--- Log opened Mon Oct 28 00:00:07 2013
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00:48 < 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.
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06:03 < sbaugh> kanzure: I messaged you the pastebin log
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08:09 <@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
08:10 < sbaugh> gentoo brlcad
08:11 < sbaugh> what's that lib do?
08:14 <@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
08:15 < sbaugh> yes, equery files package
08:15 <@kanzure> could you pastebin that list to me?
08:16 < 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
08:18 <@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
08:19 < sbaugh> No no I mean what does libbrep.so do
08:19 <@kanzure> oh interesting, libbu.so is there but libbrep.so isn't?
08:20 <@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)
08:21 <@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.
08:22 <@kanzure> so i do see this: /usr/brlcad/include/brlcad/brep.h
08:25 <@kanzure> okay i've filed a bug, https://github.com/kanzure/python-brlcad/issues/2
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08:29 < poppingtonic> ping
08:29 <@kanzure> pong
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08:31 < 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.
08:32 < poppingtonic> post-pcr
08:33 <@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?
08:34 < poppingtonic> yes. bidens pilosa.
08:34 < ParahSailin> any idea of genome size?
08:34 < ParahSailin> that will inform the amount of coverage you want
08:35 < ParahSailin> cheaper to just send in your biological to some lab like ucdavis or axeq so they can do the library preparation
08:37 < 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?
08:38 < 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
08:39 < poppingtonic> is that the cheapest?
08:39 < ParahSailin> yes
08:40 < ParahSailin> looks like your genome size is over 4 GB
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08:41 < ParahSailin> thats gonna be a full 8 lanes at minimum, probably more
08:41 < poppingtonic> where did you look?
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08:41 < ParahSailin> "bidens pilosa genome size"
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08:44 <@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
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08:45 < poppingtonic`> sorry ParahSailin, I got disconnected. where did you get that data?
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08:45 < ParahSailin> "bidens pilosa genome size"
08:46 <@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
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08:46 <@kanzure> https://github.com/tpaviot/pythonocc/blob/master/src/examples/PAF/test_gears_sympy.py
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08:48 < 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
08:50 <@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
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08:52 < poppingtonic> this is great. thank you ParahSailin.
08:53 < ParahSailin> why this particular organism
08:54 < poppingtonic> it has a soothing property against mosquito bites, and I find that interesting.
08:55 < ParahSailin> well, 370 + 3183 http://dnatech.genomecenter.ucdavis.edu/prices.html
09:01 < poppingtonic> 3553?i see
09:01 < poppingtonic> *i see
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09:09 < ParahSailin> only thing that would be on you would be getting the right mobio or qiagen kit for plant gdna
09:15 < 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.
09:17 < ParahSailin> i just told you what what you want will cost
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09:31 < ParahSailin> yeah, if you disregarded illumina's patents you might be able to do a cheaper hiseq
09:37 < dingo> nice nick ParahSailin
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10:15 < 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
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10:29 < ParahSailin> http://vicariousinc.tumblr.com/post/65316134613/vicarious-ai-passes-first-turing-test-captcha
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11:04 < nmz787> superkuh: http://diyhpl.us/~nmz787/pdf/Direction_selectivity_is_computed_by_active_dendritic_integration_in_retinal_ganglion_cells.pdf
11:07 <@kanzure> really?
11:08 < nmz787> interesting, 'lectricity follows appaent light bulb movement across visual field
11:10 < nmz787> there's no one in # or ## dairyfarmers or farmers or farming :(
11:14 < superkuh> This time the libgen link worked.
11:14 < superkuh> But thanks.
11:15 < nmz787> oh
11:15 < nmz787> didn't visually look it
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12:39 < 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
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13:55 < heath> nmz787: there's a #horticulture irc channel
13:55 < heath> or ##, i can't recall
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14:18 < jrayhawk> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/21258337
14:18 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnm.2297
14:41 < 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
14:42 < nmz787> huh the first link works
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15:10 < 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
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16:13 < nmz787> what's a good python way to discern the string '12' as being interchangable with 'twelve'?
16:14 < 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
16:15 <@kanzure> the only way to solve that problem is to never trust user input and only let the users select from possible valid choices
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16:34 < nmz787> would this fall under NLP?
16:35 <@kanzure> the overall probem, yes
16:35 <@kanzure> the specific problem of converting numbers to their words, no
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16:35 <@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.
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17:16 < 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
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17:17 < justanotheruser> paperbot: http://pubs.acs.org/doi/pdf/10.1021/jo4018777
17:17 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/a190057f763b6cd9a3ad5cefd0f441cb.pdf
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17:37 < nmz787> huh, wonder what the chinese are planning?
17:39 < nmz787> I guess that paper doesn't necessarily imply nefarious
17:40 < ParahSail1n> thats pretty impressive
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21:51 < poppingtonic> paperbot,  http://www.ncbi.nlm.nih.gov/pubmed/19829295
21:51 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnature08514
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22:35 <@kanzure> uhuh
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23:56 <@kanzure> anyone have a copy of that recent photoshop source code dump?
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--- Log closed Tue Oct 29 00:00:08 2013