: it's possible to enable this. it's disabled by default to avoid problems with namespace collisions between spaces and underbars when compiling.
12:29 < kanzure> oh i suppose the header thing should be a markdown thing, not an ikiwiki thing
12:30 < jrayhawk> Yeah, probably.
12:30 < jrayhawk> i wonder if my browser supports anchor-by-id
12:31 < kanzure> i only learned about that recently.. wish i knew it earlier, would have saved a bunch of trouble
12:33 < nmz787> i was looking at a site that didnt have IDs where it had a visual 'anchor'
12:33 < nmz787> bold and bigger text or something
12:36 < kanzure> by anchor i mean <a name="anchor_name" /> giving page.html#anchor_name a thing
12:36 < kanzure> or <element id="blah"> giving page.html#blah in more recent browsers
12:38 < jrayhawk> the links-family supports that
12:39 < jrayhawk> it appears to be a 4.01 thing, at least
12:48 < kanzure> this is what tom randall has been up to: http://www.roningenetics.org/Sequencing.html
12:49 < kanzure> "The original data represents ~600 X coverage of the 40 Mb N. crassa genome."
12:49 < kanzure> 600x coverage sounds sorta extreme
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13:11 < nmz787> kanzure: depends on the read length
13:11 < nmz787> and those wonky areas that are hard to synth/sequence
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13:12 < nmz787> http://www.youtube.com/watch?v=0LdavB22YdU
13:12 < nmz787> whoops
13:12 < nmz787> wrong im
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13:26 < superkuh> I received my first DMCA take-down request today.
13:26 < delinquentme> ^^^ nice!
13:28 < nmz787> for what?
13:31 < superkuh> Principles of Gene Manipulation and Genomics ebook, Rights Holder: John Wiley and Sons, Inc.
13:31 < superkuh> http://superkuh.com/dmca001.html
13:33 < chris_99b> w00t http://users.ecs.soton.ac.uk/msn/book/new_demo/hough/
13:34 < kanzure> http://blog.ioactive.com/2012/08/stripe-ctf-20-write-up.html
13:34 < kanzure> superkuh: congratulations! took them forever.
13:35 < nmz787> chris_99b: see that's a quick algorithm in Java :P so it would be even faster in openCV
13:35 < chris_99b> heh indeed, i was suprised how fast it was
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13:38 < chris_99b> i've almost got all the stuff to make a crude magnetic stirrer now, except the magnets :)
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14:08 < nmz787> "Cleveland BioLabs has been trying to move its lead candidate, CBLB502, along this development path. The drug is an injectable recombinant derivative of a bacterial protein flagellin that activates signaling pathways and suppresses apoptotic cell death in hematopoietic and GI cells. The firm also is exploring CBLB502 as a radioprotectant in medical procedures. It has completed animal efficacy and human safety studies, and it has regul
14:09 < nmz787> seems like you'd want radiation-damaged cells to apoptose, rather than continue to possible mutate into a cancer
14:10 < nmz787> if that actually got approved, people would think it was great, but it could in reality just keep them coming back
14:10 < nmz787> hmm, this is the stuff of shrewd marketing I think by pharma... to keep themselves in business
14:11 < kanzure> this is neat for tracing javascript execution flow on a page: https://github.com/Imaginea/FireFlow http://blog.imaginea.com/fireflow/
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15:35 < kanzure> python reverse engineering tools http://erpscan.com/wp-content/uploads/2012/06/Python-arsenal-for-RE-1.1.pdf
15:41 < kanzure> this looks like an amusing way to play with kernel memory dumps: https://github.com/trolldbois/ctypes-kernel
15:47 < chris_99b> how do you dump RAM in these days, kmem or whatever seems no longer readable
15:48 < chris_99b> *in linux
15:48 < kanzure> pastebin monitoring service: https://github.com/xme/pastemon
15:48 < kanzure> chris_99b: are you root when you try kmem?
15:48 < chris_99b> yeah
15:48 < chris_99b> they prevent you reading it now
15:48 < kanzure> uhh ask jrayhawk
15:52 < jrayhawk> IIRC it's a really stupid whitelisting-by-cmdline-string kernel option
15:53 < jrayhawk> You can probably sudo -i; ln `which bash` /root/X;
15:54 < jrayhawk> i suppose i should look up what they actually whitelist
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15:54 < loanshark> helloo
15:55 < kanzure> loanshark: get these. http://diyhpl.us/wiki/diybio/faq/books/
15:55 < kanzure> they are linked now.
15:55 < loanshark> ooh!
15:55 < loanshark> thank you
15:55 < loanshark> btw,  i have a reading suggestion
15:56 < loanshark> http://www.amazon.com/gp/product/B004H4XCVY/ref=kinw_myk_ro_title
15:57 < loanshark> Biopunk: Solving Biotech's Biggest Problems in Kitchens and Garages
15:57 < kanzure> why?
15:57 < chris_99b> have you read it loanshark?
15:57 < loanshark> I am reading it
15:57 < kanzure> yeah i mean, after reading it, i can't really recommend it
15:57 < kanzure> unless you're an anthropologist
15:57 < loanshark> xD
15:57 < loanshark> Its just an interesting read
15:57 < loanshark> in my oppinion
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15:58 < loanshark> opinion*
15:58 < kanzure> http://diyhpl.us/~bryan/papers2/diybio/biopunk.pdf
15:58 < chris_99b> i thought it was going to tell me how to create a glowing cat ;)
15:58 < loanshark> -.-
15:58 < skorket> evening everybody
15:58 < kanzure> or if you need a .mobi file for some bizarre reason http://diyhpl.us/~bryan/papers2/diybio/biopunk.mobi
15:59 < loanshark> i just spent 13 hours moving my ship from dry dock to pier side waiting for flooding/fire
15:59 < loanshark> so i had a lot of time to kill
16:00 < loanshark> so i bought that book and I think its very informative, if you are interested in DIY bioengineering projects
16:00 < jrayhawk> new solution: feed your cat https://www.unitednuclear.com/index.php?products_id=383
16:00 < chris_99b> in seriousness though the molecular biology of the cell looks awesome from skimreading it
16:00 < kanzure> chris_99b: look at the molecular cloning book
16:01 < chris_99b> ta i'll check it out
16:01 < chris_99b> haha that looks fun jrayhawk
16:01 < chris_99b> i've got one of those little tritium keyrings
16:01 < loanshark> I'm currently reading molecular biology of the cell :3
16:02 < kanzure> we used to have way more unitednuclear.com links dropped in here... i miss that
16:09 < kanzure> https://blog.gregbrockman.com/2012/08/system-design-stripe-capture-the-flag/
16:10 < kanzure> oh oops. that's not different.
16:15 < chris_99b> has anyone ordered anything from Carolinatech
16:16 < chris_99b> er, http://www.carolina.com
16:16 < chris_99b> they say something about not shipping certain stuff to residential addresses
16:22 < jrayhawk> a sure sign you're buying something good
16:24 < chris_99b> heh
16:32 < kanzure> chris_99b: i haven't personally ordered from them, but i've used a number of their products before
16:33 < chris_99b> cool, pleased with them?
16:33 < kanzure> uh, the gfp kit seemed to work
16:34 < kanzure> it was one of those lame standard projects in a biology class in high school
16:34 < chris_99b> i want some gfp to play with electroporation
16:48 < chris_99b> you can use a microinjector can't you to introduce dna into any type of cell?
17:03 < kanzure> so this looks like another patent defense pool: http://www.rpxcorp.com/
17:03 < kanzure> "As a provider of patent risk solutions, RPX helps corporations manage their exposure to patent litigation. We have introduced efficiency to the patent market by providing a rational alternative to traditional litigation strategy for our clients, offering defensive buying, acquisition syndication, patent intelligence, and advisory services."
17:03 < kanzure> 'rational patent'
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18:35 < kanzure_> beep
18:36  * ThomasEgi activates the trainhorn
18:38 -!- kanzure_ is now known as kanzure
18:40 < jk4930> beep? hi there
18:40 < brownies> boop
18:42 < kanzure> hi brownies.
18:42 < brownies> hello
18:42 < brownies> kanzure: did i tell you i cured my DelayedJob woes? ...by using it in ways other than recommended by the README? http://build.thoughtbot.com/delayed-job/
18:43 < kanzure> so the solution is the "Store IDs, not records" thing?
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18:48 < kanzure> yashgaroth: yo.
18:48 < yashgaroth> whatup
18:48 < kanzure> yashgaroth: http://diyhpl.us/wiki/diybio/faq/books
18:48 < kanzure> i need something else to add to this
18:48 < kanzure> sambrook doesn't actually go over "basic pcr" and "basic gels" or "basic cell culture"
18:50 < yashgaroth> I'll glance over what I have and see if there's anything that fits the bill
18:50 < brownies> kanzure: eh, the overall solution is to carve things out into standalone subclasses that are jobs, rather than just tacking .delay onto random things
18:51 < brownies> once you architect with that in mind, it looks like other things fall into place... i was able to clean up code in other models/controllers.
18:51 < kanzure> oh i see
18:52 < kanzure> i never got into the habit of using .delay directly when i was using delayed_job
18:52 < kanzure> i usually had tiny classes i'd write and then i'd make workers do those things somehow
18:52 < kanzure> which is also very handy for long-lived tasks that you must run over the heroku console
18:53 < brownies> apparently we have 600+ failed jobs just hanging out in the DJ table
18:53 < brownies> thanks to the geniuses who architected DJ, it didn't plug into our existing app-wide error-notification system
18:53 < brownies> and i've just been happily going on for weeks/months presuming it was all working.
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18:56 < yashgaroth> so by 'basic' do you mean the principles, or a demo protocol?
18:56 < kanzure> yashgaroth: i don't want any more books that describe biology
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18:56 < yashgaroth> sooo protocols
18:57 < kanzure> yashgaroth: yes
18:57 < kanzure> but "methods in molecular biology" seems to immediately jump off the deep end with transgenic ewoks
18:57 < yashgaroth> oh yeah that's a collection of esoterics
18:57 < kanzure> there's a lot of skills you need to pick up before your ewok cell culture is going to even live a few days
18:58 < yashgaroth> weaning ewok cells off of FBS is such a hassle
18:58 < kanzure> i'm aware that a lot of the basics are picked up in an actual lab because of oral tradition
18:58 < kanzure> buut there probably is some resource i'm forgetting?
18:59 < brownies> gather 'round the bunsen burner, kids... time to learn how to culture a wooly mammoth
18:59 < yashgaroth> hmm the protocol-online link is broken
19:00 < kanzure> http://protocol-online.org/ works for me?
19:00 < yashgaroth> pretty much, I mean pcr is just template + primers + reaction mix + water
19:00 < yashgaroth> no, their "basic PCR" link
19:00 < yashgaroth> http://www.protocol-online.org/cgi-bin/prot/jump.cgi?ID=3320
19:01 < kanzure> oh man, methodmint went down? they seem to be redirecting to some other lame thing http://methodmint.com/
19:01 < yashgaroth> guess the PI fucked one too many postdocs
19:01 < kanzure> ah.. http://research.abl.es/
19:01 < kanzure> so, nobody uses methodmint/research.abl.es because biologists are anti-compooter
19:01 < kanzure> and protocol-online.org still sucks
19:01 < yashgaroth> yeah but their 'basic gel' protocol is ok...lemme read http://www.methodbook.net/dna/agarogel.html
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19:02 < yashgaroth> I'd say more that computers are anti-biologist, but yes
19:03 < kanzure> protocol-online.org is a terrible link aggregator, but that's basically what it is
19:04 < yashgaroth> they seem to be quite old links to webpages of the rare helpful professor
19:04 < kanzure> it has a few basic protocols in a few places, but it's not reliable in terms of "will there definitely be a rtPCR protocol"
19:04 < kanzure> yeah
19:04 < kanzure> methodmint was trying to use stackoverflow's ui to do protocols/voting, but it hasn't seemed to catch on
19:04 < yashgaroth> it's not like biologists are good at organizing, like for example does rtpcr mean reverse transcriptase or real time? no one will step up and delineate
19:05 < kanzure> oh well, acronyms are a bad idea in biology anyway
19:05 < kanzure> *oh, well
19:05 < yashgaroth> unless it's cox
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19:06 < yashgaroth> hey at least they don't name proteins after the discoverer, I'd quit biology in that case
19:06 < kanzure> khandradikanicase
19:06 < kanzure> lakshomininitinate
19:06 -!- strangewarp [~strangewa@c-76-25-200-47.hsd1.co.comcast.net] has joined ##hplusroadmap
19:06 < yashgaroth> chandrasekharkinin
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19:07 < kanzure> yashgaroth: so, is there a book that goes over these basic protocols?
19:07 < kanzure> 'cause i'm not aware of it
19:08 < yashgaroth> anyway it is still a lot of 'bunsen burner tales' since the field doesn't recognize diybio at all...of course you don't need a centralized resource
19:08 < kanzure> i think i often see basic protocols muttered in supplements sometimes
19:08 < yashgaroth> oh no there's not that I know of
19:08 < yashgaroth> even an SOP won't cite some canonical version of 'a gel'
19:08 -!- loanshark [~loanshark@ip72-218-125-108.hr.hr.cox.net] has quit [Quit: loanshark]
19:08 < kanzure> SOP?
19:08 < yashgaroth> standard operating procedure
19:09 < yashgaroth> "we tell you to do it this way, which you never will, but we can blame you if you don't"
19:09 < kanzure> brownies: what do you think? i've always wanted to replace http://protocol-online.org/ but i haven't figured out all the details (besides the technical crap)
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19:12 < kanzure> yashgaroth: when i joined a lab once, i was handed some laminated cards with instructions for their basic pcr
19:12 < yashgaroth> mhm
19:12 < kanzure> and for their gel mix they just had me copy something into a notebook
19:13 < yashgaroth> there is a long, proud tradition of obfuscating sources in benchwork
19:14 < kanzure> maybe one way to motivate people to care about good protocols would be checklists
19:14 < kanzure> and they might care to update the checklist to make it easier to debug in the future, or something
19:15 < yashgaroth> yeah that's the dream
19:15 < brownies> checklists would be good
19:16 < brownies> last time i joined a lab (which was a damned long time ago...) no one told me a damn thing
19:16 < brownies> kanzure: why/how do you want to replace it?
19:16 < kanzure> i want to replace it because it's fucking awful
19:16 < brownies> wouldn't you basically have to crowdsource standard practices from all sorts of practitioners?
19:16 < kanzure> and there's no accountability or way to improve it
19:16 < brownies> and why would those practitioners want to write down stuff for you?
19:16 < kanzure> yes, probably
19:17 < brownies> unless you're a secret genius with like 18 nobel prizes, let's go with yes
19:17 < kanzure> yeah, i don't claim to have that part figured out
19:17 < kanzure> there's maybe the 'credibility' thing or the 'oh look at my publication record' thing
19:17 < kanzure> but they would just publish in journals for that ;)
19:18 < kanzure> methodmint is an interesting case for me because they applied the stackoverflow software to protocols, and it had a very small amount of activity (about 20 users)
19:18 < brownies> i mean, wikipedia is a *great* resource for e.g. pure mathematics
19:19 < kanzure> http://research.abl.es/methods/tagged/molecular-biology/
19:19 < kanzure> but the top one has '2 votes' wtf
19:19 < brownies> but how did those mathematicians converge on wikipedia? and why? i have no clue.
19:19 < kanzure> "6X DNA Loading Buffer for Agarose" and 1 user
19:19 < kanzure> brownies: actually, they also converge on mathoverflow (anton's site)
19:20 < brownies> kanzure: actually, derp. presumably the actual *methods* for many things are written down in published papers, which are... behind paywalls.
19:20 < kanzure> yes, but most of those methods verge on esoteric
19:20 < brownies> but if you're at an institution, you just find N papers who all used the technique of interest to do an expriment, read how they did it, maybe send some emails, and there you go.
19:20 < brownies> why esoteric?
19:20 < kanzure> in my experience if you're at an institution, you usually just have someone tell you once, but yeah
19:20 < brownies> presumably the boring methods are also written down?
19:20 < brownies> well, sure, that too.
19:20 < kanzure> the boring methods are just shared in lab culture
19:20 < kanzure> humans talking to humans and being friendly
19:21 < kanzure> it's possible that methodmint got no attention because its creators weren't advertising
19:21 < kanzure> yashgaroth: put on your bioglasses and tell me what you see? http://research.abl.es/methods/tagged/molecular-biology/
19:21 < brownies> yes, nerds are known for being highly socially adept and great public speakers -_-
19:22 < kanzure> well, if your prof says "hey, you will need to run a gel on that, ask tobi" you go ask tobi
19:22 < brownies> what if tobi is on vacation?
19:22 < kanzure> and tobi will show you where the parts are stored
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19:22 < kanzure> haha nobody goes on vacation in a lab man, it's a labor camp
19:22 < yashgaroth> looks ok? I seem to remember reading a couple some months ago and being aghast
19:22 < brownies> i read phd comics! there were vague mentions of occasional vacations!
19:22 < kanzure> tobi is always there because he's from china and has a dreadful fear that if he leaves, just once, ever, that he wont have a job
19:23 < yashgaroth> I guess you could scrape kit manufacturer protocols since so much benchwork is with pre-made kits nowadays
19:23 < kanzure> true, kit makers probably have an incentive to make usable protocols
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19:24 < kanzure> "your pcr mix never fucken works" is a bad review
19:24 < kanzure> s/bad/normal
19:25 < kanzure> brownies: so, i agree with you that most people who would benefit from thsi resource will just use their paywalls or colleagues
19:25 < kanzure> but presumably there's incentives for others outside that system to contribute?
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19:27  * brownies ponders
19:27 < kanzure> brownies: btw here's the "math overflow" presentation
19:27 < kanzure> http://diyhpl.us/~bryan/irc/open-science-summit-2011/Math%20Overflow%20Anton.pdf
19:27 < brownies> the question is basically the same as the one for mathematicians
19:28 < brownies> if you gave professional scientists in field X a place to collaborate with each other
19:28 < kanzure> look at the presentation :poke:
19:28 < brownies> and it *just so happened to be public* ... then the problem would be solved.
19:28  * brownies looks
19:28 < kanzure> haha, no, professional biologists would not collaborate in just one place that you give them
19:28 < kanzure> that's not how they role
19:28 < kanzure> openwetware didn't solve that
19:29 < brownies> kanzure: yeah, the worrying answer is that math is compatible with this sort of collaboration, and other fields just aren't.
19:29 < brownies> it is easy to rationalize that answer too, because for math all you need is pen and paper and brain
19:30 < yashgaroth> and stimulants
19:30 < brownies> heh
19:30 < kanzure> also on mathoverflow you can "do" math
19:30 < kanzure> you don't "talk about maybe possibly doing math"
19:30 < brownies> well, that's the thing. math *is* just hanging out and thinking about stuff. you can go to someone's office and do it.
19:31 < brownies> (or online, or whatever)
19:31 < kanzure> also math is about revisiting the same topics a lot
19:31 < brownies> whereas with e.g. biology you have to be all like "oh, good idea. let me go run 800 expreiments in the lab and get back to you in a month."
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19:31 < kanzure> in biology you might do an experiment and remember some of the methods, but you'll probably move on to something else
19:31 < kanzure> although, pcr is pretty fundamental, so that's not fair to say
19:31 < yashgaroth> each pcr takes a lot of tweaking, moreso than most labwork
19:31 < brownies> *i* don't remember how to run a PCR, but iirc it wasn't *that* complicated -_-
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19:32 < brownies> i mean, on a scale of "make a sandwich" to "produce a glowing cat" it's closer to sandwich.
19:32 < yashgaroth> sure, just with the caveat "10% of the time your sandwich will melt for no discernable reason"
19:33 < brownies> good thing we're going to make a million sandwiches, then.
19:33 < kanzure> shiiiiite http://dumps.mathoverflow.net/
19:34 < kanzure> hm, so, i find it sort of hard to believe that the answer is that "protocols can't get better because of the way that biology works"
19:35 < brownies> i thought the answer was "protocols can't get better because biologists are assholes'
19:35 < brownies> ;)
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19:35 < kanzure> jmil: how does your lab do protocols/procedures? giant binder?
19:36 < kanzure> brownies: i think the solution wouldn't target professors. it would be the undergrads/grad students.
19:37 < brownies> kanzure: sidebar: why are all the acts_as_paranoid gems abandoned? =(
19:37 < kanzure> professors aren't sitting around pipetting thing things.
19:37 < brownies> kanzure: but wouldn't the undergrads just ask the grad students...
19:37 < kanzure> i'm not sure this is for education
19:37 < kanzure> i mean, for those institutions
19:38 < kanzure> brownies: this was updated 4 months ago. is that abandoned? rails3 acts as paranoid
19:38 < kanzure> dfjdkafkl
19:38 < kanzure> https://github.com/goncalossilva/rails3_acts_as_paranoid
19:39 < kanzure> "As of April 4, 2012, there have been 16,496 registered users to MathOverflow. So far, 28,601 questions have been posted. Questions are answered an average of 3.9 hours after they are posted, and "Acceptable" answers take an average of 5.01 hours."
19:40 < brownies> kanzure: ugh.
19:40 < kanzure> oh i see. "MathOverflow is very specific about what a user can or should post. Questions must be research level mathematics questions. If not, they will be promptly removed. Questions should be well-defined and specific."
19:40 < brownies> kanzure: default_scope { where(paranoid_default_scope_sql) } # Magic!
19:40 < kanzure> so, mathoverflow does it by deleting unworthy questions
19:40 < kanzure> and only doing research-level stuff
19:40 < brownies> well, yeah, they make it clear it's *for mathematicians*
19:40 < kanzure> even mathematicians are sometimes unfamiliar with another area of math
19:41 < brownies> and, honestly, you can't enforce that kind of stuff when it comes to diybio
19:41 -!- nmz787 [~Nathan@ool-45792f2b.dyn.optonline.net] has joined ##hplusroadmap
19:41 < brownies> kanzure: yeah, but that unfamiliarity is usually couched in some research they're doing. "i'm researching X about Y, and i realized it requires basic knowledge of <obscure field>, so..."
19:41 < kanzure> being an expert at culturing ecoli will convey you absolutely no skill in designing primers
19:42 < kanzure> nmz787: how'd the meeting go?
19:43 < kanzure> brownies: so, i don't think i can imagine a "research-level-only" biology protocols overflow site
19:43 < kanzure> because most of the time when you're doing a new protocol, it's for a project that nobody is going to replicate unless it's something groundbreaking
19:44 < kanzure> (like if it confers some new level of ability to others)
19:44 < brownies> yeah, but a lot of math is like that too. it's not going to be terribly relevant, but people will still go "oh, that's interesting..."
19:47 < kanzure> it's worth noting that openwetware.org doesn't do much for the biology community in terms of 'making protocols easier/more accessible'
19:47 < kanzure> or 'organizing more protocols together'
19:47 < kanzure> http://openwetware.org/wiki/Protocols
19:48 < kanzure> oh that's hilarious: "The venerable qpcrlistserv. Anyone doing qPCR should be subscribed to this list." http://openwetware.org/wiki/Real-time_PCR
19:48 < kanzure> oh nice it's actually a yahoo group -_- http://tech.groups.yahoo.com/group/qpcrlistserver/
19:49 < kanzure> it's had activity since 2002?
19:49 < kanzure> "If you wish to join this group, your application will only succeed if you give a qPCR reason for wishing to join. "
19:49 -!- soylentbomb [~k@d149-67-118-140.col.wideopenwest.com] has quit [Quit: Leaving]
19:49 < kanzure> "Members: 3201"
19:49 < nmz787> not really here, but it went well, I talked... came up with a somewhat cool idea actually
19:49 < nmz787> but will talk later
19:49 < brownies> so... there you go?
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19:50 < kanzure> brownies: hm? a mailing list per protocol??
19:51 < brownies> no, i mean... that's where all the biologists are.
19:51 < kanzure> last comment 2008 "http://openwetware.org/wiki/Electrocompetent_cells"
19:52 < kanzure> oh but it has 10+ contributing authors on that page, that's nice
19:52 < kanzure> openwetware has only 10986 users
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19:53 < kanzure> http://openwetware.org/wiki/Special:Statistics
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19:55 < jk4930> may I interrupt with a question?
19:56 < jk4930> those protocols you're talking about are about doing (+ replicating) stuff in the lab?
19:56 < brownies> yeah, basic usage of lab equipment and basic experiments and whatnot
19:57 < kanzure> jk4930: like http://openwetware.org/wiki/DNA_Synthesis_from_Oligos
19:58 < brownies> kanzure: is that good documentation in your opinion? that link?
19:58 < jk4930> and usually there are none and most knowledge is anecdotal (varying from lab to lab)
19:58 < kanzure> brownies: you mean, in terms of "best that you're going to find on the web" or in terms of "do you like it"?
19:58 < jk4930> how is this handled in bigger labs?
19:58 < kanzure> because i hate that
19:58 < brownies> kanzure: yes, i also hate it.
19:59 < kanzure> but it's proobably the best you will find on the interwebs
19:59 < brownies> i am willing to believe, thoguh, that it's the best currently available... and i agree that is rather sad.
19:59 -!- AdrianG is now known as meth
19:59 < kanzure> the fact that it's a wiki makes it 100x better than protocols-online.org ;)
19:59 < yashgaroth> jk4930: in bigger labs, a stamp is applied to each copy of said anecdotal protocol
19:59 < jk4930> stamp meaning copyright
19:59 < jk4930> ?
19:59 < yashgaroth> nah, just a stamp
20:00 < kanzure> "so we talked to our biology greybeard, and this is what he said, so :stamp:"
20:00 < jk4930> -v
20:00 < yashgaroth> looks official
20:00 < jk4930> and they don't share
20:00 < brownies> what about corporations? surely giant research labs in corporations have documented protocols?
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20:00 < yashgaroth> sure
20:00 < kanzure> but it's probably just as bad as the other stuff that's written down
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20:01 < kanzure> and certainly on average the quality is prolly the same
20:01 < yashgaroth> no corporate research lab will ever consider releasing a protocol to "protowetment.org" though
20:01 < yashgaroth> err *mint.org" but whatevs
20:01 < kanzure> "current protocols in molecular biology" looks like a possibly useful publication
20:02 < kanzure> ad: mcb.asm.org/content/12/4/local/advertising.pdf
20:02 < kanzure> http://mcb.asm.org/content/12/4/local/advertising.pdf
20:02 < kanzure> index: http://onlinelibrary.wiley.com/book/10.1002/0471142727/homepage/archive.htm#Core
20:02 < kanzure> wtf is a "replacement page"?
20:02 < jk4930> another topic: lab automation. any opinions there?
20:02 < kanzure> jk4930: what about it?
20:03 < foucist> robots in the lab
20:03 < foucist> doing all your work for you
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20:03 < jk4930> right
20:03 < kanzure> what about it though?
20:03 < kanzure> my opinion is yes robots are real?
20:04 < jk4930> how much is it used?
20:04 < kanzure> it's not
20:04 < foucist> kanzure: maybe he's asking for opinions about if lab automation is pathetic and needs serious work
20:04 < yashgaroth> depends on the lab
20:04 < jk4930> that's what i'm currently researching
20:04 < kanzure> lab robotics is overly priced
20:04 < kanzure> and it's usually proprietary and nutty software
20:04 < yashgaroth> there's nothing below a room-sized Tecan, expect some crappy qiagen benchtop robots
20:04 < kanzure> and most labs don't use it because they have a never-ending-supply of free labor
20:05 < kanzure> "Unit 19.1 Internet Basics for Biologists"
20:05 < kanzure> from april 1998
20:05 < jk4930> i'm considering bringing some AI to the lab, maybe later some basic robotics
20:05 < jk4930> still i have to figure our their needs
20:05 < kanzure> what does "AI" mean
20:05 < yashgaroth> okay
20:06 < jk4930> artificial intelligence
20:06 < kanzure> now tell me what it actually means
20:06 < jk4930> what this AI should do?
20:06 < kanzure> why do i put up with this shit you guys give me
20:06 < kanzure> blargh
20:06 < yashgaroth> I don't want a computer deciding how to run a protocol, or rather whoever's in charge of qa/qc doesn't
20:06 < foucist> kanzure: more amphetamines for you! until you get your sense of humor back :P
20:06 < kanzure> jk4930: btw have you seen the tecan perl module/library that jonathan cline wrote?
20:06 < jk4930> nope
20:07 < kanzure> have you seen the open source liquid handling robot delinquentme built?
20:07 < jk4930> i guess not. i'm pretty new to this field
20:07 < foucist> kanzure: you mean the shaker?
20:07 < kanzure> no not the shaker
20:07 < kanzure> i haven't seen a shaker yet
20:07 < kanzure> i know jmil built an orbital shaker, but his 3d printer is more interesting to me
20:08 < jk4930> well, those AI should act as an artificial research assistant (that's the goal, not the start)
20:08 < jk4930> doing literature research, hypothesis formulation, experiment design and operation, etc.
20:09 < kanzure> okay.
20:09 < jmil> kanzure: our lab protocols are a mess of word files dumped on a server, hopefully :-(
20:09 < kanzure> by hopefully do you mean "yes we have a server with word files"
20:09 < jmil> if we are lucky
20:10 < kanzure> jmil: do you think your lab would use an online protocol thinger to clean that up?
20:10 < brownies> what did delinquentme build?
20:10 < kanzure> and possibly things with voting or rating or quality
20:10 < brownies> i would like to see this
20:10 < kanzure> brownies: https://github.com/delinquentme/lh001
20:10 < kanzure> brownies: http://www.youtube.com/watch?v=ZY5IY5CZ1es
20:10 < jmil> but ideally to keep it DRY you want each step in a protocol to be it's own entry in a task database, and each item used in a protocol to be in its own "items" database, then the protocol is just merging the tasks and items together to allow maximum reuse and dynamism
20:10 < kanzure> jmil: biologists won't ever do that manually dude
20:10 < kanzure> there's no fucking way
20:11 < jmil> kanzure: realistically they wouldn't use it. it has to come down to the user
20:11 < jmil> but if i had my own lab i would regiment it
20:11 < kanzure> hmm
20:11 < jmil> i have the item database already
20:11 < kanzure> are you the only one that uses it?
20:11 < jmil> ya
20:11 < kanzure> or do you force the others to update it :)
20:11 < kanzure> oh :(
20:11 < jmil> i don't have any power yet. just a lowly postdoc
20:12 < jmil> "if i were a professor"… cue the music...
20:12 < kanzure> jmil: what do you think of this sorta site? http://research.abl.es/questions/9/how-do-you-isolate-rna-from-skin/
20:12 < kanzure> it has little activity but it's like stackoverflow for voting up/down on protocols
20:12 < kanzure> and for q/a style debugging i guess
20:13 < brownies> kanzure: wtf @ that video
20:13 < brownies> kanzure: does it have an ON button? -_-
20:13 < kanzure> brownies: you should ask him
20:13 < kanzure> because i don't know :)
20:14 < brownies> haha
20:14 < brownies> yeah, it would be nice to see it doing something
20:14 < brownies> anything, really.
20:16 < jmil> kanzure: nature protocols does it best. with task steps, wait steps, color coded etc. they are the BEST and cover every possible kind of lab protocol
20:16 < jmil> kanzure: i don't see a protocol on that site
20:16 < brownies> Nature Protocls?
20:17 < kanzure> jmil: meh i don't want to dig; but good point. most of those were questions and not actually procedures.
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20:17 < kanzure> "current protocols in molecular biology" had a 2003 book with 29 chapters that seems fairly comprehensive.
20:18 < kanzure> jmil: have you used springerprotocols or "methods in molecular biology" and if so what do you think about these
20:18 < jmil> methods in molecular bio is amazingness
20:18 < jmil> they detail the science behind each step in the protocol
20:19 < jmil> really stellar. even better than nature protocols. but nature protocols is the most you could hope for coming from people doing the protocols since they are the ones in the trenches, not the world thought leaders like featured in methods in molecular bio
20:19 < kanzure> wait what? so who writes methods in molecular bio?
20:20 < kanzure> i mean surely it has to be people who are practicing those techniques?
20:20 < jmil> i think it's like a paper. written and done by a trainee but overseen directly by a PI
20:20 < jmil> i always saw methods mol bio stuff as kind of a victory lap publication for the PI after they get a big paper and some notoriety. nature protocols is trying to be like that idea
20:21 < kanzure> i think i've seen a few of my friends in nature protocols. usually it's something sorta edgy but still thorough.
20:21 < jmil> a lot of nature protocols are detailing useful protocols developed for landmark papers but not described there in sufficient detail to be reproduced due to lack of space or due to a huge amount of technical info really needed to describe fully
20:22 < jmil> kanzure: ya that model also applies to nature protocols
20:23 < kanzure> jmil: so the problem i'm trying to solve here is that many people coming into diybio need protocols or need to be indoctrinated
20:23 < kanzure> in a lab you have access to those books (if necessary) but most of the time you just get handed some notes from someone else
20:24 < brownies> so why don't they just read the books? o.O
20:24 < kanzure> because they cost like $20,000 a volume?
20:25 < kanzure> this looks pretty nice in terms of coverage: http://onlinelibrary.wiley.com/book/10.1002/0471142727/toc
20:25 < kanzure> (current protocols in molecular bio)
20:25 < brownies> a book costs $20,000? that ain't right.
20:25 < kanzure> well, no, it's probably like $50-$100 per book in the series
20:26 < kanzure> but methods in molecular bio is 900 books
20:26 < kanzure> oh wait
20:26 < kanzure> http://www.currentprotocols.com/WileyCDA/Section/id-810249.html
20:27 < kanzure> online subscription to current protocols is $400/series
20:27 < brownies> it appears to be 1 book?
20:27 < brownies> oh i see
20:27 < brownies> i didn't know this existed. well, there's your fucking answer. -_-
20:28 < kanzure> what, everyone pays a lot of cash to get these documents?
20:28 < brownies> why would any biologist contribute to some half-baked ghetto recreation of this, when their institution gives them *this* for free?
20:28 < kanzure> not all institutions have this
20:28 < brownies> well, no, the lab owners pay, and that's that.
20:28 < kanzure> and, most of the time, like in jmil's case, it's just some word documents on a shared server
20:29 < kanzure> i mean, the reason you go to these books is because something is broken, not because it's your first stop
20:29 < kanzure> (unless you're doing something esoteric in the first place)
20:29 < brownies> well... i don't know these things. -_-
20:30 < brownies> but what i gather is that plenty of documented protocols exist
20:30 < brownies> and there's unlikely to be much sympathy for a small ragtag poverty-stricken band of garage tinkerers
20:30 < kanzure> the situation still sucks even for people in labs, though
20:33 < kanzure> (my academic access gateways make that site say "you are not subscribed")
20:49 < AdrianG> ok
20:49 < AdrianG> so whats the biggest breakthrough needed to make bio-hackinjg a commodity
20:49 < AdrianG> like pc hacking
20:50 < foucist> what do you mean by commodity
20:52 < kanzure> what?
20:52 < kanzure> you might suffer from over-lateral-thinking syndrome
20:53 < brownies> better verticalize your thinking bro
20:54 < kanzure> *overly
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21:07 < jrayhawk> i guess it's pretty easy to hack epigenetics. quantifiedselfers and other self-improvement nerds do it all the time.
21:09 < yashgaroth> ehhhhhh
21:10 < kanzure> if they can quantify it with gene expression graphing and stuff, sure
21:12 < yashgaroth> still like saying if I binge drink and my liver upregulated alcohol dehydrogenase, I'm "hacking" my genetics
21:13 < jrayhawk> you might want to look up 'hack' on the jargon file
21:14 < yashgaroth> I try not to
21:14 < yashgaroth> also epigenetics implies they're acetylating their own histones and shit
21:16 < AdrianG> kanzure: why
21:16 < ParahSailin_> this might be a little off topic here, but does anyone know about inverters for solar on a small (home) scale?
21:16 < AdrianG> foucist: commodity as in real cheap
21:16 < AdrianG> like anyone with two brain cells and 2 bucks can do it
21:16 < kanzure> AdrianG: i think you're just being cryptic
21:16 < ParahSailin_> commercial models too expensive, it seems like it wouldn't cost too much to solder stuff together
21:17 < kanzure> AdrianG: but i would appreciate cheap reagents anyway
21:18 < AdrianG> reagents are relatively cheap
21:18 < AdrianG> its the hardware thats expensive
21:18 < kanzure> hardware is pretty cheap on ebay
21:18 < yashgaroth> yeah no reagents are the expensive part
21:19 < yashgaroth> that's true in all of bio research except, like, computational
21:21 < kanzure> i'm pretty sure some of the thermocycler designs cost less than the $200 reagent mixes
21:21 < yashgaroth> hell the vendors usually just give equipment away so you'll buy their reagents
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21:35 < nmz787> delinquentme: hey i'm prob gonna drive past greensburg on saturday
21:36 < AdrianG> i thought hardware is expensive
21:36 < AdrianG> like
21:36 < AdrianG> what reagents are we talking
21:36 < kanzure> all of them
21:36 < AdrianG> well
21:36 < AdrianG> purity ?
21:36 < kanzure> completely
21:37 < AdrianG> so then we should concentrate on cheap reagent production.
21:37 < AdrianG> are there any companies thare are trying to do that
21:37 < AdrianG> dramatically to bring down synthesis costs down?
21:38 < kanzure> if you want to do cheap reagent production, go right ahead
21:38 < kanzure> none of us will stop you
21:41 < nmz787> AdrianG: doesn't cost follow demand?
21:41 < nmz787> it depends what you're talking about
21:41 < AdrianG> yes and no
21:41 < nmz787> an antibody could be a reagent in some assay
21:41 < nmz787> but its pretty different than sugar cane
21:41 < nmz787> or salt
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21:58 < nmz787> do we know this guy http://andreasbastian.com/3dp/final_report_v2.pdf
21:59 < kanzure> i don't have any records
22:02 < nmz787> ice woodpulp composite material tested for strength http://andreasbastian.com/pykrete/pykrete.html
22:02 < nmz787> hmm, maybe useful at the poles
22:02 < nmz787> or on some other planet
22:03 < yashgaroth> pykrete is boss
22:05 < nmz787> know anyone here http://www.upmc-biosecurity.org/website/our_staff/index.html#ExecOfficers
22:05 < nmz787> ?
22:06 < nmz787> wait, huh:
22:06 < nmz787> The Center for Biosecurity of UPMC
22:06 < nmz787> The Pier IV Building
22:06 < nmz787> 621 E. Pratt Street, Suite 210
22:06 < nmz787> Baltimore, Maryland 21202
22:07 < nmz787> University of Pittsburgh Medical Center... in Baltimore???
22:08 < nmz787> oh, hmm
22:08 < nmz787> "Prior to joining UPMC in 2003 as the Center for Biosecurity, the group was founded in 1998 as the first and only academic center focused on biosecurity policy and practice. The Center’s work has helped to identify the character and potential consequences of major biological threats, the policies needed to protect the nation, and the response capacities necessary to diminish the impact of such an event."
22:08 < kanzure> none of the names jump out at me
22:10 < nmz787> Journal of.... Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science   http://online.liebertpub.com/loi/bsp/
22:11 < nmz787> only $597/year in print
22:12 < kanzure> hah
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22:13 < nmz787> this looks like a good wiki to scrape
22:13 < nmz787> http://seqanswers.com/wiki/Software
22:13 < nmz787> or copy
22:13 < nmz787> http://seqanswers.com/wiki/Service_Provider
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22:14 < nmz787> FAQ http://seqanswers.com/wiki/How-to
22:14 < nmz787> "The ultimate goal is to contain and parse some of the content that is not ideal for forums, particularly the monsterBioinformatics package thread"  http://seqanswers.com/forums/showthread.php?t=43
22:15 < nmz787> "2012 in Bioinformatics: SEQanswers: An open access community for collaboratively decoding genomes"
22:15 < nmz787> "2011 Nucleic Acids Research: The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis"
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22:18 < nmz787> oO http://seqanswers.com/wiki/SEQanswers
22:18 < nmz787> oops
22:18 < nmz787> http://www.good.is/post/a-13-year-old-s-slavery-analogy-raises-some-uncomfortable-truths-in-school/
22:18 < nmz787> school is like slavery ?
22:19 < nmz787> "Instead of truly teaching, most teachers simply "pass out pamphlets and packets" and then expect students to complete them independently, Williams wrote. But this approach fails, she concluded, because "most of my peers cannot read and or comprehend the material that has been provided." "
22:20 < nmz787> "Given that only 19 percent of School #3's eighth graders were proficient in language arts last year (and just 13 percent in math)—well below the state average of 60 percent—it's clear that the school and its teachers need to change their approach."
22:21 < nmz787> hah, so the girl wrote a good essay about how the school sucked, and the school (which does seem to suck) kicked her out
22:21 < nmz787> "Attempting to silence Williams by branding her a troublemaker and driving her off campus isn't the answer. Now she is walking away from this controversy convinced that white teachers don't want to educate black students at all."
22:21 < nmz787> I don't really think its a race thing though
22:21 < nmz787> maybe sometimes, I guess I don't know
22:21 < nmz787> I think school was pretty lame though, with the whole packet thing
22:22 < nmz787> but honestly, my parents taught me how to read
22:22 < nmz787> "As the parent of two black boys I know firsthand that white teachers can excel at teaching black children. What set those outstanding teachers apart was their genuine desire to see my boys succeed and hard work to build relationships with them and with our family. What if Williams' English teacher had used her essay to turn a critical eye on her teaching practice and her expectations for black students? What if the school had used it 
22:22 < nmz787> geez, well, good author of this article at least
22:23 < nmz787> oh wow, linked from that article http://www.good.is/post/teachers-are-awesome-meet-the-99-year-old-educator-still-on-the-job?utm_content=prev-next&utm_medium=post-page-bottom
22:23 < nmz787> hah, i bet so many old jokes are made of her
22:23 < nmz787> pretty great to hear an old person still kicking and doing good things
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22:38 < delinquentme> nmz787, you still heere?
22:38 < delinquentme> and you're going to a biosecurity spot in PGH?
22:38 < delinquentme> IM COMING.
22:43 < delinquentme> me bites brownies,
22:43  * delinquentme chews
22:43 < brownies> eh
22:43 < brownies> stop that
22:43 < delinquentme> NOM.
22:43 < delinquentme> okay.jpg
22:44 < delinquentme> no im hungry.
22:44 < delinquentme> was delish.
22:44 < delinquentme> should share more often.
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23:12 < nmz787> delinquentme: yes
23:12 < delinquentme> I'm gonna be in monroeville early this morning
23:12 < nmz787> delinquentme: no not going to anything biosecurity
23:12 < delinquentme> saturday i should be back in GBG
23:12 < nmz787> ok
23:12 < delinquentme> nmz787, I know the building so we should break in then.
23:12 < delinquentme> theres a security guard and big scanners
23:12 < delinquentme> but Itll be fun
23:12 < nmz787> we're camping fri night, then hiking somewhere east of gburgh
23:13 < delinquentme> linn run?
23:13 < nmz787> that site says UPMC biosec is in Baltimore
23:13 < nmz787> not PGH
23:13 < nmz787> which is lame
23:13 < delinquentme> Ahh well theres the BST 3
23:13 < delinquentme> which is le awesome.
23:13 < nmz787> not sure where we're hiking
23:13 < nmz787> maybe linn runn/forbes state forest
23:13 < nmz787> there's that laurel ridge
23:13 < nmz787> which is pretty cool
23:14 < nmz787> i also really like ohiopyle area tho
23:14 < nmz787> but who knows
23:14 < nmz787> kanzure: Verification RequiredPlease select the image of Albert Einstein below and click the submit button.We regret having to add this extra step for our subscribers, but have found it necessary due to systematic automated downloading of our content (in violation of our Terms and Conditions).
23:15 < nmz787> kanzure: from these guys http://prl.aps.org/abstract/PRL/v108/i25/e253901
23:15 < delinquentme> super cool
23:16 < delinquentme> umm yeah maybe starbucks on 30?
23:16 < delinquentme> 30 actually runs into all those foothills
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23:22 < delinquentme> oh and nmz787 712-610-8659
23:25 < nmz787> yeah, ok, I'll let you know ahead of time when we're passing through
23:26 < delinquentme> awesom
23:26 < nmz787> maybe i could see you on the way out too, on monday
23:26 < delinquentme> cool i should be around both days +D
23:28 < nmz787> can i text that #?
23:30 < delinquentme> yeah
23:30 < nmz787> cool
23:30 < nmz787> ttyl
23:30 < nmz787> this is a weird site
23:30 < nmz787> seems crappy but i wonder if the software is better than gOptical
23:30 < nmz787> http://www.opticalsoftware.net/
23:31 < nmz787> http://twitter.com/lensdesignapps
23:39 < kanzure> why is it 1am?
23:39 < kanzure> who are you people?
23:42 < brownies> deep questions
23:48 < nmz787> kanzure: what is this site http://www.rtbot.net/Beam_profile
23:48 < nmz787> i mean, http://www.rtbot.net/
23:48 < nmz787> it seems like a strange site to have that big (decent looking) mass of optics data
23:50 < nmz787> oh, its just ripping wikipedia
23:54 < gnusha> laser_etcher.git: 26fbb59 tons of links, chrome no longer hates me for all the open tabs
23:56 < nmz787> kanzure: ping
23:56 < kanzure> pong
23:57 < nmz787> ikiwiki seems to want URLs to be in the [text](URL), or [URL](text) format
23:57 < nmz787> hrmm
23:57 < kanzure> or <http://...>
23:57 < nmz787> i /just/ regexed all them
23:57 < nmz787> to be inside []
23:57 < kanzure> i think you can also get away with <a href=""></a>
23:57 < kanzure> [text](url)
23:58 < nmz787> ugh
23:58 < nmz787> well not tonight
23:58 < nmz787> for me at least
23:58 < nmz787> ttyl
23:58 < nmz787> bed
23:58 < nmz787> finally
23:58 < nmz787> :P
23:58 < kanzure> good night
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--- Log closed Fri Aug 31 00:00:12 2012