| --- Log opened Tue Sep 17 00:00:28 2013 | ||
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| kanzure | brlcad/python wrappers coming along nicely | 00:11 |
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| pasky | paperbot: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2637.html | 04:24 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnmeth.2637 | 04:24 |
| pasky | hmm that link is weird, it returns just 206 Partial content | 04:27 |
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| poppingtonic | paperbot: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/ | 05:39 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/554773dc1608d215f9289fe06d475ab8.txt | 05:39 |
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| poppingtonic | ping | 06:15 |
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| pasky | poppingtonic: that won't be too helpful though, will it? | 07:00 |
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| heath | https://github.com/stephencelis/ghi | 07:35 |
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| kyknos | paperbot, http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2637.html | 08:37 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnmeth.2637 | 08:37 |
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| kanzure | kyknos: hi | 08:40 |
| kanzure | Jenda`: don't i know you too | 08:40 |
| kanzure | wait you're all from that hacker country | 08:40 |
| Jenda` | kanzure: I'm from the same hackerspace as pasky and chido are :) | 08:41 |
| Jenda` | and kyknos too | 08:41 |
| kyknos | kanzure, hi | 08:41 |
| pasky | I've mentioned the channel on our biolab channel :) | 08:42 |
| pasky | and yay, paperbot or rather libgen got its act together now \o/ | 08:42 |
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| kyknos | seems like an interesting place | 08:52 |
| blueskin | >that hacker country | 08:55 |
| blueskin | define? | 08:55 |
| kanzure | czech republic | 08:58 |
| poppingtonic | Mr. Lee's Greater Hong Kong | 09:03 |
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| nalkri | poppingtonic: Diamond Age? | 09:14 |
| anannie | paperbot: http://lawfam.oxfordjournals.org/content/12/3/307.short | 09:38 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1093%2Flawfam%2F12.3.307 | 09:38 |
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| * brownies pokes gradstudentbot | 10:11 | |
| gradstudentbot | Why aren't you doing science right now? | 10:11 |
| kanzure | http://www.jwz.org/blog/2010/10/every-day-i-learn-something-new-and-stupid/ | 10:11 |
| kanzure | javascript doesn't have ints | 10:11 |
| ParahSai1in | but thats ok, since ints up to 2^51 or something can be represented as doubles | 10:20 |
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| ParahSai1in | what the hell? ncbi's standard format for sequence reads is specified only by their SRA toolkit source code? | 11:18 |
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| ParahSai1in | wow, "Guys from NCBI said me that they don't give this documentation anybody. And if you want to use the SRA format then you need to use their API." | 11:19 |
| ParahSai1in | the program to convert this .sra file to fastq is hideously slow | 11:19 |
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| kanzure | haha | 11:20 |
| kanzure | great | 11:20 |
| ParahSai1in | for comparison, extraction to fastq from .sra is about 50x slower than BWA mapping | 11:20 |
| ParahSai1in | which makes it about 1000x slower than gunzip | 11:20 |
| kanzure | time to write a paper.. i mean a haskell thing. | 11:20 |
| ParahSai1in | what, reverse engineer sra format? | 11:21 |
| kanzure | some alternative | 11:21 |
| ParahSai1in | http://seqanswers.com/forums/archive/index.php/t-12054.html | 11:22 |
| ParahSai1in | and apparently this file format is unsupported now because of budget cuts | 11:23 |
| ParahSai1in | but it is the required submission format | 11:23 |
| gradstudentbot | Wow, I'm definitely not including this data in the paper. | 11:24 |
| ParahSai1in | kanzure: there is an alternative, fastq.gz or bam | 11:28 |
| ParahSai1in | paperbot: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059190 | 11:30 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/601fca0556ee72dd6ab1e27fcd9292a8.txt | 11:30 |
| kanzure | wow it's failing on plosone | 11:32 |
| kanzure | what the hell? | 11:32 |
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| entelechios | http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0059190&representation=PDF | 11:41 |
| entelechios | seems they switched their stuff around a bit | 11:41 |
| entelechios | from what i recall | 11:41 |
| kanzure | i haven't updated zotero-translators in paperbot in a while, so maybe it's time for a version bump | 11:42 |
| kanzure | https://github.com/blog/1633-3d-file-diffs | 11:46 |
| kanzure | "Also available is the revision slider, which lets you transition between the current version of the file, and the previous one with a small slider at the top of the viewer." | 11:47 |
| entelechios | paperbot: https://www.sciencedirect.com/science/article/pii/S0003347213003060 | 11:47 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/bf49990e17829815d3546392e321c769.pdf | 11:47 |
| kanzure | "This is done using csgtool, a C library paired with a Ruby gem via FFI." | 11:47 |
| entelechios | Metabolic rate and body size are linked with perception of temporal | 11:47 |
| entelechios | information | 11:47 |
| kanzure | https://github.com/sshirokov/csgtool | 11:47 |
| entelechios | (smaller you are the slower you perceive time) | 11:47 |
| kanzure | https://help.github.com/articles/3d-file-viewer | 11:47 |
| kanzure | takes a while for their stl pages to load though | 11:48 |
| kanzure | https://github.com/carlosgs/Cyclone-PCB-Factory/commit/d389a67ab2cc1d63ec1a38f5e60f20e2f9643247 | 11:48 |
| entelechios | wow that CAD diff stuff is awesome | 11:48 |
| ParahSai1in | plosone is not though zotero | 11:49 |
| kanzure | zotero must have a plosone scraper, there's no way they skipped that | 11:50 |
| gradstudentbot | Someone's sitting at my bench space. | 11:50 |
| entelechios | i'm incredibly surprised at how performant this is on firefox in linux | 11:51 |
| entelechios | a lotta 3d crap in the browser will crash for me in these circumstances | 11:51 |
| entelechios | but this is running more smoothly than, like, standalone programs such as structure synth on this crappy box | 11:51 |
| kanzure | i think this might be the one that is just a bunch of png files they generate | 11:52 |
| entelechios | yes | 11:52 |
| entelechios | eg | 11:52 |
| entelechios | not pasting that oh god | 11:52 |
| entelechios | that's an entire base64 or w/e encoded PNG in my address bar there | 11:52 |
| entelechios | hahahahaha | 11:52 |
| entelechios | data:image/png;base64, | 11:53 |
| entelechios | and then the encoded png | 11:53 |
| entelechios | when i view image | 11:53 |
| entelechios | that's still pretty impressive rendering | 11:53 |
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| entelechios | often i gotta bust out chromium to get 3d stuff working proper in the browser | 11:54 |
| kanzure | https://news.ycombinator.com/item?id=6400895 | 11:56 |
| kanzure | https://news.ycombinator.com/item?id=5519676 | 11:56 |
| entelechios | ah so you suggested this ages ago? | 11:57 |
| entelechios | right on | 11:57 |
| kanzure | i built it ages ago and then i stopped caring | 11:57 |
| kanzure | committing stl files to a git repo is a sin, it's like committing build objcets | 11:57 |
| kanzure | *objects | 11:58 |
| entelechios | someone else pick up on your work then? | 11:58 |
| kanzure | nah, lots of people doing similar things | 11:58 |
| entelechios | oh yeah i couldn't picture that repo staying small. | 11:58 |
| entelechios | people toss around gajiggabytes like pinata candy | 11:58 |
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| ParahSai1in | "2013-09-17T19:30:05 fastq-dump.2.3.3 err: table incorrect while opening manager within database module - failed /data2/NCBI-SRA/sra/sra-instant/reads/ByExp/sra/ERX/ERX171/ERX171672/ERR196983/ERR196983.sra" | 13:04 |
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| ParahSai1in | what? a bug in an undocumented file format and toolkit api for it? | 13:05 |
| ParahSai1in | who would have ever guessed | 13:05 |
| jrayhawk | http://www.youtube.com/watch?v=Oie1ZXWceqM | 13:06 |
| jrayhawk | !title | 13:06 |
| jrayhawk | fffff | 13:06 |
| kanzure | .title | 13:12 |
| yoleaux | 3-Sweep: Extracting Editable Objects from a Single Photo, SIGGRAPH ASIA 2013 - YouTube | 13:12 |
| jrayhawk | that's the one | 13:12 |
| jrayhawk | technology is hard | 13:12 |
| kanzure | that's okay hawkbot you will understand computers eventually | 13:12 |
| entelechios | that's so cool jrayhawk | 13:47 |
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| poppingtonic | nalkri: No. Snow Crash. | 14:30 |
| nalkri | Oh right, close | 14:30 |
| poppingtonic | paperbot: http://www.nature.com/nphys/journal/v7/n5/full/nphys1915.html | 14:32 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnphys1915 | 14:32 |
| poppingtonic | I'd forgotten all of the Phyles in The Diamond Age at the time, unfortunately. The Diamond Age came off as the book with better quality hackers imo. | 14:40 |
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| heath | https://github.com/s-macke/jor1k :: "jor1k is a OpenRISC 1000 emulator written in JavaScript running Linux" | 15:28 |
| soylentbomb | Awesome. | 15:28 |
| heath | http://s-macke.github.io/jor1k/ | 15:29 |
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| heath | is there a book i can read while i'm on the beach that will actually help me with android/java/smali stuff? | 23:30 |
| * heath already has most of the online references in pdf on his kindle dx | 23:31 | |
| heath | online references for smali and dex | 23:32 |
| justanotheruser1 | .paperbot http://onlinelibrary.wiley.com/doi/10.1111/j.1745-9125.2003.tb01013.x/pdf | 23:33 |
| justanotheruser1 | .paper http://onlinelibrary.wiley.com/doi/10.1111/j.1745-9125.2003.tb01013.x/pdf | 23:33 |
| justanotheruser1 | paperbot: | 23:33 |
| justanotheruser1 | paperbot help | 23:33 |
| heath | i've got about another hour or two to queue up material before the lappy is stored securely in a secret little compartment away from me for ~1+week(s) | 23:33 |
| justanotheruser1 | heath: do you know how to work paperbot | 23:34 |
| heath | leave out the peroid | 23:34 |
| heath | or just add the link | 23:34 |
| heath | e.g. | 23:34 |
| heath | paperbot: http://onlinelibrary.wiley.com/doi/10.1111/j.1745-9125.2003.tb01013.x/pdf | 23:34 |
| paperbot | http://libgen.org/scimag2/10.1111/j.1745-9125.2003.tb01013.x.pdf | 23:34 |
| justanotheruser1 | paperbot http://onlinelibrary.wiley.com/doi/10.1111/j.1745-9125.2003.tb01013.x/pdf | 23:35 |
| paperbot | http://libgen.org/scimag2/10.1111/j.1745-9125.2003.tb01013.x.pdf | 23:35 |
| justanotheruser1 | ok thanks | 23:35 |
| heath | yw | 23:35 |
| justanotheruser1 | can paperbot ever not find it | 23:35 |
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| heath | justanotheruser1: yes | 23:37 |
| --- Log closed Wed Sep 18 00:00:29 2013 | ||
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