| --- Log opened Fri Jun 27 00:00:47 2014 | ||
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| nmz787 | 'just sweep it under the rug' paraphasing random internet person | 00:24 |
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| kanzure | http://2013.igem.org/Team:TU-Delft/Zephyr | 06:57 |
| kanzure | http://2013.igem.org/Team:TU-Delft/Zephyr_How | 06:57 |
| kanzure | "Zephyr is a low-cost Do It Yourself (DIY) machine which can scan petridishes and 96 well plates for expression of fluorescence at micrometer scale. The Typhoon is the commercial machine that does the same, only it is priced around 120.000 dollars. The main difference is the use of low-cost optics. This allows you to pick exactly which fluorescence you want to detect and not to pay for the ones you do not use. Furthermore, it does not have ... | 06:57 |
| kanzure | ... confocal optics, as this is not that often when scanning bacteria and protein gels. This DIY machine can be built by anyone with one or two days on their hands and the costs are around 1500 dollars." | 06:57 |
| Viper168_ | I assume that period should be a comma | 07:02 |
| Viper168_ | in 120.000 | 07:02 |
| Viper168_ | otherwise it means $120 | 07:02 |
| kanzure | they are probably just usin the parallel reality numbering system | 07:02 |
| dbolser | oh yeah, eu | 07:03 |
| dbolser | in germany they use . to mean , and , to mean . | 07:03 |
| dbolser | so 1.343,34 is normal | 07:03 |
| chris_99 | haha | 07:03 |
| chris_99 | thats odd | 07:03 |
| dbolser | indeed | 07:03 |
| Viper168_ | that's also dumb | 07:04 |
| kanzure | yep | 07:04 |
| dbolser | dumb is mm/dd/yy | 07:04 |
| kanzure | yep | 07:04 |
| Viper168_ | I prefer knowing the month first so I have a reference for what day it is first thing | 07:05 |
| kanzure | just use ISO 8601 | 07:05 |
| Viper168_ | what day it is in said month that is | 07:05 |
| dbolser | how does twitter count views in their summary? | 07:05 |
| kanzure | .wik ISO 8601 | 07:05 |
| yoleaux | "ISO 8601 Data elements and interchange formats – Information interchange – Representation of dates and times is an international standard covering the exchange of date and time-related data. It was issued by the International Organization for Standardization (ISO) and was first published in 1988." — http://en.wikipedia.org/wiki/ISO_8601 | 07:05 |
| dbolser | that sorts well | 07:06 |
| chris_99 | i don't think having the year first is that useful for humans though | 07:06 |
| dbolser | assuming your brain reads strictly left to right | 07:07 |
| chris_99 | mm | 07:07 |
| * archels has been spotting quotes as separation mark more and more | 07:11 | |
| archels | as in, 1'123'242.41 | 07:11 |
| eudoxia | that's horrible | 07:12 |
| kanzure | eudoxia: you should rewrite nanoengineer | 07:20 |
| eudoxia | kanzure: the first herculean labor of transhumanism? | 07:21 |
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| kanzure | eudoxia: who cares? | 07:35 |
| eudoxia | shrug | 07:36 |
| eudoxia | i actually discussed doing that with kirka before he disappeared from the internet, he was building his own in racket or something | 07:36 |
| eudoxia | maybe he got somewher | 07:36 |
| eudoxia | somewhere* | 07:36 |
| kanzure | i doubt it | 07:42 |
| kanzure | pretending that others you're not in communication with are making progress is like pretending a magical gnome will do all your work | 07:42 |
| eudoxia | i do that with zyvex labs :V | 07:43 |
| kanzure | do they even have employees? | 07:43 |
| kanzure | .gc site:linkedin.com "zyvex labs" | 07:44 |
| eudoxia | i don't even know | 07:44 |
| yoleaux | 158 (site), 148 (end), 110 (api) | 07:44 |
| kanzure | "Zyvex Labs. Privately Held; 1-10 employees; Nanotechnology industry" | 07:44 |
| kanzure | so 1 employee | 07:44 |
| ParahSailin | so, having to build gcc on this fedora core 4 machine because boost wont build because bcl2fastq wont build | 07:47 |
| kanzure | enjoying your yak shaving? | 07:49 |
| sheena | anyone here know things about an idea to supplement my upper body strength's ability to hold an object still while it's being pulled on https://docs.google.com/drawings/d/1cV5hlavzAf6eU1bAee8TzfH4vEI5WMKFipEezW5TbfM/edit?usp=sharing | 07:50 |
| ParahSailin | kanzure: im just getting started, i will probably have to install libc too | 07:51 |
| kanzure | it sounds like your office could use a snake pit | 08:07 |
| ParahSailin | this is on a vendor's machine | 08:10 |
| ParahSailin | we needed them to give us a shell; they give us something ancient | 08:10 |
| kanzure | .title http://www.genesis-ultrasound.com/venous-ultrasound.html | 08:20 |
| yoleaux | First diagnosis with venous ultrasound made by Dr. Karl Dussik | 08:20 |
| kanzure | "He used a method in which a transducer was placed on both sides of the patient and submerged in water. The patient's head was partially under water as well. They transmitted sound waves toward the patient at a known rate. The echos were then recorded on heat sensitive paper. These were among the first ultrasound images and the first to diagnose brain tumors." | 08:20 |
| kanzure | .title http://www.ob-ultrasound.net/aloka_ssd-1.html | 08:21 |
| yoleaux | The Aloka SSD-1 waterbag scanner in 1960 | 08:21 |
| kanzure | .title http://www.ob-ultrasound.net/japan_ultrasonics.html | 08:21 |
| yoleaux | history of Medical ultrasound / ultrasonography in Japan, Toshio Wagai | 08:21 |
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| kanzure | "n 1954, Tanaka published an important review entitled "Application of ultrasound to diagnostic field", and investigations had started with other body organs. By 1955, experiments and fabrication with B-mode scanning had started using a similar scope modified from the original A-mode machine coupled with a linear moving transducer gantry. This was shortly developed into the water-bag scanners." | 08:22 |
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| kanzure | this looks similar to the turret ultrasound imaging apparatus that fenn found, http://www.ob-ultrasound.net/project/japan_water-bath_s.jpg | 08:22 |
| ParahSailin | http://en.bookfi.org/ google asks me if i want to translate from russian, so i know its good | 08:25 |
| ParahSailin | cool http://bookfi.org/dl/2236252/dab1cb | 08:26 |
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| kanzure | at least russia has public access to literature | 08:27 |
| kanzure | ParahSailin: why don't these methods show up in python-brlcad? https://github.com/kanzure/brlcad/blob/master/src/librt/primitives/brep/brep.cpp | 08:43 |
| ParahSailin | im not that familiar with ctypes | 08:45 |
| kanzure | oh right, i should check if those methods are available in the shared library in the first place | 08:46 |
| kanzure | i only see somelib.rt_brep_plot and somelib.rt_brep_plot_poly | 08:47 |
| kanzure | argh this is strange. that's not true. that was just tab completion. but this works: | 08:47 |
| kanzure | In [7]: somelib.rt_brep_curve | 08:47 |
| kanzure | Out[7]: <_FuncPtr object at 0x7f5b58037bb0> | 08:47 |
| kanzure | but rt_brep_get is undefined. heh. | 08:48 |
| kanzure | nm /that/lib.so | grep rt_brep_get returns nothing, but there's 21 functions that start with rt_brep_ | 08:49 |
| mosasaur | which python module imports these functions? | 08:49 |
| kanzure | python-brlcad | 08:52 |
| mosasaur | brlcad/__init__.py seems to expect _bindings to exist | 08:59 |
| kanzure | it makes it | 08:59 |
| kanzure | if _os.path.exists(_path_bindings): | 09:00 |
| kanzure | https://github.com/kanzure/python-brlcad/blob/master/brlcad/__init__.py | 09:00 |
| mosasaur | Ah OK, I never installed brlcad so a "locate bindings | grep brlcad" gives me nothing. What does it say on your system? | 09:01 |
| kanzure | that question' doesn't make sense | 09:02 |
| kanzure | what are you trying to learn? | 09:02 |
| mosasaur | where the _bindings files are | 09:02 |
| kanzure | they are generated | 09:02 |
| mosasaur | well, do you have them, and where are they? | 09:03 |
| kanzure | if you have installed python-brlcad then you have already generated the bindings | 09:03 |
| mosasaur | you did not answer my question | 09:03 |
| kanzure | are you asking me where site-packages is? | 09:04 |
| mosasaur | no I just want to know the exact location of _bindings | 09:04 |
| ParahSailin | kanzure: that is really bizarre | 09:05 |
| kanzure | it's in brlcad/ when you install it | 09:05 |
| kanzure | committing the bindings doesn't make sense because it wont work for whatever stupid version of brlcad you have installed | 09:05 |
| kanzure | so it just generates bindings at install-time | 09:05 |
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| kanzure | in my case it's /home/kanzure/.virtualenvs/brlcad/lib/python2.7/site-packages/brlcad-0.0.1-py2.7.egg/brlcad/_bindings/ | 09:06 |
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| kanzure | hm, librt.brep_intersect_curve_surface and librt.brep_intersect_curve_curve seem to exist | 09:19 |
| gradstudentbot | You can't guarantee that. | 09:21 |
| ParahSailin | you sure the .so corresponds to that cpp file? | 09:22 |
| gradstudentbot | Cancer: still not cured. | 09:22 |
| kanzure | no | 09:22 |
| ParahSailin | https://github.com/kanzure/brlcad/blob/4ef506d738e12cc8f401a9419c0c9d89cda45459/src/librt/primitives/brep/brep.cpp the _get does not exist in this revision | 09:23 |
| ParahSailin | do you know which revision your so is from? | 09:24 |
| kanzure | huh, apparently not | 09:25 |
| kanzure | that's a reasonable explanation | 09:25 |
| kanzure | i keep forgetting that all the structs (like rt_db_internal) have the name "struct_" prepended. so it's really struct_rt_db_internal. | 09:26 |
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| kanzure | jove.com is down | 13:30 |
| kanzure | totally didn't do it | 13:34 |
| chris_99 | lol | 13:35 |
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| chris_99 | Does anyone know the name for how an enzyme can detect a particular type of molecule and then break it down accordingly, if there is such a generic name | 14:07 |
| kanzure | binding | 14:08 |
| kanzure | .wik binding affinity | 14:09 |
| yoleaux | "In biochemistry and pharmacology, a ligand (from the Latin ligandum, binding) is a substance (usually a small molecule), that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a signal-triggering molecule, binding to a site on a target protein." — http://en.wikipedia.org/wiki/Binding_affinity | 14:09 |
| chris_99 | thanks! | 14:09 |
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| kanzure | ParahSailin: i think we shuld fork the syrian electronic army ("syrian biology front", maybe) and get some of that aid money | 14:10 |
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| gradstudentbot | That's definitely a Nature paper. | 14:11 |
| ParahSailin | i think army and biology and syria just put me on a watchlist | 14:14 |
| chris_99 | lol | 14:15 |
| kanzure | would be funny to troll diybio with an email from the syrian electronic army | 14:15 |
| kanzure | "hai guys, wut media works best in the middle of the fucking desert?" | 14:16 |
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| kanzure | doc brown getting his plutonium from that region is pretty funny, now that i think about it | 14:17 |
| chris_99 | Did they/do they have nuclear reactors there? | 14:18 |
| kanzure | no, the libyan terrorists stole the plutonium | 14:19 |
| kanzure | he was going to make them a nuke | 14:19 |
| chris_99 | aha hehe | 14:20 |
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| chris_99 | I assume currently it's not possible to build arbitrary enzymes to break down arbitrary molecules | 14:21 |
| kanzure | hm wait why did brown even know libyan terrorists anyway | 14:23 |
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| kanzure | maybe that's what "heavy stuff" was always referring to | 14:23 |
| kanzure | someone should photoshop him into one of those ISIS propaganda videos | 14:23 |
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| chris_99 | maybe he made heavy water for them ;) | 14:28 |
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| chris_99 | Just found out about this http://en.wikipedia.org/wiki/Zymase thought that was clever | 14:34 |
| kanzure | .wik zymase | 14:34 |
| yoleaux | "Zymase is an enzyme complex that catalyzes the fermentation of sugar into ethanol and carbon dioxide. It occurs naturally in yeasts. Zymase activity varies among yeast strains." — http://en.wikipedia.org/wiki/Zymase | 14:34 |
| chris_99 | he extracted it in 1907 | 14:35 |
| chris_99 | *1897 | 14:35 |
| joepie91__ | paperbot: http://www.ehbonline.org/article/S1090-5138(10)00075-9/abstract | 14:46 |
| joepie91__ | (amidoingitrite) | 14:46 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/6af3d1247ab3e711097ffcda087d7ce9.txt | 14:47 |
| joepie91__ | I'm not, okay | 14:47 |
| kanzure | that just means paperbot tried really hard | 14:47 |
| joepie91__ | oh, I see | 14:47 |
| joepie91__ | paperbot: http://download.journals.elsevierhealth.com/pdfs/journals/1090-5138/PIIS1090513810000759.pdf | 14:47 |
| joepie91__ | ? | 14:47 |
| joepie91__ | yes? no? | 14:47 |
| kanzure | he is reconsidering his existence | 14:48 |
| * joepie91__ pokes it with a stick, impatiently | 14:48 | |
| kanzure | paperbot: http://download.journals.elsevierhealth.com/pdfs/journals/1090-5138/PIIS1090513810000759.pdf | 14:48 |
| * joepie91__ stabs Python 3 in the eye with the stick | 14:49 | |
| kanzure | geeze that's a lot of redirects | 14:49 |
| kanzure | at least 5 | 14:49 |
| kanzure | http://download.journals.elsevierhealth.com/pdfs/journals/1090-5138/PIIS1090513810000759.pdf -> http://loginptr.elsevierhealth.com/PhoenixWeb/PhoenixServlet?d=http://download.journals.elsevierhealth.com -> http://download.journals.elsevierhealth.com?xs=yes&sid=46443037323744412d444532452d393238302d453333372d3930353834344644383334333a3133312e3235322e3133302e3234383a31343033393035373538323138 -> ... | 14:49 |
| kanzure | ... http://www.ehbonline.org/article/S1090-5138(10)00075-9/pdf -> a few others | 14:50 |
| joepie91__ | right | 14:50 |
| joepie91__ | I guess I'm not getting a paper? :( | 14:50 |
| kanzure | paperbot tried :\ | 14:50 |
| kanzure | probably does not have access | 14:50 |
| kanzure | usually they don't redirect you if you have access | 14:51 |
| gradstudentbot | Is this going to count as my ethics training? | 14:51 |
| joepie91__ | :( | 14:54 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/1aff50d9d0ed1c6c0006e56bc71bb858.txt | 14:54 |
| joepie91__ | ...? | 14:54 |
| joepie91__ | heh | 14:55 |
| kanzure | haha | 14:55 |
| joepie91__ | persistent paperbot is persistent | 14:55 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/1a0201b63be97d4827d78edd86bb05d7.txt | 14:55 |
| kanzure | .botsnack | 14:56 |
| yoleaux | :D | 14:56 |
| kanzure | not you | 14:56 |
| chris_99 | heh | 14:57 |
| gradstudentbot | Do I have to go through the IRB for that? | 14:58 |
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| mokstar | yay | 15:54 |
| * mokstar gets a job. | 15:54 | |
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| kanzure | hm i didn't expect this code to be working already | 16:40 |
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| kanzure | "Quote "Show me papers, not links I have to filter through. " I agree with that. Discuss specific, individual papers and their conclusions. It is less worthwhile to point to blog entries or file directories of 100 pdf's." | 18:02 |
| kanzure | jonathan cline hates me :( | 18:02 |
| jrayhawk | i appreciate the ideal, at least | 18:17 |
| kanzure | but without directories of pdfs, you're not going to get any | 18:17 |
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| kanzure | https://github.com/kanzure/modelo | 19:23 |
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| ybit2 | kanzure: what made you write modelo? | 19:25 |
| kanzure | angry about orm stuff | 19:26 |
| kanzure | all muddled up with sql | 19:26 |
| kanzure | models and type validations are both generally useful across a wide range of projects | 19:26 |
| kanzure | but that doesn't mean i want to use sqlalchemy everywhere | 19:27 |
| kanzure | ugh "Panasonic has a nice, small -80 freezer for about 4K." -80 freezer costs $4k? wtf | 19:31 |
| kanzure | and why the fuck is it made by panasonic :| | 19:31 |
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| kanzure | ehsm is streaming tomorrow (day 2?) | 20:13 |
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| kanzure | ParahSailin_: what happened to operation "make antibodies yo"? | 20:26 |
| kanzure | is that still going to happen | 20:27 |
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| kanzure | nmz787: so what's the plan on the synthesier or parts | 20:45 |
| kanzure | synthesizer | 20:45 |
| nmz787 | yo | 20:56 |
| nmz787 | http://www.npr.org/2011/11/30/142714568/interpreting-the-constitution-in-the-digital-era | 20:56 |
| nmz787 | I think I can look at that stuff on Sunday | 20:57 |
| nmz787 | tonight I'm gonna try to get the BOM done for the openspectrometer | 20:58 |
| nmz787 | kanzure: i'm kind of unsure how to arrange things actually... and if I want to move all my stuff to this lab i know of | 20:58 |
| kanzure | "arrange things"? | 20:58 |
| kanzure | what, your furniture not matching the drapes? | 20:59 |
| nmz787 | its relatively private, but I don't know if my renters insurance would cover items there | 20:59 |
| nmz787 | i need to get a labelmaker | 20:59 |
| nmz787 | well like the room with the microscope has a bunch of boxes, and lacks a table for one edge of the room | 20:59 |
| nmz787 | and then I was thinking the tables kind of suck | 20:59 |
| nmz787 | but I'm not sure what I'd really like... the prob is it's kind of a small room | 21:00 |
| nmz787 | I guess I'll check about my renters insurance policy | 21:00 |
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| ||0_-_0|| | paperbot http://www.nature.com/nrg/journal/v15/n7/full/nrg3742.html | 21:47 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnrg3742 | 21:47 |
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| --- Log closed Sat Jun 28 00:00:48 2014 | ||
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