2013-05-12.log

--- Log opened Sun May 12 00:00:24 2013
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klafkahttp://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit thoughts?01:12
gene_hackerI doubt it will be very bright01:24
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archelspersonally, I think the project is way cool, also to give diybio some well-deserved positive rep. But to claim that it can be used as actually lighting, to read a book by or so, is ridiculous.01:29
klafkayes agreed on both counts01:30
klafkai was wondering if people here knew the people involved01:30
fennantony evans was a founder of senstore with rachel kalmar, a quantified self startup. http://singularityhub.com/2012/01/12/senstore-wants-to-make-a-tricorder-that-monitors-the-entire-body/01:38
fenni never met him though. curious how senstore seems to have disappeared from the internet. i guess that's what these singularity university types do, move on to the next flashy thing01:40
fennthey used to hold periodic meetups called "sensored" where people would show off prototypes and talk about electronics and stuff01:43
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kanzuremy new best friend: http://diyhpl.us/~bryan/irc/IMG_20130512_080014.jpg06:18
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kanzureneweather_: hello09:38
neweather_hi09:38
neweather_kanzure hi09:40
neweather_ah total noob09:40
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neweatherhello?09:54
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kanzureneweather: yes?10:02
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neweatherkanzure: sorry, noob trying to get my head round this10:20
kanzurearound what?10:21
neweatherhmm irc10:21
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cathalgarveyLove the topic lads!13:56
cathalgarveyJust here to abuse community resources as usual https://www.sciencedirect.com/science/article/pii/S037811190100584413:56
cathalgarvey@paperbot https://www.sciencedirect.com/science/article/pii/S037811190100584413:57
kanzurepaperbot: https://www.sciencedirect.com/science/article/pii/S037811190100584413:57
cathalgarveypaperbot: https://www.sciencedirect.com/science/article/pii/S037811190100584413:57
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Cooperative%20effects%20by%20the%20initiation%20codon%20and%20its%20flanking%20regions%20on%20translation%20initiation.pdf13:57
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Cooperative%20effects%20by%20the%20initiation%20codon%20and%20its%20flanking%20regions%20on%20translation%20initiation.pdf13:57
kanzureexcellent13:57
cathalgarveyEvery time I come here I make a fool of myself haranguing paperbot. I'm sorry paperbot.13:58
kanzuresup?13:58
cathalgarveyTY @Kanzure13:58
kanzurealso i found that "YOU MUST HAVE A PHD" email thread pretty bizarre13:58
cathalgarveyHaha, last minute workload before holidays is all! :)13:58
cathalgarveyWanna get a gene ordered ASAP and want to get the nitty-gritty of translation initiation looking good on paper first..13:58
cathalgarveyHaven't read that thread yet?13:58
kanzureah, well, whatever it's just boring stuff13:59
cathalgarveyHave been meaning to but there are so many posts and I am already so very old13:59
cathalgarveyHow about yoruself? What's news over  yonder hill14:00
kanzuretoday i am goofing off on a rom hacking marathon14:01
kanzurehttps://github.com/kanzure/pokecrystal-demo/wiki/Announcement14:01
kanzurehttp://sanqui.sweb.cz/screen/2013051221%3A53%3A49diyhpl.us-~yenatch-pokecrystal-extras-tilemonster--Chromium-c7e8.png14:02
cathalgarveyAwesome! :)14:03
cathalgarveyROM hacking at that depth must involve some assembly, no?14:05
cathalgarveyDidn't know you went that deep into SW hacking14:05
kanzurecathalgarvey: here's a presentation,14:05
kanzurehttp://diyhpl.us/~bryan/irc/pokered/crystal/aha-pokemon-crystal.pdf14:05
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kanzurecathalgarvey: also these are fun,14:06
kanzurehttps://github.com/kanzure/pokecrystal/tree/master/extras/vba.py14:06
kanzurehttps://github.com/kanzure/pokecrystal/blob/master/extras/gbz80disasm.py14:06
kanzurehttps://github.com/kanzure/pokecrystal/blob/master/extras/crystal.py14:06
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kanzureit has full test coverage: https://github.com/kanzure/pokecrystal/blob/master/extras/tests.py14:07
kanzureand 100,000+ lines of hand-crafted asm https://github.com/kanzure/pokecrystal/blob/master/main.asm14:07
* heath thinks fenn is looking for a job14:08
heathnobody uses linkedin unless they are looking, right?14:09
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klafkalol14:10
klafkai use it as an ego boost14:10
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klafkawhen people ask me if i want a job14:10
cathalgarveySome people use it as a way to have a wang-off about how many people they "employ". But for the most part, yea. Job=hunting.14:10
kanzureoh man, linkedin is a lousy way to get employment14:10
klafkais it?14:11
kanzureyeah, you get harassed by recruiters constantly14:11
cathalgarvey:P14:11
klafkaoh14:11
cathalgarveyIn Ireland that would be considered a magical place.14:12
cathalgarveyPeople chase rainbows here for jobs.14:12
klafkalike i said - i like the ego boost14:12
cathalgarveypaperbot: https://www.sciencedirect.com/science/article/pii/B978012385120800003614:12
klafkano one started doing that kanzure till i changed my job description to 'data scientist'14:12
kanzurefenn: https://news.ycombinator.com/item?id=563766314:12
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Chapter%20threeDesigning%20Genes%20for%20Successful%20Protein%20Expression.txt14:12
klafkaturns out people don't give a fuck about support engineers14:12
cathalgarveyThank you paperbot14:12
kanzureklafka: you literally put data scientist? you mad man.14:12
kanzurebrownies: ^ check that shit out14:12
klafkawhy?14:12
kanzurecathalgarvey: nope no access on that last one14:12
kanzureklafka: because nobody calls themselves a "data scientist".. that's just poor marketing.14:12
klafkaumm lots of people do14:13
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cathalgarveyAh well, it's just more noise about Gene Designer, which I'm not going to be using anyway.. :)14:13
klafkaholy crap i haven't logged into my 'professional gmail' in months14:13
cathalgarvey@kanzure In case you haven't noticed, there are oceans of stupid people with too much money desperate to get in on this "big data" they keep hearing about in TED talks.14:14
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cathalgarveyAnything with "data" in the title gets them salivating like Pavlov's dogs.14:14
* data_astronaut explores datar14:14
klafkakanzure:  maybe is should call myself 'machine learning guru '14:14
kanzureklafka: i think "machine learning" is very well defined at this point; it means you top out at SVM or something.14:14
kanzureor that you might at least have an ability to write and understand kernels14:15
klafkawhat really?14:15
klafkayou top out ?14:15
klafkai'd think it means you top out at the bleeding edge of ML research or some shit14:15
kanzurewhat? i mean, i haven't seen anyone hiring a "machine learning" person that knows things beyond svm and mcmc or something14:15
cathalgarveyMachine learning has a role in Kernels? Show me this proto-skynet, I would flash it onto my phone.14:15
kanzurecathalgarvey: wrong type of kernel14:15
kanzurecathalgarvey: unfortunately14:15
klafkacathalgarvey:  yeah14:15
klafkakernel spaces14:16
kanzureklafka: btw evidence to the contrary would be appreciated/neat14:16
klafkais what they are referring to14:16
klafkakanzure: what do people that know machine learning call themselves then?14:16
klafkalike beyond mcmc and svm14:16
klafkait's funny because svm and mcmc have nothing to do with each other14:16
klafka:P14:16
cathalgarveypaperbot: http://link.springer.com/protocol/10.1007%2F978-1-61779-564-0_1514:16
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/f7907f865e118a6fffc8b5f1076e2f2f.txt14:16
* data_astronaut doesn't understand14:16
kanzureklafka: oh sure there's definitely little relation, but i would expect a machine learning person to know both.14:16
* data_astronaut starts hiring people based on if they know what corn kernels are14:16
kanzurecathalgarvey: sorry, no access on that one14:16
klafkacathalgarvey: they refer to 'kernel machines' SVM is a good example of a kernel machine14:16
cathalgarveyStupid gene designer papers. Little signal, all paywall14:16
kanzurecathalgarvey: did you see https://news.ycombinator.com/item?id=5687832 ?14:17
* data_astronaut welcomes people to alabama's "silicon valley" with corn kernels for now on14:17
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data_astronautgotta stay on the cutting edge14:17
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cathalgarveyHow's SLF going these days? :)14:18
kanzurei have acquired 20+ TB14:18
kanzureworking out logistics14:19
cathalgarveyTB?14:19
kanzureterabytes14:19
cathalgarveyAs in, of data or capacity??14:19
kanzurecapacity; i have been running out of room for a while now and only have 20%.14:19
cathalgarveyYou realise that if you try to personally DL 20 TB of paywalled data, you'll get arrested, right?14:20
cathalgarveyThat's been pretty comprehensively proven already14:20
kanzurei think you're wrong14:20
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kanzurebut also, there's a lot of public domain and CC-BY-SA stuff that needs to be catalogged and copied too14:21
kanzureNTRS stuff was "public domain" but we fucking don't have it anymore14:21
cathalgarveyI think you can't argue with clear precedent; downloading too much science, even with a legitimate reason (as Aaron had), gets you arrested.14:21
kanzureoh, aaronsw made a bunch of mistakes14:21
cathalgarveyEven "public domain" stuff on JSTOR isn't "public domain" because it has their stupid letterhead on it, and they claim derivative work. And in the US, that works.14:21
cathalgarveyYou're making a mistake right now; Freenode have server logs and you *founded* Science Liberation Front. The Aaron prosecutors were using his blog post advocating open science as evidence.14:22
kanzurewhether or not it's legal is an interesting question, but i'm still interested in having an organization or entity with that complete collection.14:22
cathalgarveyYou're openly tied to an "organisation" that clearly advocates and encourages people to break the law in the US; that alone is enough to put you in prison, AFAIK.14:22
cathalgarveyBy all means, I'm all for freedom of science. But you're using *your real name* to do it, I'm boggled14:23
kanzurehey, i know you think i'm doing something wrong, but i haven't even told you important details that would give you enough information14:23
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kanzurei'm not using my real name to do anything 'cept paperbot maybe14:23
cathalgarveyI don't think you're doing something "wrong". Civil disobedience is great when a law is injust. I think you're doing something very, very foolish.14:23
kanzureif you thing paperbot is morally wrong, then please elaborate.14:23
kanzureor legally wrong, even14:23
kanzuresorry, i definitely meant legally wrong14:24
cathalgarveyAnd if there are mitigating details, for the love of god don't tell me! :)14:24
cathalgarveyYou've already said too much in public channels!14:24
cathalgarveyLegally?14:24
kanzureoh my god i have storage space~~~~14:24
cathalgarveyA) Advocating and encouraging copyright infringement. You might even count hosting a group as "abetting", and given how silly US copyright law is, it'd probably stick.14:24
kanzureactually, i've had takedown requests that i've replied to and had amicable resolutions14:25
cathalgarveyB) Hosting a (much appreciated) robot on a huge clearnet server (Freenode) that explicitly serves the function of evading paywalls, which the CFAA has been beefed up to make into a serious crime.14:25
kanzurei think you are reading too much into what paperbot does14:25
kanzureit's just a shortcut for me reading papers14:25
cathalgarveyGlad to hear it, but if they wanted to push for a non-amicable solution, they'd win14:25
* kanzure yawns14:26
cathalgarveyYou can say that all you like, but you're hosting a gateway to direct copyright infringement. That's even more concrete a breach of Copyright law than a torrent index, and index hosts have been put in prison.14:26
kanzurewoo http://sanqui.sweb.cz/screen/2013051223%3A26%3A45bgb-PM_CRYSTALBYTE-085e.png14:27
kanzureSanky: i am abusing your links14:27
cathalgarveyThe guys who founded TPB never once broke copyright and the US arranged for prison sentences for them. Exhausted ridiculous political capital to do so, too.14:27
kanzurecathalgarvey: by that logic everyone in the world is hosting a gateway to direct copyright infringement14:28
cathalgarvey@kanzure Copyright is innately illogical, yes. But there are clear examples of legal precedent that show what you're doing can get you arrested and convicted of a felony in your country.14:28
cathalgarveyThat's all I'm saying; not "wrong" but "foolish".14:29
kanzurei don't think reading papers is that big of a deal; this is what they are here for.14:29
cathalgarveyIf you want to help civil disobedience, host a zero-knowledge webserver for science, hope it's not abused for porn, and hope instead that it hosts articles.14:29
cathalgarveyI think anything that costs a powerful lobbying corporation in the US money is a big deal to them, and traditionally results in a crackdown.14:30
cathalgarveyElsevier have *all the lobby money* and a vested interest in their paywall; it's all they have.14:30
kanzurei think suing a mendelsevier user would look extremely poor14:30
cathalgarveyIf they see someone pulling an Aaron, they'll respond vigorously. At *best*, you'll be forced to delete your stuff and take down your server. More likely, you're looking at a felony.14:30
kanzure"pulling an Aaaron" sigh, just because we both read papers doesn't mean that we're doing anything really similar.14:31
cathalgarveyThat's why they don't sue individuals who pirate; they're not actually that stupid. But take this to the 20TB level, and it's another ballgame.14:31
kanzurebtw, in the US, storing content is not a felony (except state secrets, i think, but i'm not completely sure)14:33
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cathalgarveyFor personal use, no.14:37
cathalgarveySo if you use your accounts to make local copies and never share them, that's fine (though check for a "fair usage policy" that might get your account frozen).14:37
cathalgarveyBut you should really read the CFAA and the recent amendments they are trying to / have already added: it would make it a felony to set up a gmail account under a false name, so weigh that against what's implied by "Science Liberation Front".14:38
cathalgarveyI'm only offering my concerns here, but I do think you're treading a fine line now, and walking into fire if you push with some of your implied goals.14:38
kanzurei think you are a fearmonger14:39
kanzurei assume you also disprove of me talking with the FBI?14:39
cathalgarveyNope, because you're american.14:39
cathalgarveyAnd I didn't disapprove of "talking with the FBI", I disapproved of the FBI asserting a sort of responsibility over Europeans.14:40
klafkato be fair kanzure you are a pseudo public figure under this pseudonym14:40
klafkaeveryone knows who you are14:40
klafka:p14:40
klafkaro most people14:40
klafkaalso your whois has your name14:40
kanzureoh also pokecrystal; all sorts of "copyright law" "evil remixing" going on there. gotta hate that too.14:40
kanzureklafka: yep, my whois also has my address and phone number. nobody calls me :( it's so sad.14:40
cathalgarveyDude, you keep misunderstanding me as "hating" copyright infringement. I don't, I think copyright is a farce.14:41
cathalgarveyBut disliking copyright doesn't make it not-exist. It's one of the most unreasonably inflated legal structures in existence.14:41
cathalgarveyYou can end up with more severe penalties for downloading an mp3 than for beating someone senseless.14:41
cathalgarveyOn that basis, I was suggesting that encouraging or directly aiding in the mass-infringement of literature owned by a prototypical, exceptionally-well-funded copyright troll might not be wise.14:42
cathalgarveys/owned/"owned"/14:42
klafkakanzure:  what do you use for 3d printing stuff?14:42
kanzureklafka: my friends14:43
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kanzureklafka: i use them for things.14:43
kanzureklafka: i don't actually have a 3d printer of my own.14:43
klafkai mean software wise14:43
klafkai was considering getting one14:43
klafkaa cubex one14:44
kanzureoh, software things. depends on the device itself, they usually have "official" software. reprap's firmware is ok.14:44
klafkaoh really14:44
klafkabut don't they all take standardized formats?14:44
kanzurepeople like to use slic3r, openscad, brlcad, etc.14:44
cathalgarvey@klafka If you're talking about modelling and are not a solids purist, I recommend OpenSCAD. Oldie, but goldie.14:44
klafkai see14:45
klafkai need to think more about generative art in 3d printing a bit14:45
kanzurei would recommend brlcad or something else other than openscad for generative art14:46
kanzureopenscad has this shitty custom language14:46
kanzureand if you want stl, brlcad is fine with that.14:46
kanzure*fine for that14:47
klafkacool14:47
superkuhI recently removed all the books from my mirror for the reasons cathalgarvey suggests. Now I just host journal articles. For those I am willing to take the risk.14:52
superkuhI have a feeling a full copy of my technical books mirror might show up somewhere though. Completely unrelated to me, of course.14:52
kanzurecathal is just angry about lawsuits, paperbot is not going to cause the apocalypse.14:53
cathalgarveyEh, I'm not angry14:53
cathalgarveyI've no reason to be angry, especially as Paperbot's done me a favour today. :)14:54
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klafkapaperbot: http://onlinelibrary.wiley.com/doi/10.1592/phco.23.12.1238.32704/abstract15:16
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/55b302baaca6ff29c5f68aebb5ccdaa.txt15:16
klafkacan someone get me that rpretty please15:17
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cathalgarveypaperbot: https://www.sciencedirect.com/science/article/pii/S002228360800795X?np=y15:57
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Ribosome%20Collisions%20and%20Translation%20Efficiency%3A%20Optimization%20by%20Codon%20Usage%20and%20mRNA%20Destabilization.pdf15:58
cathalgarveypaperbot: https://www.sciencemag.org/content/324/5924/255.long16:08
paperbotSSLError: [Errno 1] _ssl.c:504: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 632, in send)16:08
cathalgarveyruh roh16:08
cathalgarveypaperbot: http://www.sciencemag.org/content/324/5924/255.long16:08
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Coding-Sequence%20Determinants%20of%20Gene%20Expression%20in%20Escherichia%20coli.pdf16:08
cathalgarveyThank goodness. I've tried opening a "free access" account with ScienceMag so many f-ing times16:09
kanzureunknown protocol :rolleyes:16:09
kanzureweird.16:09
kanzurepython-requests supports HTTPS just fine... i thought?16:09
cathalgarveyWell, it is "SSLError", so at least it's been dispatched correctly to an SSL handler16:12
cathalgarveySSL23 looks like an old SSL format though, perhaps it's not supported by Python?16:12
* cathalgarvey tries to recall what versions of SSL border the SSL/TLS divide16:13
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cathalgarveyofc, "string.replace("https://","http://") works fine too16:13
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* heath was prescribed modafinil17:49
* heath has to now find an insurance company that actually pays17:50
heath$1026/month for 200mg17:50
heath$300/month for 100mg17:50
kanzurehey congrats you're getting screwed harder than i am on adderall17:50
kanzureoh17:50
kanzurehey congrats we're both being screwed about the same17:51
heathit's ~$500/month for armodafinil17:53
heathhey cathalgarvey, where are you working these days?17:53
kanzurecathal is working out of his supervolcano lair17:55
cathalgarveyHello!17:55
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cathalgarveyStill working between the lab-in-rent's-house and my own kitchen at home (not for wetware, ofc)17:55
ParahSail1nwhat's adderall cost you?17:56
kanzureit varies by month and by pharmacy, $200-$300/mo (dose is the same each month)17:56
ParahSail1nso thats how you type so fast17:57
kanzureyes, according to http://www.seanwrona.com/typeracer/profile.php?username=kanzure i type 20-30 wpm faster on adderall17:58
ParahSail1ni can't take the physical strain of adderall unfortunately17:59
brownieskanzure: eh?17:59
cathalgarvey@ParaSail1n You need to take the ephemeral form, then? :)18:00
ParahSail1nyeah the stuff i got was the XR, i'd be cool if it lasted for 2-4 hours then able to sit down and have an appetite18:01
ParahSail1nit was XR, but i chewed the granules, but that didnt really help at being more ephemeral18:02
kanzurei am on 30mg XR for 8 hours, then 20mg tablet non-XR for whatever else i need18:02
heathanyone up for clicking so fast you have to get a robotic finger replacement? http://click-click-click.meteor.com18:07
ParahSail1nheath i will win every time18:10
heathit's on then18:10
heathawww :)18:10
heathheh, i didn't take into account more than 2 people looking at the screen at the same time :)18:11
heath..and clicking18:11
ParahSail1njavascript:for(var i=0; i<50; i++)$(".Left").click()18:11
cathalgarveyhax18:12
* heath ragequits18:12
yashgarothgo team left18:13
cathalgarveyIt broke my heart a little to use a C program as a backend, but I have finally got PySplicer set up to avoid secondary structure in mRNA output18:14
cathalgarveyI can finally, therefore, order the goddamned gene I've been working on for weeks and go to bed18:15
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cathalgarveyAny last minute advice for shit-to-avoid-in-final-constructs?18:15
cathalgarveyI've got RNAse E, will throw in biobrick enzymes etc.. what else to exclude?18:15
kanzureheath: an xhr per click seems super inefficient. have you considered websockets? like socket.io or some shit.18:16
kanzureParahSail1n: wtf, i was trying that (actually i was using $(".score")[1]) but .click() didn't seem to be working.18:17
kanzureheath: join our pokehack :o http://sanqui.sweb.cz/screen/2013051303%3A04%3A59diyhpl.us-~yenatch-pokecrystal-extras-tilemonster--Chromium-9ce8.png18:18
ParahSail1nkanzure, .Left and .Right work18:19
heathkanzure: that's a great point, re: ws://18:20
heathi had considered it, but i was mostly told to get familiar with it and have something up in a few hours :P18:20
heaththe obvious conclusion from the above being i haven't played with websockets much18:22
heathhttps://github.com/heath/btc_ticker uses them18:23
* heath will throw in ws:// per request18:23
kanzureobviously you should be using dnode18:24
kanzureover webrtc18:24
kanzurewith uh... um.. blast what the hell library is hip these days.18:24
kanzureangular.18:25
heathhah18:26
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ParahSail1npaperbot, http://onlinelibrary.wiley.com/doi/10.1002/cjce.5450690317/abstract19:01
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/a06dadafd3ae391a6c2b49761edc562a.txt19:01
ParahSail1npaperbot, http://heattransfer.asmedigitalcollection.asme.org/article.aspx?articleid=145040319:03
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Water-Heated%20Pool%20Boiling%20of%20Different%20Refrigerants%20on%20the%20Outside%20Surface%20of%20a%20Horizontal%20Smooth%20Tube.pdf19:03
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cathalgarveyOrder placed, wish me luck!19:11
cathalgarveyNow to have food and sleep, those other requirements for effective biohacking19:11
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heathspeaking of whatever the hell library is hip these days..19:37
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* heath has accepted commits in webrtc on ietf and in angular19:37
heathapparently to get something pushed on a major project, you just need to correct grammar regularly19:38
kanzurei'm afraid that most of my commits are typo fixes19:42
kanzureit seems really lame19:42
kanzuremost of my contributions to yeoman were typofixes, for example19:42
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kanzuregene_hacker: sup19:42
gene_hackerwriting an IK solver and other fun stuff19:43
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kanzure.title http://bamh1.com/2013/05/13/oh-the-places-well-go-setting-up-a-biohacking-space/23:25
yoleauxOh the places we’ll go… setting up a Biohacking space!23:25
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