--- Log opened Thu Aug 08 00:00:07 2013
--- Day changed Thu Aug 08 2013
00:00 -!- Adifex [~Adifex@75-148-41-126-Colorado.hfc.comcastbusiness.net] has quit [Quit: Adifex]
00:20 -!- valyap [~emankcin@c-76-23-254-105.hsd1.ct.comcast.net] has left ##hplusroadmap []
00:29 -!- stieruridir [47fff18b@gateway/web/freenode/ip.71.255.241.139] has quit [Ping timeout: 250 seconds]
01:01 -!- Guest55373 [~not@100.43.114.90] has quit [Ping timeout: 256 seconds]
01:06 -!- padz [~not@100.43.114.90] has joined ##hplusroadmap
01:22 -!- padz [~not@100.43.114.90] has quit [Ping timeout: 246 seconds]
01:29 -!- padz [~not@100.43.114.90] has joined ##hplusroadmap
02:00 -!- ielo [~ielo@host-92-20-142-250.as13285.net] has joined ##hplusroadmap
02:08 -!- wrldpc_ [~wrldpc@120.88.50.102] has joined ##hplusroadmap
02:09 -!- wrldpc [~wrldpc@120.88.50.102] has quit [Ping timeout: 240 seconds]
02:09 -!- wrldpc_ is now known as wrldpc
02:24 -!- padz [~not@100.43.114.90] has quit [Ping timeout: 264 seconds]
02:26 -!- padz [~not@100.43.114.90] has joined ##hplusroadmap
02:33 -!- ThomasEgi [~thomas@185.5.8.81] has joined ##hplusroadmap
02:33 -!- ThomasEgi [~thomas@185.5.8.81] has quit [Changing host]
02:33 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap
02:51 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
02:55 -!- ielo [~ielo@host-92-20-142-250.as13285.net] has quit [Ping timeout: 248 seconds]
03:27 -!- makoLime [~mako@103-9-42-133.flip.co.nz] has quit [Ping timeout: 264 seconds]
03:48 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has joined ##hplusroadmap
04:17 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Read error: No route to host]
04:18 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
04:54 -!- Jaakko97 [~Jaakko@cpc13-newc15-2-0-cust64.16-2.cable.virginmedia.com] has joined ##hplusroadmap
05:11 -!- Adillian [~Adillian@124.43.126.116] has quit [Ping timeout: 240 seconds]
05:12 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap
05:13 -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap
05:48 -!- jmil [~jmil@hive76/member/jmil] has quit [Quit: jmil]
06:17 -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap
06:41 <@kanzure> oh this is the dumbest thing i've ever seen: https://github.com/zotero/translators/blob/master/ScienceDirect.js#L88
06:41 <@kanzure> //mimetype map for supplementary attachments
06:41 <@kanzure> //intentionally excluding potentially large files like videos and zip files
06:41 <@kanzure> uh.. except maybe i really do intend you to download videos and zip files?
06:42 < drazak> lol
06:52 -!- Rk is now known as rk[]
06:57 < Lemminkainen> paperbot http://www.reportlinker.com/p0490898-summary/Life-Science-Tools-and-Reagents-Global-Markets.html
06:59 < drazak> paperbot: http://www.reportlinker.com/p0490898-summary/Life-Science-Tools-and-Reagents-Global-Markets.html
06:59 < drazak> or not
07:00 < Lemminkainen> it's an industry report
07:00 < drazak> wonder why it can't do it
07:00 < Lemminkainen> may be beyond poor paperbot's steez
07:00 < drazak> indeed
07:09 <@kanzure> you killed it
07:20 < Lemminkainen> i love you paperbot http://psycnet.apa.org/journals/rev/93/2/119/
07:21 < paperbot> RuntimeError: maximum recursion depth exceeded in cmp (file "/usr/lib/python2.7/_weakrefset.py", line 73, in __contains__)
07:22 < paperbot> RuntimeError: maximum recursion depth exceeded in cmp (file "/usr/lib/python2.7/_weakrefset.py", line 73, in __contains__)
07:23 < Lemminkainen> o_o I'm so sorry Paper Bot
07:23 < chris_99> haha
07:34 -!- jmil [~jmil@hive76/member/jmil] has quit [Ping timeout: 246 seconds]
07:43 < ThomasEgi> up the recursion limit!
07:43 < ThomasEgi> http://cdn.memegenerator.co/instances/400x/39791605.jpg
07:45 < chris_99> heh
07:57 -!- anannie [~chatzilla@unaffiliated/anannie] has quit [Ping timeout: 245 seconds]
08:07 -!- cpopell [47fff18b@gateway/web/freenode/ip.71.255.241.139] has joined ##hplusroadmap
08:12 -!- poppingtonic [~poppingto@212.49.88.110] has quit [Read error: Connection reset by peer]
08:12 -!- poppingtonic [~poppingto@212.49.88.110] has joined ##hplusroadmap
08:12 -!- oblique [~oblique@unaffiliated/oblique] has quit [Quit: leaving]
08:13 -!- poppingtonic [~poppingto@212.49.88.110] has quit [Remote host closed the connection]
08:18 -!- padz [~not@100.43.114.90] has quit [Ping timeout: 276 seconds]
08:25 < archels> so this new stuff from IBM's SyNAPSE project is pretty cool
08:25 < archels> https://dl.dropboxusercontent.com/u/91714474/Papers/020.IJCNN2013.Corelet.pdf
08:26 -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap
08:27 < archels> lots of applications
08:27 < archels> http://www.research.ibm.com/software/IBMResearch/multimedia/IJCNN2013.algorithms-applications.pdf
08:29 < archels> kurzweilai's writeup is actually relatively decent http://www.kurzweilai.net/ibm-research-creates-new-foundation-to-program-synapse-chips
08:31 < chris_99> are those chips analog?
08:31 < chris_99> in some parts
08:32 < heath> kanzure: what's wrong zotero's lookup table?
08:32 < heath> minus the horrible indentation
08:39 < archels> chris_99: no, all-digital. weights are binary :(
08:40 < chris_99> ah
08:40 < chris_99> i'd quite like to make a simple ANN with op-amps and the like just to play with
08:40 < archels> that's useless, just simulate it
08:41 < archels> you'd be building a cybernetic circuit more than a neural circuit anyway
08:41 -!- padz [~not@100.43.114.90] has joined ##hplusroadmap
08:41 < chris_99> i never said it'd serve much purpose, i'd have leds or something to view the weights etc ;)
08:43 < archels> no, that's cool, but you'd be hard pressed calling it a neural circuit
08:43 < archels> it would be an analog feedback controller
08:44 < chris_99> why couldn't i call it an ANN?
08:45 < archels> because neurons do not work remotely like op-amps
08:45 < chris_99> i didn't think ANNs worked esp. like real neurons anyway?
08:46 < archels> it's true that the level of realism varies considerably
08:46 < archels> if you stuck a few op-amps together, you could call it a neuron in the classical McCulloch-Pitts sense
08:47 < archels> but those aren't very much like real neurons either
08:48 < chris_99> it'd just be something kind of fun to play with i guess, like i could train it to act as an xor or what not
08:48 < archels> well, I guess the guys at IBM got some good results with binary synapses, so we don't need over-the-top realism
08:51  * rk[] likes MP neurons
08:52 < rk[]> i have been considering making a led lattice, implementing a ANN and viewing the weights with LEDs
08:55 < nsh> ugh, speaking of neurons...
08:55 < nsh> anyone read this: http://www.wired.com/opinion/2013/07/die-links-die-stop-worrying-about-link-rot/
08:55 < nsh> synopsis: the web is a brain! it's a brain! no really, it's just like a brain! so therefore links that aren't used should rot and die and that will make it work better!
08:56 < nsh> signed, brain scientist and all-round genius guy
08:57 < nsh> i'm really tempted to irl stalk this person and engineer getting trapped in an elevator with him so i can savagely apply the cluestick for several hours without him being able to escape in his personal helicopter
08:57 <@kanzure> heath: the code is poorly tested
08:57 <@kanzure> heath: and it's hard to decipher what it's doing
08:57 <@kanzure> heath: and it's not a state machine
09:09 -!- eudoxia [~eudoxia@r186-55-132-229.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap
09:09 < eudoxia> paperbot: http://dl.acm.org/ft_gateway.cfm?id=378823&ftid=120666&dwn=1&CFID=238345090&CFTOKEN=34506872
09:10 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/9c9eeacbe850042d120452c5348dab19.pdf
09:10 < eudoxia> yisss paperbot
09:11 < eudoxia> paperbot: http://dl.acm.org/ft_gateway.cfm?id=1065042&type=pdf&coll=DL&dl=GUIDE&CFID=238345090&CFTOKEN=34506872
09:11 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/7923b3a1efd5c07d3830d4a844850c75.pdf
09:25 -!- anannie [~chatzilla@unaffiliated/anannie] has joined ##hplusroadmap
09:25 -!- eudoxia [~eudoxia@r186-55-132-229.dialup.adsl.anteldata.net.uy] has left ##hplusroadmap ["leaving"]
09:29 -!- cpopell [47fff18b@gateway/web/freenode/ip.71.255.241.139] has quit [Ping timeout: 250 seconds]
09:33 < archels> The brain has two types of links: inbound (axons) and outbound (dendrites), and sometimes two neurons are connected by both an inbound and an outbound link — two-way links.
09:33 < archels> wait--what?
09:37 <@kanzure> they are just bad at describing basic neuroscience
09:37 < chris_99> that article looks crap in all respects
09:37 < chris_99> 'Our greatest technological network to date — the World Wide Web — is approaching a breakpoint, at which it will shrink.'
09:43 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds]
09:43 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap
09:49 < nmz787> anyone in here actually have success with ANNs?
09:50 <@kanzure> once or twice.
09:54 -!- anannie [~chatzilla@unaffiliated/anannie] has quit [Ping timeout: 246 seconds]
09:57 -!- anannie [~chatzilla@unaffiliated/anannie] has joined ##hplusroadmap
09:58 < nsh> define success
09:59 < nsh> some weights changed and now desired classification is occurs with higher frequency? or oh yeah, goldbach conjecture, solved that before breakfast
10:08 < nmz787> dunno what goldbach is
10:08 < nmz787> i guess i mean real world success, better at classification
10:09 -!- Jaakko97 [~Jaakko@cpc13-newc15-2-0-cust64.16-2.cable.virginmedia.com] has quit [Quit: Nettalk6 - www.ntalk.de]
10:16 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Remote host closed the connection]
10:35 < chris_99> have you played with weka, that's pretty cool to compare a number of different classifiers
10:39 < nmz787> no
10:39 < nmz787> fenn: sortof related to the zeolite water from air http://www.youtube.com/watch?v=FWwii1dX4v8
11:10 -!- klafka [~klafka@204-16-157-18-static.ipnetworksinc.net] has joined ##hplusroadmap
11:55 -!- cpopell [458c23cc@gateway/web/freenode/ip.69.140.35.204] has joined ##hplusroadmap
11:59 -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has joined ##hplusroadmap
12:15 -!- jmil [~jmil@hive76/member/jmil] has quit [Ping timeout: 240 seconds]
12:17 -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap
12:24 <@kanzure> http://learningthreejs.com/blog/2013/08/02/how-to-do-a-procedural-city-in-100lines/
12:25 <@kanzure> http://www.mrdoob.com/lab/javascript/webgl/city/01/
12:25 -!- yorick [~yorick@oftn/member/yorick] has quit [Read error: Connection reset by peer]
12:32 -!- AlonzoTG [~atg@pool-108-18-204-142.washdc.fios.verizon.net] has joined ##hplusroadmap
12:38 <@kanzure> heh http://blog.typeracer.com/2013/08/08/typeracer-5th-anniversary-and-1-million-users/
12:39 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap
13:23 <@kanzure> well, zotero-translators sure is an active project https://github.com/zotero/translators/pull/606
13:23 <@kanzure> https://github.com/zotero/translators/pulls
13:24 <@kanzure> ParahSail1n: apparently crossref returns more metadata than dx.doi.org https://github.com/zotero/translators/pull/452
13:29 -!- childcorn [~itodashev@c-76-23-254-105.hsd1.ct.comcast.net] has joined ##hplusroadmap
13:35 < ParahSailin> kanzure: what url do you request from for crossref
13:36 <@kanzure> no idea, i'd have to look at their implementation
13:42 < ParahSailin> i guess you can use http://www.crossref.org/guestquery
13:50 < childcorn> Korean scientists have used lazers to perforate a cell and then optical tweezers to put foreign DNA into them.
13:51 < childcorn> ABSTRACT  http://www.opticsinfobase.org/boe/fulltext.cfm?uri=boe-4-9-1533&id=260009
13:52 <@kanzure> there is also laser-induced ultrasonic poration
13:53 < gradstudentbot> Dude, you contaminated my experiment.
14:02 -!- eudoxia [~eudoxia@r186-54-220-115.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap
14:04 < yorick> kanzure: on your site, most useful qr code ever?
14:05 <@kanzure> it's a honeypot for people silly enough to scan a qr code on a website
14:05 < yorick> dammit
14:05 <@kanzure> you're the only person it has ever trapped
14:05 <@kanzure> congratulations! :confetti:
14:05 < yorick> what do I win?
14:06 < ParahSailin> what qr code
14:06 <@kanzure> eternal shame
14:06 < yorick> yay
14:06 <@kanzure> ParahSailin: http://heybryan.org/
14:07 < yorick> kanzure: also your name thingy on github is going offscreen
14:08 <@kanzure> my what?
14:08 < yorick> http://dl.dropbox.com/u/22989236/temp/2013080824.png
14:08 < yorick> or does it just say 'e'
14:08 <@kanzure> it used to say "HIRE ME" but then i realized i didn't want to work
14:08 < yorick> you could've made it 'kanzure'
14:09 <@kanzure> https://github.com/gelstudios/gitfiti
14:09 <@kanzure> also this guy did something else https://github.com/will
14:10 < yorick> it would've been nice if it actually committed every day
14:10 <@kanzure> it did.
14:10 < yorick> it didn't cheat and commit in the past?
14:10 <@kanzure> it committed in the future
14:11 < yorick> that's *also* cheating
14:11 <@kanzure> cheaters gonna cheat
14:12 <@kanzure> i would rather just do actual work anyway
14:12 <@kanzure> https://github.com/substack still trying to figure out which drugs he's on
14:13 < yorick> kanzure: well it's his only job
14:13 < yorick> I don't think he's on any drugs
14:13 < yorick> he just does modules for a living
14:13 < yorick> and sometimes combines them into moderately-well-working awesome virtualization things
14:16 <@kanzure> "only job".. same with me, right? i just write code.
14:16 <@kanzure> but i don't pump out 200 modules/year
14:17 < yorick> kanzure: he writes modules to call mkdir -p
14:17 < yorick> https://github.com/substack/node-mkdirp <-- he really does
14:17 <@kanzure> yeah, i'm aware
14:17 < yorick> and also, he doesn't maintain anything really
14:17 <@kanzure> writing small modules is an okay thing
14:17 < chris_99> lol
14:18 <@kanzure> being aware of code boundary issues is commendable because it lets you focus on the actual work
14:23 < yorick> kanzure: or on infinite subprojects "hmm my mkdir -p needs a callback on every created dir, and to be able to automatically mount volumes according to fstab if mkdir -ping across it, and automatically calling sudo"
14:24 <@kanzure> callbacks on each created directory would be cool
14:24 <@kanzure> but your file system isn't async anyway
14:24 <@kanzure> so it's a bit of a loss
14:26 -!- poppingtonic [~poppingto@212.49.88.107] has joined ##hplusroadmap
14:30 < ParahSailin> sure, any syscall could be considered async
14:36 -!- makoLime [~mako@103.9.42.133] has joined ##hplusroadmap
14:36 -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has quit [Read error: Connection reset by peer]
14:45 -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has joined ##hplusroadmap
14:52 < drazak> wtf is an MFC?
14:56 <@kanzure> mere field communicator
14:56 < drazak> I... I don't think so
14:57 < drazak> refering to this https://groups.google.com/forum/#!msg/diybio/2LiRM1OCwIA/8bbD2r0CUNAJ
14:58 < drazak> is it.. a battery?
14:58 < ParahSailin> microbial fuel cell
14:58 <@kanzure> fuel cell
14:58 <@kanzure> damn it he beat me
14:58 < ParahSailin> really shitty sort of batter
14:58 < ParahSailin> y
14:58 < drazak> gotcha
14:58 < ParahSailin> well, not shitty, but nobody's figured out how to make it useful yet
14:58 < drazak> seems awful
14:59 < chris_99> what do the microbes do in it?
14:59 < ParahSailin> electron donors to an electrode
14:59 < chris_99> intriguing
14:59 < chris_99> what sort of microbes?
14:59 < drazak> this idea just seems awful
14:59 < ParahSailin> shewanella
15:00 <@kanzure> hahah funny to see mark hamalainen at synthego. basically he's jumping ship now.
15:00 < drazak> chris_99: please tell me you're not 13
15:00 <@kanzure> wasn't he working at halcyon molecular
15:00 < chris_99> i'm not heh
15:00 <@kanzure> and immunepath
15:00 < ParahSailin> lol
15:01 <@kanzure> and mitosens
15:01 < chris_99> http://en.wikipedia.org/wiki/Microbial_fuel_cell has lots of info
15:01 < ParahSailin> mfcs tend not to be very useful
15:01 < ParahSailin> if you want to get usable energy out of microbial fermentation, protip is methanogenesis
15:02 < ParahSailin> you can put the methane into a fuel cell if you want
15:02 < drazak> mfcs seem awful, you're probably better off using some sort of enzyme than an actual bacterium.
15:03 < ParahSailin> loose "enzymes" tend to be even less productive
15:04 < drazak> it just seems like a losing value
15:04 < drazak> er, battle
15:04 < drazak> it's my bed time
15:04 < ParahSailin> the cool thing about bacteria is that they recycle their degraded enzymes for you
15:04 < drazak> but I can't think of a way in which something biological magically gets you more energy out of electrons skipping levels
15:04 < ParahSailin> drazak: it actually works, its just low power denisty
15:04 < ParahSailin> its not "magic"
15:05 < drazak> to be frank low power density is the same as not working at all
15:05 < drazak> and what do you get, like, 100mv extra per cell?
15:05 <@kanzure> what does power density mean in units?
15:05 < drazak> come off it
15:05 <@kanzure> huh?
15:06 < nmz787> pfft
15:06 < nmz787> ya'll are nuts
15:07 < nmz787> there are lots of interesting research directions that MFCs are the intersection of
15:07 < drazak> show me papers
15:07 <@kanzure> ha ha http://www.theverge.com/2013/8/7/4595876/kickstarter-founder-yancey-strickler-explains-ban-GMOs
15:07 < nmz787> hooking up wires to bio stuff, speeding up water treatment, sludge powered sensors
15:07 < ParahSailin> kanzure: power density = W/ m2 of electrode area in this case
15:07 < nmz787> drazak: use google scholar
15:08 < drazak> nmz787: if you think it's cool show me papers to prove it
15:08 < gradstudentbot> The autoclave smells really good.
15:08 < ParahSailin> kanzure: do we like drazak for some reason?
15:10 < drazak> probably not, I'm kind of an asshole
15:10 < chris_99> look at all the cool stuff they can do on the wikipedia article
15:10 <@kanzure> ParahSailin: he knows chemistry things sometimes
15:10 < drazak> ParahSailin: also electronics things
15:11 < nmz787> drazak: i don't think it's cool enough right now to show you papers
15:11 < drazak> nmz787: ok so it's not that cool yet, that I can understand
15:11 -!- eudoxia [~eudoxia@r186-54-220-115.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving]
15:11 < nmz787> it's more my mood
15:11 < drazak> let me rephrase things so that I'm less of an asshole
15:12 < nmz787> my interest in MFCs lies in that some species grow wires from themselves to their electrode
15:12 < nmz787> and I think that could be useful in other applications
15:12 < drazak> I don't think MFCs are a good research path if you're a small lab and it's your only thing you're researching
15:12 < nmz787> and the idea of charge separation
15:12 < drazak> nmz787: I like bateria growing their own wires
15:12 < drazak> that's cool and somethign with a lot of applications that doesn't lock you into a hard to fight battle
15:13 < nmz787> drazak: MFCs are cheap and easy though, why wouldn't they be a good hit for small labs?
15:13 < drazak> nmz787: because it's hard to get somewhere with it in a constructive way, you make little improvements, but there's never an ah-hah moment, and it's going to take a LOT of time
15:13 < drazak> nmz787: I think small labs want to have a lot of small projects
15:13 < nmz787> there's research into basically adding a wire in waste treatment plants that simply dumps current to ohmic resistance (resistance makes heat)
15:13 < drazak> nmz787: shotgun vs sniper
15:14 < nmz787> so it speeds up waste treatment simply by heating itself
15:14 < drazak> yep
15:14 < nmz787> it's more of optimization
15:14 < ParahSailin> theres some reason why mfcs seem to be a dead end
15:14 < nmz787> ah hahs don't happen often in isolated science
15:14 < nmz787> these days at least
15:14 < ParahSailin> lots of labs throw lots of money into them and it never seem to go anywhere
15:15 < nmz787> there's some collaboration or knowledge transfer
15:15 < drazak> yes, optimization projects are almost always of diminishing returns
15:15 < drazak> nmz787: yes, which is why the shotgun approach is great
15:15 < drazak> nmz787: you get to collaborate with a lot of people on a lot of things
15:15 <@kanzure> drazak: it's hard to tell what other people are in diybio for
15:15 < nmz787> they don't seem mutually exclusive
15:15 < ParahSailin> if you want to get energy out of waste sludge, methane fermentation is well proven and scalable
15:17 < chris_99> i just saw the wiki page 'Electrohydrogenesis' know anything about that?
15:17 < drazak> kanzure: dunno, I thin you know I'm in it to help people make actual science happen and not pseudoscience or just science for show, which is why I'm an asshole
15:17 < ParahSailin> electrolysis?
15:17 < nmz787> ParahSailin: more like methanogenesis
15:18 < chris_99> http://www.sense.nl/graduations/2648 is the paper they cite
15:18 < ParahSailin> nmz787: that was to chris_99
15:18 < chris_99> ' biocatalyzed electrolysis '
15:19 < ParahSailin> if you're electrolysing water, you're already doing something dumb in most cases
15:19 < nmz787> paperbot: http://pubs.acs.org/doi/abs/10.1021/es803531g
15:19 < ParahSailin> exceptions would be a nuclear submarine making oxygen for human crew and other weird applications like that
15:19 < paperbot> http://libgen.org/scimag/get.php?doi=10.1021%2Fes803531g%26pubId%3D340422328
15:20 < ParahSailin> http://sci-hub.org/pdfcache/cb4cc1b556cc422eac80ed3f495ed704.pdf
15:20 < ParahSailin> well thats garbage
15:20 <@kanzure> drazak: "actual science". i see. that's not entirely why i'm here.
15:20 < ParahSailin> hey im pretty sure my former pi is the editor of that journal
15:21 <@kanzure> drazak: i mean, i certainly don't mean pseudoscience. but spending $100M to prove that a certain drug isn't effective.. doesnt' matter to me.
15:21 < drazak> kanzure: heh, well, for some value of actual science, it's kind of a moving target
15:21 <@kanzure> ParahSailin: got anything in the black book against him? you can bribe him into publishing.. er.. something.
15:21 < drazak> kanzure: yeah that's not the type of science I'm talking about, and I think you know that
15:21 < ParahSailin> ah, associate editor
15:21 <@kanzure> associate editor means he does all the work, i think
15:21 < ParahSailin> theres like 10 of those
15:22 < drazak> kanzure: I simply mean doing things to some sort of standard, and that projects like lets make a kit to show off bioluminescent bacteria that a 5 year old can do don't interest me and I think they're a waste of time
15:23 < drazak> if ou're not documenting hat you're doing it's useless, etc
15:23 <@kanzure> ParahSailin: haha. i wonder how that works.
15:23 < ParahSailin> http://pubs.acs.org/page/esthag/editors.html
15:23 < drazak> nobody will take diy bio seriously if thing saren't documented well, if it's not repeatable, etc
15:23 < ParahSailin> diybio is already a joke
15:24 < drazak> ParahSailin: yeah well
15:24 < drazak> ParahSailin: I can only do what I can do to help fix that
15:24 <@kanzure> avery is finally pushing code up via git
15:24 <@kanzure> https://github.com/AveryLouie/BlogDocs/tree/master/DNACrusher
15:24 < ParahSailin> it will be a joke until methods come within the reach of diyers
15:24 <@kanzure> ugh he had images dumped into the repo whaaaat
15:24 < nmz787> drazak: you must not value enhancing the educational effectiveness for coming generations
15:24 <@kanzure> and .pyc files argh
15:24 < ParahSailin> lol pyc
15:25 <@kanzure> oh it's his blogdocs repo wtf
15:25 <@kanzure> still.. pyc :(
15:25 <@kanzure> and .tar files
15:25 < ParahSailin> i think that guy has not heard of biopython which basically makes all that code he just pushed redundant
15:26 <@kanzure> well, at least it's python. so now instead of cathal and avery making crap in different languages, i only have to fix their crap in one.
15:26 <@kanzure> win-win-lose... :|
15:27 < drazak> nmz787: not really, no
15:27 < gradstudentbot> I could never be a PI.
15:28 < nmz787> drazak: well that stuff matters, so just know that some projects you might think are stupid, but it's more stupid to worry about them, unless they're causing trouble
15:28 < ParahSailin> lol ^I tabs ftw
15:28 < drazak> nmz787: that's why those projects I don't comment on
15:28 < drazak> nmz787: I just let them go
15:28 < nmz787> glowing gfp ecoli with an elecron microscope to accompany would be an awesome kit for a 5 yr old
15:28 < drazak> nmz787: I do comment on bad science
15:28 < drazak> why do you need an electron microscope o.O
15:29 < nmz787> seems avery could have done what he did with biopython, but i guess that would be heavier?
15:29 < ParahSailin> heavier but kanzure wouldnt have to fix it
15:29 <@kanzure> biopython is poorly written in a bunch of places, but at least the general community has agreed to maintaining it or something
15:30 < ParahSailin> also his fasta file parser is probably broken
15:32 < nmz787> i can't really tell what it's use is really supposed to be... or rather what his graph is showing... I've only sequenced stuff like twice, and used sequencher once and can't remember the second time
15:32 < drazak> nmz787: I know a guy in ##chemistry who do some awesome sythetic chemistry stuff in their garage, can't remember his f-ing name but kanzure probably remembers who it is
15:32 < nmz787> or what's wrong with phred phrap consed?
15:33 < drazak> nmz787: he has a legit lab notebook and could probably publish if that was to his liking if he had a novel method for his synthesis
15:33 < drazak> UC235
15:33 < drazak> derp
15:35 < nmz787> was it synbio?
15:35 <@kanzure> no i don't remember the person
15:35 < nmz787> or for synbio?
15:35 < drazak> nmz787: no he has youtube vids
15:35 < drazak> he posted images of his lab notebook a couple time sin ##chemistry
15:36 < drazak> nmz787: http://www.youtube.com/watch?v=-PGtoZEZnzc is a good one, he has better chemistry in his other ones
15:36 < drazak> he had some cool new synthesis pathways and stuff
15:37 -!- tequals0 [47e80ef8@gateway/web/freenode/ip.71.232.14.248] has joined ##hplusroadmap
15:37 < drazak> oh
15:37 < drazak> nmz787: didn't realize you were nathan
15:38 <@kanzure> tequals0: hi there
15:38 <@kanzure> tequals0: do you know about biopython?
15:38 < tequals0> hi
15:38 < tequals0> yep
15:38 <@kanzure> are you aware that your git repo has a .pyc file in it?
15:38 < tequals0> yes
15:38 <@kanzure> these are precompiled python files that usually aren't distributed around
15:38 <@kanzure> okay cool. welcome to the fold.
15:38 < tequals0> it also has the source, or it should
15:39 < nmz787> tequals0: hi!
15:39 < tequals0> hey nathan (?)
15:40 < gradstudentbot> If I break my arm, do I still have to present tomorrow?
15:40 < nmz787> ea
15:40 < nmz787> yea
15:40 < nmz787> i just replied on the list
15:40 <@kanzure> gradstudentbot: yes, go write that paper
15:40 < gradstudentbot> The paper was rejected.
15:40 < nmz787> can't tell what your plot is supposed to be helpful for
15:40 < nmz787> lol
15:40 < nmz787> gradstudentbot: you're getting smarter!
15:40 < gradstudentbot> Oh that's interesting, do you want to write a paper together?
15:44 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving]
15:44 < tequals0> its supposed to give you a hint as to where the two overlap
15:45 < tequals0> The advantage vs other things is that it has less documetnation to read
15:45 <@kanzure> tequals0: btw what are the items you are selling?
15:45 < tequals0> ?
15:45 < tequals0> the gel box?
15:45 <@kanzure> you started to sell a transilluminator i think?
15:45 <@kanzure> oh a gel box
15:45 <@kanzure> okay
15:46 < nmz787> tequals0: you defintely want a good diffuser
15:46 -!- wrldpc [~wrldpc@120.88.50.102] has quit [Quit: wrldpc]
15:46 < nmz787> mac posted some pics on facebook a while back of some illuminator he was testing and it looked horrible (he had no diffuser)
15:46 < nmz787> the image looked horrible i should say
15:47 < nmz787> you would have a harder time extracting data from it, such as peak intensity
15:47 < tequals0> yea
15:47 < nmz787> tequals0: it would be great if you could re-imagine a plate gel system
15:47 < tequals0> I am working one
15:48 < tequals0> you can read details here https://tequals0.wordpress.com/2013/08/04/gelis-illuminator/
15:48 < nmz787> that iphone screen simon mentioned sounded good, as they should be aiming for equal illumination, though they can def bleed or be uneven
15:48 < nmz787> tequals0: i actually stopped doing gels because i don't have capillaries or thin lanes between plates
15:48 < tequals0> illumination experiments here https://tequals0.wordpress.com/2013/08/03/the-guide-to-diy-gel-illumination/
15:49 < tequals0> i had a capilary design, but it's not what I am going with for the time being
15:49 < nmz787> gels in long glass pipette tips might work, but it might be better to have a flat capillary for imaging
15:50 < tequals0> http://tequals0.files.wordpress.com/2013/08/img_4577.jpg
15:50 < tequals0> flat 1 ml gel/channel
15:51 < nmz787> i would beta test that
15:52 < tequals0> good
15:52 < nmz787> if tomkinsc were idling here, he'd have some optics input
15:53 < tequals0> The transluminator/psu/gel box are going to get rolled out together first, but after that I want to play with different gel boxes, like half-gel box for running fewer samples, capilaries etc.
15:55 < tequals0> I thought about a circular gel box, but that might be too avant-garde
15:55 < nmz787> realistically you could just make it automated completely. with a lased or LED at the end and a photodiode detector
15:55 < nmz787> and not worry about diffusers
15:55 < nmz787> laser*
15:56 < nmz787> or work up to that
15:57 < drazak> nmz787: anyway I'm gonna get some sleep, but we can talk about this more later
15:58 < tequals0> i like the laser/led idea
15:58 < tequals0> I agree that is how it should be done
15:58 < tequals0> like a drum scanner
15:59 < tequals0> but unfortunately people are fixated on SEEING THE DNA
15:59 < tequals0> i mean, ideally, robots would do it all
16:01 < tequals0> you would just do something like
16:02 < nmz787> drazak: see ya
16:02 < tequals0> gel_electrophoresis(100v, 50ma, 2h, DNA_SAMPLES) and then in 2 hours you would have a picture+metadata
16:02 < nmz787> drum scanner?
16:02 < nmz787> i was thinking more like a sanger sequencer or RFLP analyzer
16:03 < nmz787> plain capillary gel electrophoresis
16:03 < tequals0> http://www.luminous-landscape.com/reviews/scanners/drum_scans.shtml
16:03 < nmz787> has a single detector like all the other chromatographs
16:03 < tequals0> right, but "drum scanning" with a head instead of a photo
16:03 < tequals0> much higher resolution
16:04 < tequals0> even illumination
16:04 < tequals0> etc. good stuff
16:04 < nmz787> i don't get it
16:04 < nmz787> no
16:04 < tequals0> we are talking about the same thing, i think
16:04 < tequals0> well, basically the same thing
16:05 < nmz787> sanger and normal capillary and other chromatograms don't move the sensor
16:05 < nmz787> you just get elution time
16:05 < tequals0> ah
16:05 < nmz787> which happens to corellate to lenght
16:05 < nmz787> length
16:05 < tequals0> but it is the same idea
16:05 < tequals0> that you have a single read head
16:05 < tequals0> instead of many
16:05 < nmz787> this also eases purification of said band
16:05 < nmz787> cause it just dumps out the end
16:05 < tequals0> that has identical illumination/sensing
16:05 < nmz787> sure
16:06 < tequals0> instead of vingetting/pixels
16:06 < tequals0> yea
16:06 < nmz787> i'm saying move it with electrics
16:06 < nmz787> not mechanics
16:06 < tequals0> right
16:06 < nmz787> well it's still pixels
16:06 < nmz787> just a single row in that scanner
16:06 < nmz787> but yeah no lens falloff
16:06 < tequals0> right, but your pixels are arbitrarily close together instead of whatever sensor you have
16:07 < nmz787> a drum scanner might still have a diffuser, but more likely a bar fluoro lamp
16:07 < nmz787> tube
16:08 < tequals0> mmhm
16:08 < gradstudentbot> You know, I hear you make more money being a garbage man.
16:09 < tequals0> gradstudentbot: also, health benifits and $20 on xmas
16:09 < gradstudentbot> She keeps talking about her Nature paper, but she was only third author.
16:10 < gradstudentbot> Well, you can't guarantee that.
16:10 < gradstudentbot> Yeah, it's significant.
16:20 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has quit [Quit: - nbs-irc 2.39 - www.nbs-irc.net -]
16:22 < cpopell> I missed the MFC discussion
16:22 < cpopell> but if you guys want I can put you in touch with one of the people working on it...
16:23 < cpopell> err, at a business scale
16:23 -!- balrog [~balrog@discferret/developer/balrog] has quit [Remote host closed the connection]
16:34 -!- tomkinsc [~tomkinsc@c-24-4-11-202.hsd1.ca.comcast.net] has joined ##hplusroadmap
16:37 < tomkinsc> Anyone know of good free software for doing image stacking for astrophotography?
16:42 <@kanzure> sudo apt-get install gcx
16:52 < tomkinsc> thanks
16:55 -!- yorick [~yorick@oftn/member/yorick] has quit [Read error: Connection reset by peer]
16:56 < tomkinsc> Registax seems to also be popular, and can run under wine apparently http://www.astronomie.be/registax/
17:01 -!- tomkinsc [~tomkinsc@c-24-4-11-202.hsd1.ca.comcast.net] has quit [Quit: My computer has gone to sleep. ZZZzzz…]
17:06 -!- tequals0 [47e80ef8@gateway/web/freenode/ip.71.232.14.248] has quit [Quit: Page closed]
17:28 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection]
17:33 -!- makoLime [~mako@103.9.42.133] has quit [Ping timeout: 240 seconds]
17:54 -!- anannie [~chatzilla@unaffiliated/anannie] has quit [Ping timeout: 256 seconds]
18:29 -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has joined ##hplusroadmap
18:36 <@kanzure> "The National Security Agency, hit by disclosures of classified data by former contractor Edward Snowden, said Thursday it intends to eliminate about 90 percent of its system administrators to reduce the number of people with access to secret information."
18:36 < gradstudentbot> I think the centrifuge is broken.
18:42 < cpopell> wut
18:42 < cpopell> but Snowden was Booz
18:42 -!- tomkinsc [~tomkinsc@c-24-4-11-202.hsd1.ca.comcast.net] has joined ##hplusroadmap
19:05 -!- poppingtonic [~poppingto@212.49.88.107] has quit [Ping timeout: 248 seconds]
19:07 -!- poppingtonic [~poppingto@212.49.88.107] has joined ##hplusroadmap
19:10 -!- JayDugger [~jwdugger@pool-71-164-182-91.dllstx.fios.verizon.net] has joined ##hplusroadmap
19:11 -!- JayDugger [~jwdugger@pool-71-164-182-91.dllstx.fios.verizon.net] has quit [Client Quit]
19:17 -!- klafka [~klafka@204-16-157-18-static.ipnetworksinc.net] has quit [Remote host closed the connection]
19:50 -!- tomkinsc [~tomkinsc@c-24-4-11-202.hsd1.ca.comcast.net] has quit [Quit: http://takeitapart.com http://cht-t.com]
19:52 -!- lichen_ [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap
19:54 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds]
19:57 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap
19:59 -!- lichen_ [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds]
20:00 -!- jmil [~jmil@hive76/member/jmil] has quit [Read error: Operation timed out]
20:08 <@kanzure> "Looks like there are going to be 900 disenfranchised sysadmins out in the wild.... I wonder what information they'll have."
20:14 -!- yashgaroth [~ffffff@cpe-75-80-50-28.san.res.rr.com] has joined ##hplusroadmap
20:17 -!- lichen_ [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap
20:21 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds]
20:25 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap
20:27 -!- poppingtonic [~poppingto@212.49.88.107] has quit [Ping timeout: 246 seconds]
20:45 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap
20:48 -!- lichen_ [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds]
20:50 -!- klafka_ [~klafka@c-67-174-253-229.hsd1.ca.comcast.net] has joined ##hplusroadmap
20:53 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Read error: Operation timed out]
20:58 -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has quit [Ping timeout: 248 seconds]
20:59 -!- klafka_ [~klafka@c-67-174-253-229.hsd1.ca.comcast.net] has quit [Remote host closed the connection]
21:02 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap
21:07 -!- lichen_ [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap
21:10 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds]
21:34 -!- cpopell [458c23cc@gateway/web/freenode/ip.69.140.35.204] has quit [Ping timeout: 250 seconds]
21:56 -!- cpopell [47fff18b@gateway/web/freenode/ip.71.255.241.139] has joined ##hplusroadmap
22:00 -!- cpopell is now known as stieruridir
22:01 -!- rk[] [~rak@108-245-58-182.lightspeed.clmboh.sbcglobal.net] has quit [Read error: Operation timed out]
22:02 -!- makoLime [~mako@103-9-42-133.flip.co.nz] has joined ##hplusroadmap
22:02 -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap
22:03 < heath> hrm
22:03 < heath> https://www.ourlab.net/Default.asp
22:03 < heath> https://www.youtube.com/watch?v=ZeL1nrt76V4
22:03 < heath> .title
22:03 < yoleaux> OURLab Intro.mov - YouTube
22:03 < heath> oppenheimer offered his lab for the diybio meetup :)
22:09 -!- childcorn [~itodashev@c-76-23-254-105.hsd1.ct.comcast.net] has left ##hplusroadmap []
22:10 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap
22:11 -!- padz [~not@100.43.114.90] has quit [Read error: Connection reset by peer]
22:13 -!- padz [~not@100.43.114.90] has joined ##hplusroadmap
22:13 -!- lichen_ [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Ping timeout: 264 seconds]
22:18  * brownies pokes gradstudentbot 
22:18 < gradstudentbot> When are you going to publish?
22:18  * brownies pokes gradstudentbot 
22:18 < gradstudentbot> Well, it looks better if you see it through a UV scope.
22:20 < heath> gradstudentbot: you can't like brownies poke you around like that
22:20 < gradstudentbot> Well, the IRB rejected that, so I'm going to rewrite it and try again.
22:24 -!- anannie [~chatzilla@unaffiliated/anannie] has joined ##hplusroadmap
22:26 -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has quit [Read error: Connection reset by peer]
22:57 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Remote host closed the connection]
23:25 -!- poppingtonic [~poppingto@212.49.88.107] has joined ##hplusroadmap
23:25 -!- yashgaroth [~ffffff@cpe-75-80-50-28.san.res.rr.com] has quit [Quit: Leaving]
23:27 < heath> gradstudentbot: you
23:27 < gradstudentbot> Blah, I'm going to quit.
23:38 -!- jmil [~jmil@hive76/member/jmil] has quit [Quit: jmil]
--- Log closed Fri Aug 09 00:00:50 2013