2013-10-28.log

--- Log opened Mon Oct 28 00:00:07 2013
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nmz787sbaugh: 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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sbaughkanzure: I messaged you the pastebin log06:03
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@kanzuresbaugh: was this gentoo brlcad or was this brlcad's upstream build?08:09
@kanzurecause the error is: ImportError: /usr/brlcad/lib/libbrep.so not found08:09
@kanzureit's interesting that files like /usr/brlcad/include/brlcad/bu.h were present08:09
sbaughgentoo brlcad08:10
sbaughwhat's that lib do?08:11
@kanzurehuh?08:14
@kanzureso anyway, is there an easy way in gentoo land to see where it installs packages to?08:14
@kanzurei mean, to see where files are dumped on your file system08:14
@kanzurebased on the package08:14
sbaughyes, equery files package08:15
@kanzurecould you pastebin that list to me?08:15
sbaughand, i ask what the lib does because perhaps it wasn't compiled08:16
@kanzurebrlcad does solid modeling08:16
@kanzureit has like 400 sublibraries or something08:16
@kanzurethe "bu" module is its core utilities module08:16
@kanzurei don't know much about gentoo.. does its package manager allow you to install things without compiling?08:18
sbaughhttp://sprunge.us/VbhT08:18
sbaughNo no I mean what does libbrep.so do08:19
@kanzureoh interesting, libbu.so is there but libbrep.so isn't?08:19
@kanzurelibbrep.so provides boundary representations for modeling curves08:20
@kanzurehmm i'm not sure if i should support this situation. i didn't anticipate libbrep.so not being present.08:20
sbaughah, so not something you would avoid compiling in (gentoo lets you pass modify compile time flags)08:20
@kanzurei would very much expect it to be a default that someone would choose08:21
sbaugh(and perhaps the packager had some weird defaults)08:21
sbaughindeed08:21
@kanzurewhich version was this, again?08:21
sbaugh7.18.408:21
@kanzureit's possible that libbrep is newer... but i sorta doubt it.08:21
@kanzureso i do see this: /usr/brlcad/include/brlcad/brep.h08:22
@kanzureokay i've filed a bug, https://github.com/kanzure/python-brlcad/issues/208:25
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poppingtonicping08:29
@kanzurepong08:29
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poppingtonicdo 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
poppingtonicpost-pcr08:32
@kanzurepoppingtonic: http://diyhpl.us/skdb/BOMs/diybio-equipment.yaml08:33
@kanzurehttp://diyhpl.us/skdb/BOMs/pcr08:33
poppingtonicthank you kanzure08:33
ParahSailinyou want to sequence a plant?08:33
poppingtonicyes. bidens pilosa.08:34
ParahSailinany idea of genome size?08:34
ParahSailinthat will inform the amount of coverage you want08:34
ParahSailincheaper to just send in your biological to some lab like ucdavis or axeq so they can do the library preparation08:35
ParahSailin3k per hiseq lane, might get a discount if you need 8 lanes08:37
poppingtonicI 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
ParahSailinive never prepared a library or commissioned a genome sequencing08:38
@kanzurescienceexchange.com will probably have some okay prices on sequencing08:38
ParahSailin~3k per hiseq lane is the price08:38
poppingtonicis that the cheapest?08:39
ParahSailinyes08:39
ParahSailinlooks like your genome size is over 4 GB08:40
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ParahSailinthats gonna be a full 8 lanes at minimum, probably more08:41
poppingtonicwhere did you look?08:41
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ParahSailin"bidens pilosa genome size"08:41
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@kanzureParahSailin: could you try https://github.com/kanzure/python-brlcad at some point08:44
@kanzureParahSailin: this is the continuation of that post-install script BS08:44
ParahSailinkanzure: sure, in a bit08:44
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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
@kanzurei thought that pythonocc had some simplifying wrapper on top of opencascade, not just swig bindings08:46
@kanzurebut i'm looking around and can't find anything that looks pythonic08:46
@kanzurehttps://github.com/tpaviot/pythonocc08:46
@kanzureall of the examples look like vanilla opencascade calls.. https://github.com/tpaviot/pythonocc/tree/master/src/examples08:46
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@kanzurehttps://github.com/tpaviot/pythonocc/blob/master/src/examples/PAF/test_gears_sympy.py08:46
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ParahSailinand that 3k is for paired end 100nt reads08:48
@kanzureby comparisong the work we did in skdb on top of opencascade looks way better, http://diyhpl.us/cgit/skdb/tree/geom/geom.py08:48
@kanzure*comparison08:50
ParahSailinpoppingtonic: you could get enough coverage for a decent assembly on one hiseq lane it looks like08:50
ParahSailin675 million * 2 100nt reads08:50
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poppingtonicthis is great. thank you ParahSailin.08:52
ParahSailinwhy this particular organism08:53
poppingtonicit has a soothing property against mosquito bites, and I find that interesting.08:54
ParahSailinwell, 370 + 3183 http://dnatech.genomecenter.ucdavis.edu/prices.html08:55
poppingtonic3553?i see09:01
poppingtonic*i see09:01
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ParahSailinonly thing that would be on you would be getting the right mobio or qiagen kit for plant gdna09:09
poppingtonicI'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
ParahSailini just told you what what you want will cost09:17
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ParahSailinyeah, if you disregarded illumina's patents you might be able to do a cheaper hiseq09:31
dingonice nick ParahSailin09:37
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superkuhpaperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.3565.html10:15
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fnn.356510:15
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ParahSailinhttp://vicariousinc.tumblr.com/post/65316134613/vicarious-ai-passes-first-turing-test-captcha10:29
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nmz787superkuh: http://diyhpl.us/~nmz787/pdf/Direction_selectivity_is_computed_by_active_dendritic_integration_in_retinal_ganglion_cells.pdf11:04
@kanzurereally?11:07
nmz787interesting, 'lectricity follows appaent light bulb movement across visual field11:08
nmz787there's no one in # or ## dairyfarmers or farmers or farming :(11:10
superkuhThis time the libgen link worked.11:14
superkuhBut thanks.11:14
nmz787oh11:15
nmz787didn't visually look it11:15
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superkuhpaperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.3547.html12:39
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fnn.354712:39
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heathnmz787: there's a #horticulture irc channel13:55
heathor ##, i can't recall13:55
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jrayhawkpaperbot: http://www.ncbi.nlm.nih.gov/pubmed/2125833714:18
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fnm.229714:18
nmz787paperbot: http://www.sciencemag.org/content/266/5188/1247.short714:41
paperbothttp://libgen.org/scimag/get.php?doi=10.1126%2Fscience.266.5188.124714:41
nmz787paperbot: http://dx.doi.org/10.1126/science.266.5188.124714:41
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/fda4e11ed90cb3df120872388e00c976.txt14:41
nmz787huh the first link works14:42
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nmz787paperbot: http://www.sciencemag.org/content/143/3602/111.full.pdf15:10
paperbothttp://libgen.org/scimag/get.php?doi=10.1126%2Fscience.143.3602.11115:10
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nmz787what's a good python way to discern the string '12' as being interchangable with 'twelve'?16:13
nmz787this 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
@kanzuredumb way: https://github.com/ghewgill/text2num/blob/master/text2num.py16:14
@kanzurepossibly smarter way: probably a feature inside regular expressions16:14
@kanzurethe only way to solve that problem is to never trust user input and only let the users select from possible valid choices16:15
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nmz787would this fall under NLP?16:34
@kanzurethe overall probem, yes16:35
@kanzurethe specific problem of converting numbers to their words, no16:35
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@kanzurei 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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justanotheruserpaperbot: http://pubs.acs.org/doi/abs/10.1021/jo401877717:16
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Total%20Synthesis%20of%20%28%2B%29-Lysergic%20Acid.txt17:16
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justanotheruserpaperbot: http://pubs.acs.org/doi/pdf/10.1021/jo401877717:17
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/a190057f763b6cd9a3ad5cefd0f441cb.pdf17:17
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nmz787huh, wonder what the chinese are planning?17:37
nmz787I guess that paper doesn't necessarily imply nefarious17:39
ParahSail1nthats pretty impressive17:40
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poppingtonicpaperbot,  http://www.ncbi.nlm.nih.gov/pubmed/1982929521:51
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fnature0851421:51
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@kanzureuhuh22:35
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@kanzureanyone 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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