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nmz787 | sbaugh: funny, i just mentioned on a meetup.com introduction that i used to like and use gentoo because I thought programs and the system would run more efficiently/faster if I compiled them all on that system... and that today I'm glad for apt-get. | 00:48 |
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sbaugh | kanzure: I messaged you the pastebin log | 06:03 |
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@kanzure | sbaugh: was this gentoo brlcad or was this brlcad's upstream build? | 08:09 |
@kanzure | cause the error is: ImportError: /usr/brlcad/lib/libbrep.so not found | 08:09 |
@kanzure | it's interesting that files like /usr/brlcad/include/brlcad/bu.h were present | 08:09 |
sbaugh | gentoo brlcad | 08:10 |
sbaugh | what's that lib do? | 08:11 |
@kanzure | huh? | 08:14 |
@kanzure | so anyway, is there an easy way in gentoo land to see where it installs packages to? | 08:14 |
@kanzure | i mean, to see where files are dumped on your file system | 08:14 |
@kanzure | based on the package | 08:14 |
sbaugh | yes, equery files package | 08:15 |
@kanzure | could you pastebin that list to me? | 08:15 |
sbaugh | and, i ask what the lib does because perhaps it wasn't compiled | 08:16 |
@kanzure | brlcad does solid modeling | 08:16 |
@kanzure | it has like 400 sublibraries or something | 08:16 |
@kanzure | the "bu" module is its core utilities module | 08:16 |
@kanzure | i don't know much about gentoo.. does its package manager allow you to install things without compiling? | 08:18 |
sbaugh | http://sprunge.us/VbhT | 08:18 |
sbaugh | No no I mean what does libbrep.so do | 08:19 |
@kanzure | oh interesting, libbu.so is there but libbrep.so isn't? | 08:19 |
@kanzure | libbrep.so provides boundary representations for modeling curves | 08:20 |
@kanzure | hmm i'm not sure if i should support this situation. i didn't anticipate libbrep.so not being present. | 08:20 |
sbaugh | ah, so not something you would avoid compiling in (gentoo lets you pass modify compile time flags) | 08:20 |
@kanzure | i would very much expect it to be a default that someone would choose | 08:21 |
sbaugh | (and perhaps the packager had some weird defaults) | 08:21 |
sbaugh | indeed | 08:21 |
@kanzure | which version was this, again? | 08:21 |
sbaugh | 7.18.4 | 08:21 |
@kanzure | it's possible that libbrep is newer... but i sorta doubt it. | 08:21 |
@kanzure | so i do see this: /usr/brlcad/include/brlcad/brep.h | 08:22 |
@kanzure | okay i've filed a bug, https://github.com/kanzure/python-brlcad/issues/2 | 08:25 |
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poppingtonic | ping | 08:29 |
@kanzure | pong | 08:29 |
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poppingtonic | do you have, somewhere, a bill-of-materials for a small genomics lab? something that might be used to record a plant genome, for instance. | 08:31 |
poppingtonic | post-pcr | 08:32 |
@kanzure | poppingtonic: http://diyhpl.us/skdb/BOMs/diybio-equipment.yaml | 08:33 |
@kanzure | http://diyhpl.us/skdb/BOMs/pcr | 08:33 |
poppingtonic | thank you kanzure | 08:33 |
ParahSailin | you want to sequence a plant? | 08:33 |
poppingtonic | yes. bidens pilosa. | 08:34 |
ParahSailin | any idea of genome size? | 08:34 |
ParahSailin | that will inform the amount of coverage you want | 08:34 |
ParahSailin | cheaper to just send in your biological to some lab like ucdavis or axeq so they can do the library preparation | 08:35 |
ParahSailin | 3k per hiseq lane, might get a discount if you need 8 lanes | 08:37 |
poppingtonic | I don't know how large it is yet. I'm just compiling information right now so I can formulate a plan. Thanks for the tip. Have you sequenced? | 08:37 |
ParahSailin | ive never prepared a library or commissioned a genome sequencing | 08:38 |
@kanzure | scienceexchange.com will probably have some okay prices on sequencing | 08:38 |
ParahSailin | ~3k per hiseq lane is the price | 08:38 |
poppingtonic | is that the cheapest? | 08:39 |
ParahSailin | yes | 08:39 |
ParahSailin | looks like your genome size is over 4 GB | 08:40 |
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ParahSailin | thats gonna be a full 8 lanes at minimum, probably more | 08:41 |
poppingtonic | where did you look? | 08:41 |
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ParahSailin | "bidens pilosa genome size" | 08:41 |
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@kanzure | ParahSailin: could you try https://github.com/kanzure/python-brlcad at some point | 08:44 |
@kanzure | ParahSailin: this is the continuation of that post-install script BS | 08:44 |
ParahSailin | kanzure: sure, in a bit | 08:44 |
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poppingtonic` | sorry ParahSailin, I got disconnected. where did you get that data? | 08:45 |
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ParahSailin | "bidens pilosa genome size" | 08:45 |
@kanzure | i thought that pythonocc had some simplifying wrapper on top of opencascade, not just swig bindings | 08:46 |
@kanzure | but i'm looking around and can't find anything that looks pythonic | 08:46 |
@kanzure | https://github.com/tpaviot/pythonocc | 08:46 |
@kanzure | all of the examples look like vanilla opencascade calls.. https://github.com/tpaviot/pythonocc/tree/master/src/examples | 08:46 |
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@kanzure | https://github.com/tpaviot/pythonocc/blob/master/src/examples/PAF/test_gears_sympy.py | 08:46 |
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ParahSailin | and that 3k is for paired end 100nt reads | 08:48 |
@kanzure | by comparisong the work we did in skdb on top of opencascade looks way better, http://diyhpl.us/cgit/skdb/tree/geom/geom.py | 08:48 |
@kanzure | *comparison | 08:50 |
ParahSailin | poppingtonic: you could get enough coverage for a decent assembly on one hiseq lane it looks like | 08:50 |
ParahSailin | 675 million * 2 100nt reads | 08:50 |
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poppingtonic | this is great. thank you ParahSailin. | 08:52 |
ParahSailin | why this particular organism | 08:53 |
poppingtonic | it has a soothing property against mosquito bites, and I find that interesting. | 08:54 |
ParahSailin | well, 370 + 3183 http://dnatech.genomecenter.ucdavis.edu/prices.html | 08:55 |
poppingtonic | 3553?i see | 09:01 |
poppingtonic | *i see | 09:01 |
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ParahSailin | only thing that would be on you would be getting the right mobio or qiagen kit for plant gdna | 09:09 |
poppingtonic | I've heard & read the phrase "$1000 genome" being bandied about. is the development of cheaper kits the only thing stopping people from getting there? like working around current hardware patents etc. | 09:15 |
ParahSailin | i just told you what what you want will cost | 09:17 |
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ParahSailin | yeah, if you disregarded illumina's patents you might be able to do a cheaper hiseq | 09:31 |
dingo | nice nick ParahSailin | 09:37 |
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superkuh | paperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.3565.html | 10:15 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnn.3565 | 10:15 |
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ParahSailin | http://vicariousinc.tumblr.com/post/65316134613/vicarious-ai-passes-first-turing-test-captcha | 10:29 |
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nmz787 | superkuh: http://diyhpl.us/~nmz787/pdf/Direction_selectivity_is_computed_by_active_dendritic_integration_in_retinal_ganglion_cells.pdf | 11:04 |
@kanzure | really? | 11:07 |
nmz787 | interesting, 'lectricity follows appaent light bulb movement across visual field | 11:08 |
nmz787 | there's no one in # or ## dairyfarmers or farmers or farming :( | 11:10 |
superkuh | This time the libgen link worked. | 11:14 |
superkuh | But thanks. | 11:14 |
nmz787 | oh | 11:15 |
nmz787 | didn't visually look it | 11:15 |
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superkuh | paperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.3547.html | 12:39 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnn.3547 | 12:39 |
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heath | nmz787: there's a #horticulture irc channel | 13:55 |
heath | or ##, i can't recall | 13:55 |
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jrayhawk | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/21258337 | 14:18 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnm.2297 | 14:18 |
nmz787 | paperbot: http://www.sciencemag.org/content/266/5188/1247.short7 | 14:41 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscience.266.5188.1247 | 14:41 |
nmz787 | paperbot: http://dx.doi.org/10.1126/science.266.5188.1247 | 14:41 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/fda4e11ed90cb3df120872388e00c976.txt | 14:41 |
nmz787 | huh the first link works | 14:42 |
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nmz787 | paperbot: http://www.sciencemag.org/content/143/3602/111.full.pdf | 15:10 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscience.143.3602.111 | 15:10 |
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nmz787 | what's a good python way to discern the string '12' as being interchangable with 'twelve'? | 16:13 |
nmz787 | this is regarding matching tool names and their descriptions, to try and reduce duplicate items when the tools are user-generated (so spelling variations, numerals vs spelled out numbers) | 16:14 |
@kanzure | dumb way: https://github.com/ghewgill/text2num/blob/master/text2num.py | 16:14 |
@kanzure | possibly smarter way: probably a feature inside regular expressions | 16:14 |
@kanzure | the only way to solve that problem is to never trust user input and only let the users select from possible valid choices | 16:15 |
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nmz787 | would this fall under NLP? | 16:34 |
@kanzure | the overall probem, yes | 16:35 |
@kanzure | the specific problem of converting numbers to their words, no | 16:35 |
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@kanzure | i highly recommend just presenting them with options that they click. they can search through options by typing words but they must select a pre-generated option. if their actual thing doesn't exist, then that's a bug/error that they should report. | 16:35 |
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justanotheruser | paperbot: http://pubs.acs.org/doi/abs/10.1021/jo4018777 | 17:16 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Total%20Synthesis%20of%20%28%2B%29-Lysergic%20Acid.txt | 17:16 |
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justanotheruser | paperbot: http://pubs.acs.org/doi/pdf/10.1021/jo4018777 | 17:17 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/a190057f763b6cd9a3ad5cefd0f441cb.pdf | 17:17 |
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nmz787 | huh, wonder what the chinese are planning? | 17:37 |
nmz787 | I guess that paper doesn't necessarily imply nefarious | 17:39 |
ParahSail1n | thats pretty impressive | 17:40 |
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poppingtonic | paperbot, http://www.ncbi.nlm.nih.gov/pubmed/19829295 | 21:51 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnature08514 | 21:51 |
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@kanzure | uhuh | 22:35 |
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@kanzure | anyone have a copy of that recent photoshop source code dump? | 23:56 |
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--- Log closed Tue Oct 29 00:00:08 2013 |
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