| --- Log opened Mon Aug 12 00:00:53 2013 | ||
| -!- Adifex [~Adifex@71-211-196-62.hlrn.qwest.net] has joined ##hplusroadmap | 00:40 | |
| -!- poppingtonic [~poppingto@212.49.88.97] has quit [Remote host closed the connection] | 01:06 | |
| -!- k4tZz [~bird@pool-173-79-34-40.washdc.fios.verizon.net] has quit [Ping timeout: 240 seconds] | 01:49 | |
| nmz787 | paperbot: http://online.liebertpub.com/doi/pdf/10.1089/15311070152757465 | 02:04 |
|---|---|---|
| paperbot | http://libgen.org/scimag3/10.1089/15311070152757465.pdf | 02:04 |
| nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/ja903635y?journalCode=jacsat | 02:10 |
| paperbot | http://libgen.org/scimag5/10.1021/ja903635y.pdf | 02:10 |
| 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 | 02:12 |
| nmz787 | kanzure: ParahSail1n ^ that pdf seems to not exist, I'm getting a 404 | 02:13 |
| -!- aelinoea [~aelinoea@a88-113-45-152.elisa-laajakaista.fi] has joined ##hplusroadmap | 02:15 | |
| nmz787 | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/0471142700.nc0310s18/pdf | 02:21 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/bdf80d948010ba7b55c10161abf8726f.txt | 02:22 |
| nmz787 | paperbot: http://www.currentprotocols.com/WileyCDA/CPUnit/refId-nc0310.html | 02:23 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/1f7526be7b04806a4f1a40958b2a858e.txt | 02:23 |
| nmz787 | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/0471142700.nc0315s26/abstract | 02:26 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/f450b3be56ec8bf4a89e83d1c50d5d5a.txt | 02:26 |
| 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 | 02:31 |
| -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds] | 02:32 | |
| 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 | 02:41 |
| -!- Adifex [~Adifex@71-211-196-62.hlrn.qwest.net] has quit [Quit: Adifex] | 02:44 | |
| nmz787 | paperbot: http://www.springerprotocols.com/Abstract/doi/10.1385/0-89603-281-7:391 | 02:44 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/b6bedf5808ef2df82964d97aa34d456a.txt | 02:45 |
| -!- poppingtonic [~poppingto@212.49.88.97] has joined ##hplusroadmap | 02:54 | |
| poppingtonic | gradstudentbot: you | 02:55 |
| gradstudentbot | I hope they kick me out. | 02:55 |
| -!- ThomasEgi [~thomas@185.5.8.81] has joined ##hplusroadmap | 02:56 | |
| -!- ThomasEgi [~thomas@185.5.8.81] has quit [Changing host] | 02:56 | |
| -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap | 02:56 | |
| -!- EnLilaSko [~Nattzor@unaffiliated/enlilasko] has joined ##hplusroadmap | 03:00 | |
| poppingtonic | paperbot: http://www.jstor.org/stable/2008268 | 03:19 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.2307%2F2008268 | 03:19 |
| 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 | 03:21 |
| poppingtonic | nmz787: hmm, thanks! | 03:25 |
| -!- augur_ [~augur@208.58.5.87] has joined ##hplusroadmap | 03:45 | |
| -!- augur [~augur@208.58.5.87] has quit [Read error: Connection reset by peer] | 03:45 | |
| -!- strangewarp_ [~quassel@67.176.51.26] has joined ##hplusroadmap | 03:45 | |
| -!- augur_ [~augur@208.58.5.87] has quit [Read error: Connection reset by peer] | 03:45 | |
| -!- HEx1 [~HEx@hexwab.plus.com] has quit [Ping timeout: 240 seconds] | 03:46 | |
| -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap | 03:46 | |
| -!- HEx1 [~HEx@hexwab.plus.com] has joined ##hplusroadmap | 03:47 | |
| -!- strangewarp [~quassel@c-67-176-51-26.hsd1.co.comcast.net] has quit [Ping timeout: 240 seconds] | 03:47 | |
| -!- anannie [~chatzilla@unaffiliated/anannie] has joined ##hplusroadmap | 04:00 | |
| -!- strangewarp [~quassel@67.176.51.26] has joined ##hplusroadmap | 04:09 | |
| -!- strangewarp_ [~quassel@67.176.51.26] has quit [Ping timeout: 240 seconds] | 04:11 | |
| -!- makoLime [~mako@103-9-42-133.flip.co.nz] has quit [Ping timeout: 246 seconds] | 04:32 | |
| -!- weles [~mariusz@c-71-234-3-169.hsd1.ct.comcast.net] has quit [Ping timeout: 260 seconds] | 04:35 | |
| archels | well, it's official. The government now owns my fingerprints. | 04:42 |
| * archels new passport | 04:42 | |
| anannie | I wonder if the HyperLoop is going to be the next segway | 05:07 |
| -!- chido [chidori@pasky.or.cz] has quit [Remote host closed the connection] | 05:16 | |
| @kanzure | elon denies the hyperpoop | 06:10 |
| 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 | 06:12 |
| anannie | Interesting | 06:15 |
| -!- Adillian [~Adillian@97e0b193.skybroadband.com] has joined ##hplusroadmap | 06:27 | |
| -!- AshleyWaffle [~quassel@c-76-121-59-64.hsd1.wa.comcast.net] has joined ##hplusroadmap | 06:33 | |
| -!- AshleyWaffle [~quassel@c-76-121-59-64.hsd1.wa.comcast.net] has quit [Changing host] | 06:33 | |
| -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has joined ##hplusroadmap | 06:33 | |
| -!- strangewarp_ [~quassel@c-67-176-51-26.hsd1.co.comcast.net] has joined ##hplusroadmap | 06:40 | |
| -!- strangewarp [~quassel@67.176.51.26] has quit [Ping timeout: 240 seconds] | 06:42 | |
| -!- poppingtonic [~poppingto@212.49.88.97] has quit [Ping timeout: 256 seconds] | 06:54 | |
| -!- strangewarp_ [~quassel@c-67-176-51-26.hsd1.co.comcast.net] has quit [Read error: Connection reset by peer] | 07:10 | |
| -!- strangewarp [~quassel@67.176.51.26] has joined ##hplusroadmap | 07:10 | |
| -!- Adillian [~Adillian@97e0b193.skybroadband.com] has quit [Ping timeout: 240 seconds] | 07:21 | |
| -!- aelinoea [~aelinoea@a88-113-45-152.elisa-laajakaista.fi] has quit [Quit: Leaving] | 07:21 | |
| -!- k4tZz [~bird@pool-173-79-34-40.washdc.fios.verizon.net] has joined ##hplusroadmap | 07:46 | |
| -!- k4tZz [~bird@pool-173-79-34-40.washdc.fios.verizon.net] has quit [Ping timeout: 264 seconds] | 07:51 | |
| -!- Jaakko97 [~Jaakko@cpc13-newc15-2-0-cust64.16-2.cable.virginmedia.com] has joined ##hplusroadmap | 07:51 | |
| -!- Jaakko97 [~Jaakko@cpc13-newc15-2-0-cust64.16-2.cable.virginmedia.com] has quit [Client Quit] | 07:52 | |
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap | 08:00 | |
| -!- poppingtonic [~poppingto@212.49.88.101] has joined ##hplusroadmap | 08:05 | |
| -!- ianmathwiz7 [~chatzilla@67.51.113.178] has joined ##hplusroadmap | 08:22 | |
| -!- randallagordon [~randall@75-175-62-76.ptld.qwest.net] has quit [Ping timeout: 264 seconds] | 08:35 | |
| -!- randallagordon [~randall@75-175-62-76.ptld.qwest.net] has joined ##hplusroadmap | 08:35 | |
| -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has joined ##hplusroadmap | 08:40 | |
| -!- anannie [~chatzilla@unaffiliated/anannie] has quit [Ping timeout: 264 seconds] | 08:41 | |
| -!- anannie [~chatzilla@unaffiliated/anannie] has joined ##hplusroadmap | 08:49 | |
| -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Ping timeout: 246 seconds] | 09:08 | |
| -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap | 09:09 | |
| -!- aelinoea [~aelinoea@a88-113-45-152.elisa-laajakaista.fi] has joined ##hplusroadmap | 09:17 | |
| @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 | 10:01 |
| -!- Not-001 [~notifico@198.199.82.216] has joined ##hplusroadmap | 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. | 10:38 |
| -!- Not-001 [~notifico@198.199.82.216] has quit [Remote host closed the connection] | 10:39 | |
| 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 | 10:40 |
| -!- poppingtonic [~poppingto@212.49.88.101] has quit [Ping timeout: 256 seconds] | 10:44 | |
| @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) | 10:48 |
| @kanzure | these are the worst hackers ever | 10:49 |
| ParahSailin | i dont have shell to any of the illumina machines here | 10:51 |
| 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 | 10:53 |
| 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. | 10:54 |
| heath | kanzure: link to these people doing the teardown? | 11:01 |
| @kanzure | https://groups.google.com/forum/#!topic/diybio/uzbIMP8-9mc | 11:03 |
| @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. | 11:04 |
| -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap | 11:07 | |
| archels | I agree with you on principle, but are the binaries from this sequencer really of much general interest? | 11:17 |
| archels | "high level control logic on a PC" is a bit vague | 11:19 |
| @kanzure | yes i think it would be of general interest | 11:24 |
| @kanzure | what if their software is wrong? that would be cool. | 11:24 |
| archels | like those Xerox copiers substituting 8 for 6? :) | 11:28 |
| heath | how do you normally obtain rom dumps in the first place? | 11:31 |
| -!- makoLime [~mako@103-9-42-133.flip.co.nz] has joined ##hplusroadmap | 11:31 | |
| 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. | 11:33 |
| heath | eh? | 11:35 |
| * heath imagines sticking a super mario brothers cartridge in his head | 11:35 | |
| -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap | 11:36 | |
| archels | that's very steampunk of you, heath | 11:49 |
| archels | :) | 11:49 |
| -!- ianmathwiz7 [~chatzilla@67.51.113.178] has quit [Ping timeout: 260 seconds] | 12:06 | |
| -!- chido [chidori@pasky.or.cz] has joined ##hplusroadmap | 12:08 | |
| -!- poppingtonic [~poppingto@212.49.88.101] has joined ##hplusroadmap | 12:11 | |
| -!- fireprfHydra [~fireprfHy@ool-44c01f50.dyn.optonline.net] has joined ##hplusroadmap | 12:18 | |
| -!- stieruridir [47fff18b@gateway/web/freenode/ip.71.255.241.139] has joined ##hplusroadmap | 12:21 | |
| -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap | 12:26 | |
| -!- jmil [~jmil@hive76/member/jmil] has quit [Ping timeout: 264 seconds] | 12:29 | |
| -!- fredox [~chatzilla@c27-253-21-32.brodm4.vic.optusnet.com.au] has quit [Quit: ChatZilla 0.9.90.1 [Firefox 21.0/20130511120803]] | 12:35 | |
| -!- fredox [~chatzilla@c27-253-21-32.brodm4.vic.optusnet.com.au] has joined ##hplusroadmap | 12:36 | |
| @kanzure | archels: yes | 12:40 |
| @kanzure | heath: also it might be running linux and then you just have to use a root exploit | 12:40 |
| 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 | 12:52 |
| nmz787 | heath: which articles specifically? | 12:53 |
| nmz787 | heath: i kinda downloaded a bunch last night, a bunch not through here | 12:53 |
| -!- ianmathwiz7 [~chatzilla@67.51.113.178] has joined ##hplusroadmap | 12:59 | |
| -!- _Sol_ [~Sol@c-174-57-58-11.hsd1.pa.comcast.net] has quit [Read error: Connection reset by peer] | 12:59 | |
| -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has quit [Ping timeout: 276 seconds] | 13:03 | |
| @kanzure | nmz787: thank you | 13:04 |
| @kanzure | nmz787: we need closeups of the chips. not just general shots. we need things like layouts and chip numbers and names. | 13:05 |
| -!- stieruridir [47fff18b@gateway/web/freenode/ip.71.255.241.139] has quit [Ping timeout: 250 seconds] | 13:05 | |
| -!- anannie [~chatzilla@unaffiliated/anannie] has quit [Remote host closed the connection] | 13:06 | |
| -!- fireprfHydra [~fireprfHy@ool-44c01f50.dyn.optonline.net] has quit [Ping timeout: 264 seconds] | 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 | 13:08 |
| nmz787 | hmm, 15% RH in Death Valley | 13:09 |
| nmz787 | even there the synringe method would need septa | 13:10 |
| nmz787 | syringe* | 13:10 |
| -!- fireprfHydra [~fireprfHy@ool-44c01f50.dyn.optonline.net] has joined ##hplusroadmap | 13:10 | |
| -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap | 13:12 | |
| -!- aelinoea [~aelinoea@a88-113-45-152.elisa-laajakaista.fi] has quit [Ping timeout: 240 seconds] | 13:19 | |
| 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 | 13:29 |
| 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 | 13:30 |
| nmz787 | Win NT passwd changer | 13:35 |
| ParahSailin | i dont think it was implied that illumina was giving them the server that goes with the machine | 13:42 |
| @kanzure | then the machine is useless? | 13:44 |
| ParahSailin | it has the microcontroller for the microscope and stage, and stuff to control the fluidics | 13:45 |
| @kanzure | sigh | 13:46 |
| ParahSailin | that stuff is pretty crucial, and you can find all the image analysis shit in CASAVA | 13:46 |
| @kanzure | well, they haven't confirmed that yet | 13:47 |
| nmz787 | so any more legit info on this http://www.unexplainable.net/simply-unexplainable/the-ice-woman-of.php | 13:48 |
| 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? | 13:49 |
| nmz787 | yeah, because you need to equalize the pressure | 13:50 |
| -!- jmil [~jmil@hive76/member/jmil] has quit [Quit: jmil] | 13:50 | |
| 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 | 13:51 |
| 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? | 13:52 |
| 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. | 13:53 |
| @kanzure | oh i guess he did announce his hyperloop https://news.ycombinator.com/item?id=6201586 | 13:55 |
| @kanzure | http://www.spacex.com/sites/spacex/files/hyperloop_alpha-20130812.pdf | 13:56 |
| @kanzure | http://www.spacex.com/hyperloop | 13:56 |
| gradstudentbot | Yeah, that's a really good question. I don't know, but I'll have to look into that. | 13:58 |
| ParahSailin | so it was just an evacuated tube after all | 14:06 |
| -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has quit [Read error: Connection reset by peer] | 14:08 | |
| -!- jmil [~jmil@hive76/member/jmil] has joined ##hplusroadmap | 14:23 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap | 14:31 | |
| nmz787 | welp read most of the pdf on the hyperloop, looks like they thought out most of the stuff | 14:41 |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] | 14:43 | |
| nmz787 | paperbot: http://link.springer.com/article/10.1251%2Fbpo2 | 14:45 |
| paperbot | http://libgen.org/scimag3/10.1251/bpo2.pdf | 14:46 |
| 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... | 14:52 |
| @kanzure | wait we don't have chemists? that's odd. | 14:54 |
| @kanzure | drazak: ping? | 14:54 |
| heath | i know a guy who's willing to help out of toronto | 14:55 |
| heath | i'll drag him in | 14:55 |
| heath | surely someone in ##chemistry would also help | 14:56 |
| heath | i think he's in the lab currently, might be awhile before he drops by | 14:57 |
| -!- Burninate [~Burn@pool-108-18-159-219.washdc.fios.verizon.net] has quit [Read error: Connection reset by peer] | 15:01 | |
| -!- Burninate [~Burn@pool-108-18-159-219.washdc.fios.verizon.net] has joined ##hplusroadmap | 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) | 15:02 |
| -!- audy [~audy@unaffiliated/audy] has quit [Quit: ZNC - http://znc.sourceforge.net] | 15:04 | |
| -!- yorick_ [~yorick@oftn/member/yorick] has joined ##hplusroadmap | 15:04 | |
| -!- wrldpc [~wrldpc@120.88.50.102] has quit [Read error: Connection reset by peer] | 15:05 | |
| @kanzure | i think i'm the op in there | 15:06 |
| -!- wrldpc [~wrldpc@120.88.50.102] has joined ##hplusroadmap | 15:06 | |
| @kanzure | maybe i'm not doing my job well enough | 15:06 |
| -!- AlonzoTG [~atg@pool-108-18-204-142.washdc.fios.verizon.net] has quit [Ping timeout: 248 seconds] | 15:06 | |
| -!- fireprfHydra_ [~fireprfHy@ool-44c01f50.dyn.optonline.net] has joined ##hplusroadmap | 15:07 | |
| -!- fireprfHydra [~fireprfHy@ool-44c01f50.dyn.optonline.net] has quit [Read error: Connection reset by peer] | 15:07 | |
| -!- yorick [~yorick@oftn/member/yorick] has quit [Ping timeout: 256 seconds] | 15:08 | |
| -!- AlonzoTG [~atg@pool-108-18-204-142.washdc.fios.verizon.net] has joined ##hplusroadmap | 15:08 | |
| nmz787 | op? | 15:10 |
| nmz787 | original poster? | 15:10 |
| ParahSailin | opertron | 15:10 |
| -!- audy [~audy@heyaudy.com] has joined ##hplusroadmap | 15:10 | |
| nmz787 | paperbot: http://psr.sagepub.com/content/early/2013/08/02/1088868313497266.full | 15:13 |
| @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 | 15:14 |
| @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 | 15:15 |
| nmz787 | but i win for finding the interesting article | 15:20 |
| nmz787 | when will paperbot simply find and give me the papers I need | 15:21 |
| @kanzure | well... soon. | 15:25 |
| nmz787 | that was a joke | 15:26 |
| gradstudentbot | Heh, undergrads. | 15:28 |
| drazak | kanzure: | 15:34 |
| @kanzure | hey, so, we need more chemistry people | 15:34 |
| @kanzure | preferably crazy chemistry people | 15:34 |
| drazak | you got me | 15:35 |
| @kanzure | organic chemists. | 15:35 |
| @kanzure | nmz787: cool, bug drazak a lot | 15:35 |
| 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 | 15:38 |
| 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) | 15:40 |
| nmz787 | (it's essentially copolymer synthesis) | 15:41 |
| ParahSailin | its for partitioning purposes yes | 15:41 |
| gradstudentbot | That's definitely not repeatable. | 15:41 |
| 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 | 15:42 |
| nmz787 | kinetics | 15:43 |
| ParahSailin | thats what i said | 15:43 |
| nmz787 | (just adding to my thoughts) | 15:43 |
| 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 | 15:49 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has joined ##hplusroadmap | 15:50 | |
| 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 | 15:56 |
| -!- fireprfHydra_ [~fireprfHy@ool-44c01f50.dyn.optonline.net] has quit [Ping timeout: 240 seconds] | 15:58 | |
| 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.." | 16:06 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has quit [Ping timeout: 264 seconds] | 16:08 | |
| 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? | 16:10 |
| @kanzure | beads | 16:11 |
| @kanzure | micron-sized beads | 16:11 |
| heath | i thought those were specifically for microfluidics | 16:14 |
| 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." | 16:15 |
| heath | am i wrong to think they are only used within microfluidics? | 16:16 |
| 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 | 16:20 |
| 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 | 16:21 |
| 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 | 16:22 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has joined ##hplusroadmap | 16:28 | |
| heath | what are the types of solid support? | 16:33 |
| heath | "Fig. 2. Protected nucleoside linked to controlled-pore glass support with a long-chain alkylamine spacer and succinyl link." | 16:34 |
| 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 | 16:35 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has quit [Ping timeout: 246 seconds] | 16:39 | |
| -!- yorick_ is now known as yorick | 16:40 | |
| -!- makoLime [~mako@103-9-42-133.flip.co.nz] has quit [Ping timeout: 246 seconds] | 16:41 | |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has joined ##hplusroadmap | 16:41 | |
| nmz787 | heath: the support in that case, i believe, is the whole glass bead and linker | 16:43 |
| * 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 :) | 16:44 |
| 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 | 16:45 | |
| -!- AshleyWaffle [~quassel@c-76-121-59-64.hsd1.wa.comcast.net] has joined ##hplusroadmap | 16:46 | |
| -!- AshleyWaffle [~quassel@c-76-121-59-64.hsd1.wa.comcast.net] has quit [Changing host] | 16:46 | |
| -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has joined ##hplusroadmap | 16:46 | |
| -!- EnLilaSko [~Nattzor@unaffiliated/enlilasko] has quit [Quit: - nbs-irc 2.39 - www.nbs-irc.net -] | 16:46 | |
| ParahSail1n | spacer is spacer between solid phase and your thing that is attached | 16:46 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has quit [Ping timeout: 264 seconds] | 16:48 | |
| 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 | 16:49 |
| 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 | 16:50 |
| 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 | 16:51 |
| 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) | 16:52 |
| gradstudentbot | The gel is streaking. | 16:53 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has joined ##hplusroadmap | 16:54 | |
| 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 | 16:55 |
| -!- ielo [~ielo@host-92-20-135-177.as13285.net] has quit [Ping timeout: 240 seconds] | 16:59 | |
| -!- yorick [~yorick@oftn/member/yorick] has quit [Remote host closed the connection] | 17:14 | |
| -!- poppingtonic [~poppingto@212.49.88.101] has quit [Ping timeout: 264 seconds] | 17:28 | |
| -!- poppingtonic [~poppingto@212.49.88.101] has joined ##hplusroadmap | 17:28 | |
| -!- yashgaroth [~ffffff@cpe-75-80-50-28.san.res.rr.com] has joined ##hplusroadmap | 17:40 | |
| -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has joined ##hplusroadmap | 18:05 | |
| 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 | 18:13 |
| -!- weles [~mariusz@c-71-234-3-169.hsd1.ct.comcast.net] has joined ##hplusroadmap | 18:28 | |
| -!- 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 | 18:32 |
| ParahSail1n | hi | 18:33 |
| -!- Reinhard [Reinhard@198-84-225-88.cpe.teksavvy.com] has quit [Read error: Connection reset by peer] | 18:34 | |
| -!- Reinhard [Reinhard@198-84-225-88.cpe.teksavvy.com] has joined ##hplusroadmap | 18:35 | |
| -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap | 18:40 | |
| -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 248 seconds] | 18:43 | |
| -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] | 18:45 | |
| @kanzure | Reinhard: welcome | 18:54 |
| superkuh | paperbot: http://proceedings.aip.org/resource/2/apcpcs/1539/1/442_1 | 18:54 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1063%2F1.4811080 | 18:55 |
| -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has quit [Ping timeout: 248 seconds] | 19:00 | |
| Reinhard | thank you :) | 19:04 |
| -!- poppingtonic [~poppingto@212.49.88.101] has quit [Ping timeout: 240 seconds] | 19:06 | |
| -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has joined ##hplusroadmap | 19:09 | |
| -!- jmil_ [~jmil@hive76/member/jmil] has joined ##hplusroadmap | 19:37 | |
| -!- aristarchus [~aristarch@unaffiliated/aristarchus] has joined ##hplusroadmap | 19:37 | |
| * heath is curious what the restrictions are for diybio in EU | 19:37 | |
| heath | hey Reinhard | 19:37 |
| heath | ^ chemist | 19:37 |
| 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 | 19:38 |
| -!- jmil [~jmil@hive76/member/jmil] has quit [Ping timeout: 246 seconds] | 19:39 | |
| -!- jmil_ is now known as jmil | 19:39 | |
| heath | hey look, a graduat chemist who knows how IRC works | 19:39 |
| heath | nmz787: here ya go, go wild | 19:40 |
| 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 | 19:41 |
| 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* | 19:42 |
| 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 | 19:43 |
| Noryokusha | lives?!!? | 19:44 |
| Noryokusha | TSK | 19:44 |
| gradstudentbot | Where did you put the revisions to the paper? | 19:44 |
| -!- KnightSirThom [~thomas@97-85-134-200.static.stls.mo.charter.com] has joined ##hplusroadmap | 19:46 | |
| -!- aristarchus [~aristarch@unaffiliated/aristarchus] has quit [Quit: Leaving] | 19:56 | |
| heath | drazak: what are you studying these days? | 19:58 |
| -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has quit [Ping timeout: 260 seconds] | 20:00 | |
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Read error: Connection reset by peer] | 20:02 | |
| 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? | 20:12 |
| heath | i wouldn't mind moving to spain, but i don't want to into those restrictions | 20:13 |
| heath | +walk | 20:17 |
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap | 20:17 | |
| heath | walk|enter|fly :) | 20:17 |
| heath | kanzure: whatever happened to quantumg? | 20:17 |
| -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has joined ##hplusroadmap | 20:19 | |
| @kanzure | heath: he hated me and got out | 20:24 |
| @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 :) | 20:25 |
| 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? | 20:26 |
| * brownies pokes gradstudentbot | 20:38 | |
| gradstudentbot | I can't do science if you're going to be like that. | 20:38 |
| 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? | 20:41 |
| 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 | 20:42 |
| 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 | 20:44 |
| heath | but caramel on tortilla chips right now, best idea ever :) | 20:45 |
| 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 | 20:46 |
| 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 | 20:47 |
| -!- makoLime [~mako@wireless-nat-7.auckland.ac.nz] has quit [Ping timeout: 240 seconds] | 20:57 | |
| -!- AshleyWaffle [~quassel@unaffiliated/anastasiawyatt] has quit [Read error: Connection reset by peer] | 21:06 | |
| -!- cpopell_ [47fff18b@gateway/web/freenode/ip.71.255.241.139] has joined ##hplusroadmap | 21:32 | |
| -!- cpopell_ is now known as stieruridir | 21:32 | |
| -!- oblique [~oblique@unaffiliated/oblique] has quit [Ping timeout: 246 seconds] | 21:57 | |
| -!- ParahSail1n [~parahsail@unaffiliated/parahsailin] has quit [Ping timeout: 245 seconds] | 22:20 | |
| -!- makoLime [~mako@103-9-42-133.flip.co.nz] has joined ##hplusroadmap | 22:25 | |
| -!- ParahSail1n [~parahsail@99-25-202-211.lightspeed.hstntx.sbcglobal.net] has joined ##hplusroadmap | 22:26 | |
| -!- ParahSail1n [~parahsail@99-25-202-211.lightspeed.hstntx.sbcglobal.net] has quit [Changing host] | 22:26 | |
| -!- ParahSail1n [~parahsail@unaffiliated/parahsailin] has joined ##hplusroadmap | 22:26 | |
| -!- ParaSa1lin [~parahsail@99-25-202-211.lightspeed.hstntx.sbcglobal.net] has joined ##hplusroadmap | 22:32 | |
| -!- ParaSa1lin [~parahsail@99-25-202-211.lightspeed.hstntx.sbcglobal.net] has quit [Changing host] | 22:32 | |
| -!- ParaSa1lin [~parahsail@unaffiliated/parahsailin] has joined ##hplusroadmap | 22:32 | |
| -!- ParahSail1n [~parahsail@unaffiliated/parahsailin] has quit [Ping timeout: 246 seconds] | 22:35 | |
| stieruridir | /query jmil hey man | 22:54 |
| stieruridir | welp, I'm a tard | 22:54 |
| -!- Adifex [~Adifex@75-148-41-126-Colorado.hfc.comcastbusiness.net] has joined ##hplusroadmap | 23:16 | |
| -!- ianmathwiz7 [~chatzilla@67.51.113.178] has quit [Ping timeout: 264 seconds] | 23:23 | |
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Remote host closed the connection] | 23:38 | |
| -!- Adifex [~Adifex@75-148-41-126-Colorado.hfc.comcastbusiness.net] has quit [Quit: Adifex] | 23:43 | |
| --- Log closed Tue Aug 13 00:00:40 2013 | ||
Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!