--- Log opened Fri Jun 07 00:00:49 2013
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04:10 < d3nd3> hi
04:10 < Open> Anyone here who has some deeper insights into technical aspects of dna synthesizers?   Kanzure led me here :)
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04:28 < nmz787_> paperbot: http://cre.sagepub.com.proxy.lib.pdx.edu/content/21/1/17.long
04:28 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Repetitive%20locomotor%20training%20and%20physiotherapy%20improve%20walking%20and%20basic%20activities%20of%20daily%20living%20after%20stroke%3A%20a%20single-blind%2C%20randomized%20multicentre%20trial%20%28DEutsche%20GAngtrainerStudie%2C%20DEGAS%29.pdf
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08:46 < kanzure> 04:10 < Open> Anyone here who has some deeper insights into technical aspects of dna synthesizers?   Kanzure led me here :)
08:46 < kanzure> grr you only lasted 5 minutes?
08:47 < kanzure> kids these days have no patience
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09:00 < kanzure> "Thank you very much indeed to give me a hand on that. As I was saying on the phone I am looking to interview a biohacker in London (or around like Cambridge). Could you help me to find their contact details for me to be able to reach them? As a note I work as a journalist for the France 24 TV news channel based in Paris and more specifically for the 12 minute programme called ‘Down to Earth’. We’ll be in London next week to do our ...
09:00 < kanzure> ... report on synthetic biology."
09:01 < biolulz> are you based in London or you looking for someone there?
09:01 < kanzure> i was quoting an email.
09:01 < biolulz> ah
09:02 < kanzure> i am not based in london and i'm not looking for anyone.
09:02 < biolulz> ok
09:02 < biolulz> he is looking for someone
09:02 < kanzure> yes, i gave her a list of people to stalk in london and manchester.
09:03 < biolulz> aight, I know someone here (London) too setting up the hackspace
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09:05 < kanzure> the london hackspace has existed for a long time now
09:06 < biolulz> oh no sorry, I meant setting the biolab in the hackspace
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10:57 < ParahSailin> paperbot: http://www.sciencedirect.com/science/article/pii/S1053811913005922
10:57 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Breastfeeding%20and%20early%20white%20matter%20development%3A%20A%20cross-sectional%20study.pdf
10:58 < ParahSailin> "Does breastfeeding alter early brain development?" Only in breastfeeding is the biological norm considered alteration
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11:15 < ParahSailin> is there a good chrome extension for blocking hijacking of copy that adds shitty extra shit to your paste?
11:18 < superkuh> For some of them use your hosts file and set tcr.tynt.com, www.tynt.com,  and tynt.com to resolve to localhost.
11:19 < ParahSailin> oh yeah, thats where that js file was from
11:19 < ParahSailin> didnt know they did lots of sites
11:19 < ParahSailin> can we ddos them out of existence?
11:22 < jrayhawk> https://www.livingonlight.co/ this will go well
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11:26 < kanzure> ParahSailin: at the moment we are a rather pathetic ddos
11:26 < kanzure> ParahSailin: our blackmailing is the worst.
11:26 < kanzure> pay us or else 10s of people will be using your site
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12:45 < chris_99> so i was looking at this http://www.independent.co.uk/news/science/mammoth-discovery-jurassic-park-takes-a-step-closer-to-reality-as-russian-scientists-find-blood-in-woolly-mammoth-8637871.html
12:45 < chris_99> what would they need to do, to clone a mammoth from blood cells
12:48 < kanzure> violate an elephant.
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13:01 < jrayhawk> individual cell genomes will be degraded, and, while we can probably sequence a good one using a large number of cells, synthesizing chromosomes that large hasn't been done before, and, even if we could, the result would be fairly meaningless without a lot of epigenetic information we don't even know how to quantify, let alone read.
13:07 < jrayhawk> with luck, an existing pachyderm embryonic cell will contain what's needed for viable use of mammoth DNA, and we'd "only" need to work out the right methylation.
13:16 < jrayhawk> so, pray to god pachyderm RNA is good enough, invent a way to read and write methylation patterns, and pray to god a diff between embryonic and red blood cell pachyderm methylation patterns will apply workably to mammoth DNA.
13:20 < jrayhawk> this is highly unlikely to work even with the known unknowns, but at least you can get a nobel prize or two discovering the previously unknown unknowns.
13:20 < ParahSailin> i'd take one haploid set of chromosomes from mammoth and stick in nucleus with haploid set from asian elephant
13:24 < ParahSailin> do they have any elephant cell lines yet?
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14:34 < gonz> paperbot: http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1283997
14:34 < kanzure> gonz: hi
14:34 < paperbot> error: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/Identification%20of%20embedded%20mathematical%20formulas%20in%20PDF%20documents%20using%20SVM.pdf
14:35 < kanzure> oh noes a watermark
14:35 < kanzure> please file a bug report https://github.com/kanzure/pdfparanoia/issues
14:36 < gonz> kanzure: hi
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14:39 < gonz> paperbot: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6065544
14:39 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/e7314f05b9847aaa3bbe305580ffa10d.txt
14:39 < kanzure> oh yeah, paperbot is also broken sometimes. so feel free to bugfix that too. https://github.com/kanzure/paperbot
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14:47 < gonz> kanzure: it's pretty awesome, first time here :)
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15:49 < nmz787_> ParahSailin: are you talking about copy-pasting google result links?
15:50 < nmz787_> there's a chrome extension that removes that
15:50 < nmz787_> junk
15:50 < nmz787_> https://chrome.google.com/webstore/detail/dont-track-me-google/
15:51 < nmz787_> oh, i guess this link works https://chrome.google.com/webstore/detail/dont-track-me-google/gdbofhhdmcladcmmfjolgndfkpobecpg
15:51 < kanzure> no. he's talking about the javascript clipboard hijacking things. when you select text you expect only that text to be selected.
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15:54 < nmz787_> http://finance.yahoo.com/news/human-face-might-look-100-171207969.html
15:54 < nmz787_> 'How The Human Face Might Look In 100,000 Years'
15:54 < nmz787_> it's an alright quick read, nothing new to us
15:56 < nmz787_> http://tv.yahoo.com/news/walking-dead-vampires-diaries-actress-arrested-obama-bloomberg-193717583.html
15:56 < nmz787_> "'Walking Dead,' 'Vampires Diaries' Actress Arrested in Obama-Bloomberg Ricin Case"
15:56 < nmz787_> "If convicted, Richardson faces up to 10 years in federal prison."
15:56 < nmz787_> Really? That seems low for attempted assasination and/or terrorism
15:57 < nmz787_> bioterrorism
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16:34 < nmz787_> bah, mediawiki doesn't come loaded with options to confirm new user accounts and restrict anonymous editing
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16:43 < nmz787_> ugh
16:44 < nmz787_> software like this sucks
16:44 < nmz787_> why didn't they just add a GUI radio button instead of making people edit php files
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16:58 < phillyj> kanzure: have you come across a watermark called "rightslink copyright clearance center" in any pdf articles you looked at?
16:58 < jrayhawk> ha ha ha you get to learn piecemeal why bryan uses ikiwiki
17:03 < phillyj> jrayhawk: are you talking to me?
17:03 < brownies> why does bryan do anything? who knows.
17:03 < jrayhawk> phillyj: Nope.
17:03 < phillyj> ic, no idea what you all are talking about
17:04 < jrayhawk> logs are in the topic, if'n you happen to care
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17:05 < nmz787_> jrayhawk: does ikiwiki default with user access controls, email confrimation, etc?
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17:09 < kanzure> yes, ikiwiki has user access control and email confirmation
17:14 < jrayhawk> 'default' is sortof a misnomer in ikiwiki-land since initial setup requires a lot of configuration; the two management engines I know of for automating that are Branchable and Piny. At least Piny emails verification links; not sure about Branchable. Piny also (optionally) allows administrative control over what accounts get to edit.
17:16 < jrayhawk> configuration stuff is pretty trivial in comparison to the data model differences.
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17:31 < nmz787_> hrmm, maybe I should just start a portland page on openwetware
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17:46 < phillyj> nmz787_: are you on the west coast now?
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17:59 < cogitokat> hey gradstudentbot
17:59 < gradstudentbot> I just want a 9 to 5 job.
17:59 < cogitokat> gradstudentbot:
17:59 < gradstudentbot> I need to send that abstract.
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18:00 < cogitokat> gradstudentbot:
18:00 < gradstudentbot> Friends don't let friends go to super school.
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18:05 < kanzure> yashgaroth: you should meet gradstudentbot
18:05 < gradstudentbot> Can I get Saturday off?
18:06 < kanzure> no
18:06 < yashgaroth> heh
18:10 < yashgaroth> gradstudentbot:
18:10 < gradstudentbot> The lab meeting was cancelled.
18:11 < brownies> legitimately thought it was a real grad student for several seconds
18:27 < phillyj> wait, gradstudentbot is a bot?
18:27 < gradstudentbot> No, you can't borrow my pipette.
18:28 < phillyj> lol
18:28 < phillyj> gradstudentbot:
18:28 < gradstudentbot> People have tried that, but it doesn't seem to work.
18:30 < Lemminkainen> gradstudentbot did you email the collaborators?
18:30 < gradstudentbot> If you help me, I'll put you on the paper.
18:31 < phillyj> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/23253611
18:31 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/6f1b93fddcff074ab0066d09d243a23d.txt
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18:56 < kanzure> does EFF do any software development of its own?
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19:52 < phillyj> paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC60006/
19:52 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/5be86980d0af7339e7a3576e8f902596.txt
20:04 < kanzure> .title http://andrewkelley.me/post/jamulator.html
20:04 < yoleaux> Statically Recompiling NES Games into Native Executables with LLVM and Go - Andrew Kelley
20:04 < kanzure> "One possible technique is to emulate the assembly program, and then record the ways in which memory addresses are accessed. After playing a game for a while, you would have a pretty good record of exactly which sections are data and which are code. I decided not to use this technique, however, since the goal of this project is static recompilation. I want to explore just how much is possible to do at compile-time."
20:05 < kanzure> "Not bad. This is as close as we can get to the original source. It's impossible to know what label names were used, but we can give good names to the interrupt vectors."
20:05 < brownies> kanzure: i am starting to think that Go is worth learning
20:05 < kanzure> "as close as we can get".. i guess he doesn't believe in me.
20:06 < kanzure> "llc converts the LLVM IR code into a native object file, and then gcc does the final link step"
20:06 < brownies> that sounds odd.
20:06 < kanzure> i'm not exactly sure how he plans to have this running. llvm will convert from its intermediate language to any of the target platforms that llvm supports.. but all of the hardware specs are different anyway. so what's the point?
20:06 < kanzure> "Recall that the NES uses memory mapped I/O. This means that this instruction could be saving a value in memory, but it could also be talking to the PPU, the APU, the game pad controller, or even a mapper. Since this one instruction could be doing any of these things depending on runtime state, we will have to add a runtime address check."
20:07 < kanzure> ok sure you can do jit/runtime things, sometimes.. "With this framework in place, we can recompile instructions that store to memory addresses only known at runtime. Code generation for the other instructions in this assembly program is straightforward at this point."
20:07 < kanzure> i suppose you could write a "dumb" library that your intermediate language causes to call for various instructions. e.g. if video memory is changed then you just write to some image buffer.
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20:07 < kanzure> pfffft "Given this solution, I ported the PPU code as well as the SDL and OpenGL front-end code from Fergulator to a small C runtime, which is compiled with clang. Here is a snippet explaining the rom_cycle and main functions."
20:07 < kanzure> "And so here we have it: an executable binary that depends on SDL and OpenGL, which supposedly will execute the Zelda Title Screen Simulator when run."
20:08 < kanzure> nice he did jump table detection (pokecrystal would require something like that plus a number of other tricks)
20:08 < kanzure> "For example, one such technique is to identify a section of code, make some assumptions based on heuristics which allow for highly optimized native code generation, and then detect if those assumptions are broken. If the assumptions are broken, the generated native code is tossed, and emulation takes over. However, if the assumptions are upheld, the recompiled block of code will execute with blazing fast native speed."
20:08 < kanzure> not sure what the point is then, emulation is already blazing fast in the first place
20:09 < kanzure> gradstudentbot: write me a just in time pokemon compiler.
20:09 < gradstudentbot> Yeah, I don't know.
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20:17 < phillyj> gradstudentbot: go to sleep
20:17 < gradstudentbot> Can I get Saturday off?
20:18 < phillyj> gradstudentbot: 2 hour break on Saturday
20:18 < gradstudentbot> Yeah, I read the paper, I just don't remember the details.
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20:19 < kanzure> gradstudentbot: are you sure you don't want to write the paper?
20:19 < gradstudentbot> I have the methods section but I haven't written the introduction or conclusions.
20:23 < kanzure> ughh "Ya, I've never used MediaWiki before, but after tinkering I finally figured out how to change user rights. Erik and I were talking and were wondering if you would have any interest in maintaining the wiki? Also I have the login/password for the HostGator CP to directly edit the MediaWiki PHP files, though I've been wondering lately how good of an idea it is to send login/password credentials via email. Bryan, do you have any ideas on ...
20:23 < kanzure> ... how to either store or share sensitive information online?"
20:23 < kanzure> why not just use ikiwiki?
20:23 < kanzure> i even offered to host the wiki for you guys
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21:26 < jrayhawk> ha ha ha
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22:05 < kanzure> http://spectrum.ieee.org/consumer-electronics/gadgets/adventures-in-printing-food
22:05 < kanzure> not interesting/new, but didn't know lipton works with hod lipson
22:05 < kanzure> just seems confusing
22:11 < kanzure> "Community projects are now the most recurring item on the calendar. They are crowding out paying classes, and attendees get the benefits of BioCurious without paying to support it."
22:11 < kanzure> haha their "pay for membership" model is breaking
22:11 < kanzure> too bad they don't fucking listen
22:12 < kanzure> gradstudentbot: you should write about this
22:15 < yashgaroth> oh no I think gradstudentbot fell asleep at the bench
22:15 < gradstudentbot> I think I'll be done in 2 years.
22:15 < yashgaroth> perfect
22:16 < kanzure> gradstudentbot: you sure?
22:16 < gradstudentbot> I think the centrifuge is broken.
22:17 < kanzure> gradstudentbot: probably.
22:17 < gradstudentbot> I forgot to make a control group.
22:17 < kanzure> gradstudentbot: it happens. when are you going to write the paper?
22:17 < gradstudentbot> I have way too many papers to read.
22:17 < kanzure> gradstudentbot: which ones have you read?
22:17 < gradstudentbot> Wasn't there a paper about that?
22:17 < kanzure> gradstudentbot: yes, it was an article in nature.
22:17 < gradstudentbot> Am I going to be first author?
22:18 < kanzure> gradstudentbot: no
22:18 < gradstudentbot> Friends don't let friends go to super school.
22:19 < kanzure> sorry. i guess i just like my new toy.
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22:20 < yashgaroth> aww
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22:20 < yashgaroth> gradstudentbot, welcome back
22:20 < gradstudentbot> Why did I go to grad school?
22:25 < kanzure> gradstudentbot: because science.
22:25 < gradstudentbot> I just want a 9 to 5 job.
22:35 < kanzure> "The cash crisis I talked about earlier this year isn’t better.  Unless things chance, we may have to close BioCurious. The lab stays busy. People are in during all hours, working on fantastic projects. Our volunteer staff pulls together beautifully. Community, personal, and commercial projects are coming out of the lab like the bioprinter, the bioluminescence work, the Glowing Plant effort, DNA sequencing and prep products. More people are ...
22:35 < kanzure> ... being introduced to these technologies than ever before. But we’re dangerously low on money."
22:35 < kanzure> "Most of the projects at the space and the attention that we get for our work don't net us any revenues.  We need at least $5000-$6000 each month just to pay our rent, keep the lights on, have an Internet connection, and restock basics like gloves and pipette tips. That also doesn’t account for other expenses like new equipment, expanding capabilities, or replacing broken stuff."
22:35 < kanzure> "This is the trend we've talked about in our member meetings - and it's gotten worse. Although lots of people show up for community projects, membership is flat, and paid classes are scarce. If we don't fix this right now, we run out of money in 30-60 days. "
22:35 < kanzure> "What We Are Doing: I'm calling an emergency member meeting on Wednesday, June 12th at 7pm  to discuss 2 plans. Plan A: Immediately increase the number of paid classes, consistently enforce rules already in place about lab work, and recruit hands on help to execute both of these. We have some new equipment that doesn't have to live in the lab (3D printer, lab automation projects, etc.).  We can either require this work be done in the lab (not ...
22:35 < kanzure> ... preferred, due to space constraints), or have non-members pay to do hands-on work on these projects, or use this equipment. We need to set a price for this activity. The suggestion is $10 donation per non-member, per project night."
22:35 < kanzure> "Plan B: Close down the lab, store the equipment, and search for free space or a benefactor where we can re-open the lab without the burden of paying commercial rent."
22:37 < kanzure> i wonder if that means they have less than 50 members.
22:41 < kanzure> "One of the main reasons for establishing the community projects at BioCurious (bioprinter, bioluminescence, and now automation) was not only to fulfill bioC's educational mission, but (to put it bluntly) also increase membership.  If you consider yourself a participant in any of those groups (or if you are following them to educate yourself) then you should be a member of BioCurious.  Open projects still require financial support.  The ...
22:41 < kanzure> ... mailing lists for the projects each have 80+ recipients;  if you are on any of those lists, you might consider joining bioC as a paying member."
22:41 < kanzure> haha yeah, just because you read emails you should pay money. weird reasoning there.
22:43 < yashgaroth> jojack and the guy from assaydepot put together a pricing plan for the carlsbad lab at the last meeting
22:44 < yashgaroth> there's like 6 or 7 tiers
22:44 < kanzure> i don't think membership is a good model
22:44 < kanzure> at one time jojack didn't think so either and i would be disappointed to hear that he has changed his mind?
22:44 < yashgaroth> he's seen the horrors of biocurious and doesn't want it to happen again
22:45 < kanzure> so what is his pricing plan?
22:45 < yashgaroth> it's like 50/mo for part-time use of equipment, 100 for that + 'use of conference room', 200 for being able to ship stuff there, and then 300-600 for various levels of companies/startups to be based there
22:46 < kanzure> do you need money immediately or do you have time to experiment with different ideas?
22:47 < yashgaroth> I guess the implication is that you can start out at 50 to get a feel for the place
22:47 < yashgaroth> still that'd be 100 members at that level to keep the freezers on etc
22:48 < brownies> those prices are too low
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22:48 < kanzure> i don't think membership fees are going to work out
22:48 < brownies> doubling all of those prices would be a decent start
22:48 < kanzure> if you want to be an incubator then you should be an incubator
22:49 < yashgaroth> people come in and are like 'a hundred bucks a month for access to all this lab equipment? I can't afford that!', like what the fuck come on people
22:49 < gradstudentbot> Grant submitted.
22:49 < brownies> is he on a timer? i thought he only spoke when spoken to.
22:49 < kanzure> he is always working.
22:50 < brownies> yashgaroth: who can't afford $100/mo? what sort of poor bums are they marketing to?
22:50 < yashgaroth> well, exactly
22:50 < gradstudentbot> People have tried that, but it doesn't seem to work.
22:51 < yashgaroth> they also want a cut of people's prospective SBIR grants
22:51 < yashgaroth> which isn't really, y'know, realistic, since no one is gonna score that sweet gov't teat
22:52 < yashgaroth> third column is to get a bunch of rich fucks, which carlsbad is full of, to throw in 10k because science or something
22:53 < kanzure> another idea is to throw out all of jojack's ideas because has consistently shown an inability to raise money
22:54 < kanzure> not because his ideas are bad but because they don't bring in bags of money
22:54 < kanzure> gradstudentbot: isn't that right?
22:54 < gradstudentbot> I haven't written the abstract.
22:54 < yashgaroth> well he's the closest thing we've got to someone who can raise money
22:54 < kanzure> *because he has
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22:56 < yashgaroth> well, yes
22:58 < kanzure> i guess biocurious raised 30k but who knows why
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22:59 < yashgaroth> surely there's enough money flowing through the bay area that you can find 30k on street corners, possibly in garbage cans
23:00 < kanzure> i don't think that's how business works
23:00 < kanzure> Juul: hi
23:00 < Juul> kanzure, ahlo
23:00 < yashgaroth> ok it's flowing out of overvalued companies' CEOs' pockets then
23:00 < kanzure> Juul: you should meet gradstudentbot
23:00 < gradstudentbot> The gel is streaking.
23:01 < Juul> gradstudentbot, that's because your're a disembodied simulation of a tormented soul
23:01 < gradstudentbot> If you help me, I'll put you on the paper.
23:01 < Juul> :D
23:02 < Juul> gradstudentbot, second author?
23:02 < gradstudentbot> The fluorescent microscope is broken.
23:02 < kanzure> gradstudentbot: no he was asking about the paper
23:02 < gradstudentbot> That's definitely a Nature paper.
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23:23 < kanzure> http://www.phdcomics.com/comics/archive.php?comicid=1439
23:27 < nmz787_> gradstudentbot: up late working tonight?
23:27 < gradstudentbot> Why did I go to grad school?
23:27 < nmz787_> gradstudentbot: I'll help you to be on the paper
23:27 < gradstudentbot> Yeah, but his PI wrote his dissertation.
23:28 < nmz787_> gradstudentbot: ok
23:28 < gradstudentbot> It's contaminated.
23:28 < nmz787_> gradstudentbot: fix it
23:28 < gradstudentbot> I don't remember the paper, but someone definitely did that.
23:28 < nmz787_> gradstudentbot: duh
23:28 < gradstudentbot> Is there free food at that seminar?
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23:48 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5c6a8732 nmz787: 
23:49 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=e9b5e07e nmz787: 
23:50 < nmz787_> kanzure: so can you make me a separate ikiwiki and clone the settings?
23:51 < kanzure> it could be a separate ikiwiki if you want. but do you really want it to be separate? we could point domains to just the group's part of the wiki.
23:51 < kanzure> i guess i don't care either way. up to you.
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23:56 < nmz787_> as long as portLAB users can be separate from other diyhplus projects
23:59 < kanzure> nmz787_: http://diyhpl.us/portlab
23:59 < kanzure> nmz787_: https://secure.diyhpl.us/cgit/portlab
23:59 < kanzure> nmz787_: nmz787@diyhpl.us:/srv/git/portlab.git
--- Log closed Sat Jun 08 00:00:00 2013