--- Log opened Mon Aug 12 00:00:53 2013
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02:04 < nmz787> paperbot: http://online.liebertpub.com/doi/pdf/10.1089/15311070152757465
02:04 < paperbot> http://libgen.org/scimag3/10.1089/15311070152757465.pdf
02:10 < nmz787> paperbot: http://pubs.acs.org/doi/abs/10.1021/ja903635y?journalCode=jacsat
02:10 < paperbot> http://libgen.org/scimag5/10.1021/ja903635y.pdf
02:12 < nmz787> paperbot: http://pubs.acs.org/doi/pdf/10.1021/ja903635y
02:12 < paperbot> http://libgen.org/scimag5/10.1021/ja903635y.pdf
02:12 < nmz787> paperbot: http://pubs.acs.org/doi/pdf/10.1021/ja903635y
02:12 < paperbot> http://libgen.org/scimag5/10.1021/ja903635y.pdf
02:12 < nmz787> paperbot: http://pubs.acs.org/doi/pdf/10.1021/ja903635y
02:12 < paperbot> http://libgen.org/scimag5/10.1021/ja903635y.pdf
02:13 < nmz787> kanzure: ParahSail1n ^ that pdf seems to not exist, I'm getting a 404
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02:21 < nmz787> paperbot: http://onlinelibrary.wiley.com/doi/10.1002/0471142700.nc0310s18/pdf
02:22 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/bdf80d948010ba7b55c10161abf8726f.txt
02:23 < nmz787> paperbot: http://www.currentprotocols.com/WileyCDA/CPUnit/refId-nc0310.html
02:23 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/1f7526be7b04806a4f1a40958b2a858e.txt
02:26 < nmz787> paperbot: http://onlinelibrary.wiley.com/doi/10.1002/0471142700.nc0315s26/abstract
02:26 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/f450b3be56ec8bf4a89e83d1c50d5d5a.txt
02:31 < nmz787> paperbot: http://pubs.acs.org/doi/abs/10.1021/ja973731g
02:31 < paperbot> http://libgen.org/scimag/get.php?doi=10.1021%2Fja973731g%26pubId%3D40031785
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02:41 < nmz787> paperbot: http://nar.oxfordjournals.org/content/21/5/1213.full.pdf
02:41 < paperbot> http://libgen.org/scimag/get.php?doi=10.1093%2Fnar%2F21.5.1213
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02:44 < nmz787> paperbot: http://www.springerprotocols.com/Abstract/doi/10.1385/0-89603-281-7:391
02:45 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/b6bedf5808ef2df82964d97aa34d456a.txt
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02:55 < poppingtonic> gradstudentbot: you
02:55 < gradstudentbot> I hope they kick me out.
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03:19 < poppingtonic> paperbot: http://www.jstor.org/stable/2008268
03:19 < paperbot> http://libgen.org/scimag/get.php?doi=10.2307%2F2008268
03:21 < nmz787> poppingtonic: using google gave me this free link http://www.ams.org/journals/mcom/1987-49-179/S0025-5718-1987-0890272-3/S0025-5718-1987-0890272-3.pdf
03:25 < poppingtonic> nmz787: hmm, thanks!
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04:42 < archels> well, it's official. The government now owns my fingerprints.
04:42  * archels new passport
05:07 < anannie> I wonder if the HyperLoop is going to be the next segway
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06:10 <@kanzure> elon denies the hyperpoop
06:12 < anannie> kanzure: That's just juvenile :p
06:12 <@kanzure> well, it's true though, he publicly announced that it wasn't a real thing or something
06:12 <@kanzure> or that he regrets saying he had thoughts of fancy about such structures
06:12 <@kanzure> i don't remember the url that showed these comments from him
06:15 < anannie> Interesting
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10:01 <@kanzure> https://github.com/nh2/hemokit emokit in haskell.. for whatever that's worth. why not just bindings to emokit, though?
10:01 <@kanzure> the python version of emokit should probably be removed from emokit.git
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10:38 < Not-001> [kanzure/papermonk-downloader-plosone] kanzure pushed 1 commit to master [+0/-0/±1] http://git.io/3_-8BA
10:38 < Not-001> [kanzure/papermonk-downloader-plosone] kanzure 57f71ee - make a callable pipe for each downloadable file The returned dictionary now includes files that each have a property called "pipe" that can be given a writable stream.
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10:40 < heath> archels: same here, as does google
10:40 < heath> nmz787: thanks for the paper requests last night, those will be useful
10:40 < heath> or if anything fun
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10:48 <@kanzure> AAAAAAHHH they do the worst teardowns
10:48 <@kanzure> they are going to teardown another sequencer
10:48 <@kanzure> but they are refusing to grab the software (again)
10:49 <@kanzure> these are the worst hackers ever
10:51 < ParahSailin> i dont have shell to any of the illumina machines here
10:53 < ParahSailin> id be surprised if they give anyone root though
10:53 < ParahSailin> ion torrent does not
10:53 <@kanzure> of course they don't give you root
10:53 <@kanzure> but the point is to get it by any means necessary
10:53 <@kanzure> that's what hacking is all about
10:54 < ParahSailin> obviously, hardware access == root access, but then you need a higher level of commitment
10:54 < ParahSailin> wetlab people are all afraid of losing their jobs
10:54 <@kanzure> you don't just take pictures of you modeling with the machine while you take off the case. you take pics of the exact chips, get model numbers, hack the system, get root and tarball everything for analysis.
11:01 < heath> kanzure: link to these people doing the teardown?
11:03 <@kanzure> https://groups.google.com/forum/#!topic/diybio/uzbIMP8-9mc
11:04 <@kanzure> "What we're willing to do, with the generous help and assistance of Illumina and their Chief Engineer, is take apart a previous generation sequencer and use it to explain the process of genome sequencing and get firsthand insight into the design decisions that they made in scaling up from this model to the current generation of machines. This machine was delivered as surplus hardware components and that is all we are tearing down. I have no ...
11:04 <@kanzure> ... idea if there are legalities that we could be running afoul of, if this were a competitive or adversarial situation with Illumina we might have to worry about that, but as it happens we are in  communication with them and thus if there is any ambiguity about what they intended for us to use or release we will simply ask. And it doesn't currently seem like there is any software worth asking them about, which I'm sure is not accidental."
11:04 <@kanzure> man.... so disappointing.
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11:17 < archels> I agree with you on principle, but are the binaries from this sequencer really of much general interest?
11:19 < archels> "high level control logic on a PC" is a bit vague
11:24 <@kanzure> yes i think it would be of general interest
11:24 <@kanzure> what if their software is wrong? that would be cool.
11:28 < archels> like those Xerox copiers substituting 8 for 6? :)
11:31 < heath> how do you normally obtain rom dumps in the first place?
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11:33 < archels> in the olden days, you'd pick the ROM out of the socket and place it in a programmer. Modern serial ROMs, just plug into the data lines with some sort of logic interface.
11:35 < heath> eh?
11:35  * heath imagines sticking a super mario brothers cartridge in his head
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11:49 < archels> that's very steampunk of you, heath
11:49 < archels> :)
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12:40 <@kanzure> archels: yes
12:40 <@kanzure> heath: also it might be running linux and then you just have to use a root exploit
12:52 < nmz787> derek responded to me personally saying to let him know if any of the pics they post suck, and that he'll be around for a week to grab more pics if I tell him to
12:53 < nmz787> heath: which articles specifically?
12:53 < nmz787> heath: i kinda downloaded a bunch last night, a bunch not through here
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13:04 <@kanzure> nmz787: thank you
13:05 <@kanzure> nmz787: we need closeups of the chips. not just general shots. we need things like layouts and chip numbers and names.
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13:08 < nmz787> kanzure: so the syringe method looks kinda PITA since you need to do everything with a needle and piercing rubber septa so you keep out potential moisture
13:08 <@kanzure> of course it's PITA :)
13:08 <@kanzure> oh, i wasn't aware of piercing anything
13:08 <@kanzure> that's cool/annoying
13:09 < nmz787> hmm, 15% RH in Death Valley
13:10 < nmz787> even there the synringe method would need septa
13:10 < nmz787> syringe*
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13:29 < heath> kanzure: dumping the rom doesn't seem like a thing they'd do in a day, and my guess is they want this to be a day of taking it apart  and discussing it, not giving away the software?
13:29 < heath> dumping the rom in a day seems like it would take longer than a day :)
13:29 < heath> unless illumina is willing to help
13:30 < heath> s/in\ a\ day//
13:30 <@kanzure> well, it's a pc. you can just root it.
13:30 <@kanzure> i think it's a pc, at least
13:30 <@kanzure> the point is, they are hackers, not geeksquad or something
13:35 < nmz787> Win NT passwd changer
13:42 < ParahSailin> i dont think it was implied that illumina was giving them the server that goes with the machine
13:44 <@kanzure> then the machine is useless?
13:45 < ParahSailin> it has the microcontroller for the microscope and stage, and stuff to control the fluidics
13:46 <@kanzure> sigh
13:46 < ParahSailin> that stuff is pretty crucial, and you can find all the image analysis shit in CASAVA
13:47 <@kanzure> well, they haven't confirmed that yet
13:48 < nmz787> so any more legit info on this http://www.unexplainable.net/simply-unexplainable/the-ice-woman-of.php
13:49 < nmz787> ?
13:49 < nmz787> http://www.nytimes.com/1981/01/03/us/dakota-teen-ager-recovers-after-being-frozen-stiff.html
13:49 < ParahSailin> i think it was the thetans
13:49 <@kanzure> nmz787: so if you use the rubber gasket thing, do you still have to have nitrogen or argon or whatever?
13:50 < nmz787> yeah, because you need to equalize the pressure
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13:51 < nmz787> otherwise the septa will eventually pop off or get sucked in... even if it doesn't totally come off, air would leak i guess
13:51 <@kanzure> all of the synthesizers from azco biotech use pressurized gasses?
13:51 < nmz787> yeah
13:51 <@kanzure> they hide it well
13:51 < nmz787> it's just some small quick-release port most likely that connects the main tank to the system
13:52 < nmz787> so i doubt it'd be super noticeable
13:52 <@kanzure> do they cycle the gas in a chamber?
13:52 <@kanzure> each reaction, replace the gas?
13:53 < gradstudentbot> Oh yeah, I'll pay you once my stipend posts.
13:53  * brownies pokes gradstudentbot 
13:53 < gradstudentbot> I can't do science if you're going to be like that.
13:55 <@kanzure> oh i guess he did announce his hyperloop https://news.ycombinator.com/item?id=6201586
13:56 <@kanzure> http://www.spacex.com/sites/spacex/files/hyperloop_alpha-20130812.pdf
13:56 <@kanzure> http://www.spacex.com/hyperloop
13:58 < gradstudentbot> Yeah, that's a really good question. I don't know, but I'll have to look into that.
14:06 < ParahSailin> so it was just an evacuated tube after all
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14:41 < nmz787> welp read most of the pdf on the hyperloop, looks like they thought out most of the stuff
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14:45 < nmz787> paperbot: http://link.springer.com/article/10.1251%2Fbpo2
14:46 < paperbot> http://libgen.org/scimag3/10.1251/bpo2.pdf
14:52 < nmz787> kanzure: so we don't have any chemists in this room
14:52 < nmz787> I need to find a chemist who's disenchanted by their B.S. or Masters or PhD program locally...
14:54 <@kanzure> wait we don't have chemists? that's odd.
14:54 <@kanzure> drazak: ping?
14:55 < heath> i know a guy who's willing to help out of toronto
14:55 < heath> i'll drag him in
14:56 < heath> surely someone in ##chemistry would also help
14:57 < heath> i think he's in the lab currently, might be awhile before he drops by
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15:02 < nmz787> all the people in ##chemistry seem to be uninterested in collaborative/multi-disciplinary projects, at least from the few times I've tried to 'hang out' over there (i idle in there all/most times)
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15:06 <@kanzure> i think i'm the op in there
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15:06 <@kanzure> maybe i'm not doing my job well enough
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15:10 < nmz787> op?
15:10 < nmz787> original poster?
15:10 < ParahSailin> opertron
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15:13 < nmz787> paperbot: http://psr.sagepub.com/content/early/2013/08/02/1088868313497266.full
15:14 <@kanzure> nmz787: ops in irc are channel wizards that can kickban and do other amazing things
15:14 < nmz787> sorry paperbot http://diyhpl.us/~nmz787/pdf/The_Relation_Between_Intelligence_and_Religiosity__A_Meta-Analysis_and_Some_Proposed_Explanations.pdf
15:14 < paperbot> http://pdf.highwire.org/stamped/sppsr/early/2013/08/02/1088868313497266.full.pdf
15:14 < nmz787> i don't think that non-collaboratively-minded people should be kicked or banned
15:14 <@kanzure> it just took a while
15:14 < ThomasEgi> actualy.. op is short for optimus prime. which pretty much is the same as an irc channel operator
15:14 < nmz787> if that's what you were thinking
15:15 <@kanzure> nmz787: of course not, but ##chemistry has had its share of trolls
15:15 < nmz787> I win for speed and filename
15:15 <@kanzure> yeah i'm not sure why paperbot failed on the filename on that one
15:15 <@kanzure> that's unacceptable
15:15 < nmz787> but lose for not processing with pdfparanoia
15:15 <@kanzure> btw i updated papermonk things earlier today i think
15:15 <@kanzure> https://github.com/kanzure/papermonk-downloader-plosone/blob/master/index.js
15:15 < nmz787> and i lose for not uploading anonymously
15:20 < nmz787> but i win for finding the interesting article
15:21 < nmz787> when will paperbot simply find and give me the papers I need
15:25 <@kanzure> well... soon.
15:26 < nmz787> that was a joke
15:28 < gradstudentbot> Heh, undergrads.
15:34 < drazak> kanzure:
15:34 <@kanzure> hey, so, we need more chemistry people
15:34 <@kanzure> preferably crazy chemistry people
15:35 < drazak> you got me
15:35 <@kanzure> organic chemists.
15:35 <@kanzure> nmz787: cool, bug drazak a lot
15:38 < nmz787> drazak: are you interested in helping with DNA synthesis at all?
15:38 < drazak> yes
15:38 < nmz787> drazak: do you know anyone that is a chemist in portland Oregon that would be interested in helping with DNA synthesis?
15:38 < drazak> no
15:40 < nmz787> drazak: it seems the only reason people use supports (soluble or insoluble) is to make purification faster and/or easier... but I can't tell if they're actually required for the synthesis to procede (seems not so far)
15:41 < nmz787> (it's essentially copolymer synthesis)
15:41 < ParahSailin> its for partitioning purposes yes
15:41 < gradstudentbot> That's definitely not repeatable.
15:42 < nmz787> cause PAGE and HPLC get single-base resolution
15:42 < nmz787> so I'm guessing they were developed purely to aid purification
15:42 < nmz787> rather than reaction kinteics
15:43 < nmz787> kinetics
15:43 < ParahSailin> thats what i said
15:43 < nmz787> (just adding to my thoughts)
15:49 < nmz787> actually, i know a polymer chemist in india
15:49 < nmz787> is there some preffered IRC client for India?
15:49 < nmz787> oh I guess he's in Singapore now
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15:56 < nmz787> paperbot: http://pubs.rsc.org/en/Content/ArticleLanding/2011/CC/c0cc04746e
15:56 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Synthesis%20of%20DNA%20block%20copolymers%20with%20extended%20nucleic%20acid%20segments%20by%20enzymatic%20ligation%3A%20cut%20and%20paste%20large%20hybrid%20architectures.pdf
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16:06 < nmz787> "I believe theoretically they should affect the rate of reaction, in turn kinetics...but its the function of solvent properties, polymer structure-properties etc... basically you need to optimize the system to get best yield with highest rate and purity... I read about these long time back but am quite sure they do affect rate.."
16:08 -!- ielo [~ielo@host-92-20-135-177.as13285.net] has quit [Ping timeout: 264 seconds]
16:10 < nmz787> and he posted this too http://ytchang.science.nus.edu.sg/pages/reprint/2003%20COCB.pdf
16:10 < nmz787> Understanding the effects of the polymer support on reaction
16:10 < nmz787> rates and kinetics: knowledge toward efcient synthetic design
16:10 < heath> what's a solid support group btw?
16:11 <@kanzure> beads
16:11 <@kanzure> micron-sized beads
16:14 < heath> i thought those were specifically for microfluidics
16:15 < heath> the question arose when reading "manual oligonucleotide synthesis using the phosphoramidite method" by h.a. white... "Oligodexoyribonucleotides may be synthesized on a solid support, which allows for the elongation of the chain without intermediate purifications."
16:16 < heath> am i wrong to think they are only used within microfluidics?
16:20 < nmz787> yes
16:20 <@kanzure> solid supports are used everywhere
16:20 < nmz787> so are liquid phase supports too
16:20 <@kanzure> which liquid phase support?
16:20 < nmz787> but they're usually employed in large scale syntheses
16:21 < nmz787> PEG, polyvinyl alcohol
16:21 < nmz787> umm, others I don't remember
16:21 <@kanzure> oh, PEG
16:21 < nmz787> lots
16:21 < nmz787> the more generic polymer synthesis literature calls either a support differentiating soluble vs insoluble
16:22 < nmz787> s/either//
16:22 < nmz787> err
16:22 < nmz787> they just say support
16:22 < gradstudentbot> The real reason I wanted to join this lab was because I love to clean glassware.
16:22 < nmz787> and then soluble or insoluble
16:22 < nmz787> vs solid phase or liquid phase
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16:33 < heath> what are the types of solid support?
16:34 < heath> "Fig. 2. Protected nucleoside linked to controlled-pore glass support with a long-chain alkylamine spacer and succinyl link."
16:35 < heath> http://www.sigmaaldrich.com/chemistry/chemistry-products.html?TablePage=16040627
16:35 < heath> .title
16:35 < yoleaux> Controlled Pore Glass (CPG) - SAFC® Proligo® Reagents | Sigma-Aldrich
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16:43 < nmz787> heath: the support in that case, i believe, is the whole glass bead and linker
16:44  * heath is now looking for introductory material for organic chemistry
16:44 < heath> i don't know what supports do, i'm guessing they support :)
16:45 < heath> there's mention of spacer supports, and i'm trying to figure that out as well
16:45 < heath> they support reactions by spacing elements away from one another?
16:45  * heath keeps searching
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16:46 < ParahSail1n> spacer is spacer between solid phase and your thing that is attached
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16:49 < nmz787> heath: as ParahSail1n said earlier, they mainly aid in purification... but as my friend said (and the paper he gave me a link to) it might also affect kinetics
16:49 < ParahSail1n> well yes, partitioning will slow kinetics
16:49 < nmz787> heath: basically with a solid support you can flush reagents past the synthesis reaction center and use a sieve to retain the solid support
16:50 < nmz787> with liquid phase, you just keep adding reagents to a vat, with the volume increasing with every step, or using the soluble support as a differentiator in crystallisation purification
16:51 < nmz787> so rather than purifiying with HPLC (which is better for analytical rather tha preparative)
16:51 < nmz787> you could just cut the polymer off the solid support, after you're done synthesizing and rinsing off nasty reagents
16:52 < nmz787> or with liquid phase, you do a crystallisation
16:52 -!- HEx1 [~HEx@hexwab.plus.com] has quit [Ping timeout: 260 seconds]
16:52 < nmz787> but the support makes the crystallisation characteristics much different than synthesis noise (other reagents, impurities)
16:53 < gradstudentbot> The gel is streaking.
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16:55 < ParahSail1n> paperbot, http://jhmas.oxfordjournals.org/content/39/4/469.extract
16:55 < paperbot> http://libgen.org/scimag/get.php?doi=10.1093%2Fjhmas%2F39.4.469
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18:13 < Burninate> paperbot, http://psr.sagepub.com/content/early/2013/08/02/1088868313497266
18:13 < paperbot> http://pdf.highwire.org/stamped/sppsr/early/2013/08/02/1088868313497266.full.pdf
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18:32 -!- Reinhard [Reinhard@198-84-225-88.cpe.teksavvy.com] has joined ##hplusroadmap
18:32 < Reinhard> hello all
18:32 < Reinhard> newcomer here
18:32 < Reinhard> i'm a chemist
18:33 < ParahSail1n> hi
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18:54 <@kanzure> Reinhard: welcome
18:54 < superkuh> paperbot: http://proceedings.aip.org/resource/2/apcpcs/1539/1/442_1
18:55 < paperbot> http://libgen.org/scimag/get.php?doi=10.1063%2F1.4811080
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19:04 < Reinhard> thank you :)
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19:37  * heath is curious what the restrictions are for diybio in EU
19:37 < heath> hey Reinhard
19:37 < heath> ^ chemist
19:38 < Reinhard> :D
19:38 < Reinhard> hola heath
19:38 < Reinhard> thanks for inviting me here
19:38 < Reinhard> this nick is registered though :(
19:38 -!- Reinhard is now known as Noryokusha
19:38 < Noryokusha> i'll switch to this
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19:39 < heath> hey look, a graduat chemist who knows how IRC works
19:40 < heath> nmz787: here ya go, go wild
19:41 < Noryokusha> hehe :3
19:41 < Noryokusha> i just started grad school
19:41 < Noryokusha> !!
19:41 < heath> i don't even know what you're studying :P
19:42 < heath> your undergrad thesis was on supramolecular thingies iirc
19:42 < Noryokusha> i work on organic photovoltaics now
19:42 < heath> organic chemist? even better
19:42 < Noryokusha> synthesis, characterization and study the devices
19:42 < Noryokusha> yay
19:42 < Noryokusha> of the*
19:43 < heath> Noryokusha: it looks like people have lives outside of IRC
19:43 < heath> ya might have to wait around a little while before activity
19:44 < Noryokusha> lives?!!?
19:44 < Noryokusha> TSK
19:44 < gradstudentbot> Where did you put the revisions to the paper?
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19:58 < heath> drazak: what are you studying these days?
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20:12 < heath> wasn't cathal and some other guise in the EU getting together to sponsor a few synbio startups?
20:12 < heath> as well as discuss the issues within EU in doing synbio from within your own basement?
20:13 < heath> i wouldn't mind moving to spain, but i don't want to into those restrictions
20:17 < heath> +walk
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20:17 < heath> walk|enter|fly :)
20:17 < heath> kanzure: whatever happened to quantumg?
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20:24 <@kanzure> heath: he hated me and got out
20:25 <@kanzure> Noryokusha: we are doing these things http://diyhpl.us/wiki/dna-synthesis.html
20:25 < Noryokusha> bookmarking. will take a look after i play some firefall
20:25 < Noryokusha> thanks for the link :)
20:26 < heath> kanzure: do you recall if it was an email or some article online where cathal was partnering with some group in the EU to discuss laws in the EU which affect diybio?
20:38  * brownies pokes gradstudentbot 
20:38 < gradstudentbot> I can't do science if you're going to be like that.
20:41 < heath> gradstudentbot: you gotta use new material when someone pokes you
20:41 < gradstudentbot> Oh that's interesting, do you want to write a paper together?
20:42 < heath> nmz787: hey when you query Noryokusha, will you make it public so i can learn as well?
20:42 < heath> s/query/converse with
20:44 < brownies> heath: i know. he's gotten boring.
20:44 < heath> irc while under the influence isn't always the greatest idea as it turns out
20:45 < heath> but caramel on tortilla chips right now, best idea ever :)
20:46 < Noryokusha> im exhausted. going to sleep for now. will read it in the morning.
20:46 < Noryokusha> thanks for showing me this place heath!
20:46 < heath> np Noryokusha
20:46 < heath> do you mind if we copy everything you say into gradstudentbot?
20:46 < gradstudentbot> The autoclave smells really good.
20:46  * brownies pokes gradstudentbot 
20:46 < gradstudentbot> Can't this wait? I am busy doing science.
20:46 < heath> it only makes sense :)
20:46 < Noryokusha> sure heath
20:47 < Noryokusha> i thought it was a real person
20:47 < Noryokusha> lol
20:47 < heath> hah :)
20:47 < heath> adíos
20:47 < heath> thanks for making your way over here
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22:54 < stieruridir>  /query jmil hey man
22:54 < stieruridir> welp, I'm a tard
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--- Log closed Tue Aug 13 00:00:40 2013