2015-08-14.log

--- Log opened Fri Aug 14 00:00:40 2015
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nmz787the price is not terribly student friendly: http://www.edn.com/design/design-tools/development-kits/4440137/Student-version-of-MATLAB-Simulink-drives-Raspberry-Pi-to-new-heights00:36
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nmz787kanzure: that intel history link is pretty awesome, especially since I am working on test equipment development01:25
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kanzurehttps://www.reddit.com/r/chemistry/comments/3gx7kg/seeking_collaborators_for_a_selffunded/04:05
gradstudentbotNo no no no! Use your key commands!04:07
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kanzuregreetings CyberelfJess07:36
fennwho is trollzyme?07:41
fennor rather, why use a new account07:41
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kanzureone-directional privacy07:43
fenn"There are already DNA synthesizers on the market that work nicely" lol yeah right07:44
fennefficient market fallacy07:45
kanzurepraise unto the market07:45
kanzuretake the wheel, supply side jesus07:45
fennsome photos from that port explosion http://pixel.nymag.com/imgs/daily/intelligencer/2015/08/13/tianjin-explosion/tianjin-china-explosion13.w529.h352.2x.jpg http://pixel.nymag.com/imgs/daily/intelligencer/2015/08/13/tianjin-explosion/tianjin-china-explosion11.w529.h352.2x.jpg http://pixel.nymag.com/imgs/daily/intelligencer/2015/08/13/tianjin-explosion/tianjin-china-explosion05.w529.h352.2x.jpg07:49
kanzureit's weird how you have to argue for every inch everywhere you go even if you're offering money07:55
kanzurejust once i'd rather not explain the entire philosophical context of everything ever07:55
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xtalmaththat clip just stays so incredible https://www.youtube.com/watch?v=H_nnZntSYjo08:09
kanzure.title08:11
yoleauxThe Tianjin Explosion - Stabilized - YouTube08:11
JayDuggerGood morning, everyone.08:22
kanzureare you guys done with your disaster porn yet08:24
xtalmathits not disaster porn, its a reminder of how important safety precautions are08:25
* fenn straps on a hard hat in case oakland explodes08:42
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kanzurebeep boop11:38
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chris_99i'm wondering if anyone can point me in the right direction, i'm going to try to automate the stage of my microscope which i think i've figured out how to do roughly now, i'm going to be driving the steppers via DRV8825 using an STM32F429 dev board, attached to my PC via USB11:55
chris_99i'm gonna write some very simple software for the devboard, but i'm wondering if theres some fairly simple PC software i could use to control everything11:56
kanzurelinuxcnc11:57
chris_99so i just looked at their page, isn't it a full distro though?11:57
kanzurei dunno if you can use linuxcnc without realtime mode, but my guess is probably, so just throw it in a virtual machine11:57
chris_99i was wondering if theres not a core piece of their distro i could just install instead, or is it all heavily interlinked11:59
kanzurei'm not the right person to ask, try fenn or CaptHindsight or #linuxcnc12:01
chris_99ta, i'll try in their channel12:02
fennuse grbl and arduino unless you specifically need the dev board12:02
chris_99i don't have any arduinos12:03
fennUSB is terrible for motion control and negates the benefit of linuxcnc12:03
fennalso i don't think linuxcnc even works with any usb libraries because the devs hate it12:03
chris_99ah heh12:03
fennactually that's not right, but it will be hard to set up something controlling motion via usb12:04
kanzureah i see12:04
kanzurei was hoping that using linuxcnc would make up for the horribleness of usb12:04
fennno, it's the other way around12:04
fennusb is so terrible even linuxcnc can't fix it12:04
kanzuresome sort of net project karmic measurement12:04
kanzureah i see.12:04
chris_99what other candidates are there that i could use on a laptop, i can only think of ethernet, but is that much better12:05
fennjust buy an atmega328 for $5 sheesh12:06
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chris_99i don't want to use arduinos though :P12:06
kanzurefenn: did you hang out with t12 by any chance?12:09
fennno12:10
kanzuregot a reply about cambrian genomics.. at least they are topical.12:14
kanzurehaving trouble figuring out why i know P212121.. he's not in my stalkmatrix, but i know about p212121.com?12:14
xtalmathfenn: you propose connecting an arduino through something else than USB to the computer?12:23
fennthe arduino would be running the timing-sensitive motion control software12:24
kanzureobviously you should use gsm https://www.usenix.org/system/files/conference/usenixsecurity15/sec15-paper-guri-update.pdf12:24
chris_99heh is that the gsmem paper12:24
xtalmathchris_99: what kind of motion control do you need? CNC & closed loop feedback? or just some pan left/right/up/down where it doesnt matter if it overshot a little?12:24
gradstudentbotWhen is he back from sabbatical?12:24
fennit's stepper motors so open loop12:25
kanzureyes that is the gsmem paper12:25
xtalmathfenn: what is the application? direct write or viewing slides?12:25
chris_99oh it's to image chips12:25
fennfuck if i know12:25
* fenn goes away and stews12:26
xtalmathchris_99: then I can't imagine the setup you propose to be troublesome in the sense of needing tight path control12:26
xtalmathchris_99: the important imaging will always happen when the stage is stationary?12:27
chris_99yeah12:28
xtalmaththen why sweat about such an issue?12:28
xtalmathor your question was more general? if so, I don't have enough experience/data to see if your components are suitable for your steppers...12:29
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chris_99i'm also wondering for other cnc stuff too, just asking in #linuxcnc re. I/O mechanism12:30
nmz787_wkanzure: wiley error dump showing some python stuff http://pastebin.com/pnVzq91p12:31
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nmz787_wkanzure: when I hit this link http://onlinelibrary.wiley.com/store/10.1002/anie.201501779/asset/supinfo/anie_201501779_sm_miscellaneous_information.pdf?v=1&s=7a2594f665c25453d028c5a73dba9b33359563c812:31
nmz787_wkanzure: coming from this accessible link http://onlinelibrary.wiley.com/doi/10.1002/anie.201501779/suppinfo12:32
kanzurethank you12:32
kanzuremod_python haha12:33
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kanzurethat pdf loads for me12:33
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nmz787_wkanzure: anything interesting in the PDF, still doesn't work here12:49
nmz787_wi'm guessing nothing too interesting... since the main paper doesn't seem to indicate any kind of DNA work12:53
nmz787_winteresting to me12:53
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justanotheruserokay, what happens today14:39
kanzure"oh that sounds like an engineering problem"15:02
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kanzure"just call glenn research's tech support line, they will tell you all the details"15:04
kanzureer, glen research's15:05
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jrayhawkwhat's funny about mod_python17:03
kanzurereally you should be using mod_wsgi17:06
jrayhawkwhy17:06
jrayhawkunlike most web developers, i can actually read apache documentation and not run the damned thing in prefork17:07
jrayhawknot that there's clear benefits either way17:07
jrayhawkeither way on mod_wsgi vs. mod_python17:08
jrayhawkmod_wsgi gets more scheduling pressure, mod_python gets interpreter overhead17:08
kanzurehm..17:08
jrayhawkthe scheduling pressure is extra funny when apache starts bouncing between minsparethreads and maxrequestworkers/threadlimit on wsgi17:13
jrayhawkor the prefork equivalent17:13
jrayhawkso web developers first convince themselves that mod_python is useless because they don't know how to configure apache, then they convince themselves that mod_wsgi is useless because they don't know how to configure apache17:14
jrayhawkso then they switch to nginx17:14
jrayhawki will say doing privilege separation without wsgi is pretty horrible17:18
jrayhawkpossible, but horrible17:18
kanzuresurely it's not an apache configuration issue17:21
jrayhawkapache makes sane privilege separation incredibly hard17:24
jrayhawknginx "solves" this problem by just not supporting dynamic execution17:25
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jrayhawkwhich i guess is a good thing in an Apple sort of design philosophy paradigm17:33
gradstudentbotShould this be on ice?17:35
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kanzurehttp://www.glenresearch.com/Reference/oligohouses.html18:05
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kanzurehttp://www.glenresearch.com/Reference/background.html18:15
kanzure"As we endeavor to improve on existing products for DNA synthesis, we focus on areas of weakness in the synthesis process. Our work on the redesign of synthesis columns has culminated in the development of TWIST™ columns for routine synthesis. In addition to being virtually leak-proof, TWIST columns allow users, if necessary, to gain access to the support simply by twisting off the retaining cap."18:16
kanzure"Purification and isolation of synthetic oligodeoxynucleotides remains the most time-consuming and labor-intensive portion of the synthesis process. We are happy to have participated in alleviating this production bottleneck with the introduction of the Poly-Pak™ group of DNA purification products. Poly-Pak cartridges allow users to purify and isolate synthetic oligos in a fraction of the time needed in the past. This technique has ...18:16
kanzure... gained popularity with core facilities, commercial producers, as well as with individual researchers. Glen Research supports the technique with a comprehensive User Guide to DNA Purification."18:17
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kanzure"Ultrafast DNA synthesis - 10 minute deprotection" (december 1993) http://www.glenresearch.com/GlenReports/GR6-22.html18:19
kanzure"Non-enzymatic ligation of single-stranded and duplex DNA" http://www.glenresearch.com/GlenReports/GR10-18.html18:23
kanzurean announcement about the mermade synthesizer http://www.glenresearch.com/GlenReports/GR12-14.html18:24
kanzure"which chemical phosphorylation reagent?" http://www.glenresearch.com/GlenReports/GR12-16.html18:24
kanzure"A rapid method for atomic mutagenesis of nucleic acids" http://www.glenresearch.com/GlenReports/GR13-12.html18:25
kanzure96-well 30-mer synthesizer http://www.glenresearch.com/GlenReports/GR13-14.html (polyplex synthesizer / genemachines)18:25
kanzure"Trityl groups in the 3rd millenium" http://www.glenresearch.com/GlenReports/GR13-13.html <--- this looks good18:26
kanzurephotocleavable biotin http://www.glenresearch.com/GlenReports/GR14-14.html18:27
kanzurepreparation of methyl triester linkages http://www.glenresearch.com/GlenReports/GR14-16.html18:27
kanzureimmobilizing oligos to gold surfaces using thiol anchors http://www.glenresearch.com/GlenReports/GR16-12.html18:28
kanzure"Unicap phosphoramidite, an alternative to acetic anhydride capping" http://www.glenresearch.com/GlenReports/GR17-13.html18:29
kanzure"A detailed comparison of seven commercially available universal supports, which have been examined for their ability to support the synthesis of short and long oligodeoxynucleotides (DNA oligomers) and also oligoribonucleotides (RNA oligomers), is reported herein." http://www.glenresearch.com/GlenReports/GR17-2.html18:31
kanzure"Precautions during packaging of phosphoramidites and transfers into alternate vials" http://www.glenresearch.com/GlenReports/GR19-13.html18:32
kanzurehmm looks like they do a lot of work with ellington18:33
kanzurepreventing impurities http://www.glenresearch.com/GlenReports/GR19-18.html18:34
kanzuresynthesis and deprotection of synthetic RNA http://www.glenresearch.com/GlenReports/GR19-22.html18:34
kanzuretetrazole and other activators http://www.glenresearch.com/GlenReports/GR19-29.html18:34
kanzurephosphonoacetate oligonucleotides with enhanced nuclease resistance http://www.glenresearch.com/GlenReports/GR20-21.html and http://www.glenresearch.com/GlenReports/GR20-2CONT.html18:36
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kanzureoptimal deprotection strategies http://www.glenresearch.com/GlenReports/GR20-24.html18:36
kanzureavoiding trityl loss during oligonucleotide synthesis http://www.glenresearch.com/GlenReports/GR21-19.html18:38
kanzureazobenzene phosphoramidite http://www.glenresearch.com/GlenReports/GR21-27.html (cute)18:38
kanzure"Synthesis of long oligonucleotides" http://www.glenresearch.com/GlenReports/GR21-211.html18:39
kanzure"Alternatives to ammonium hydroxide for deprotection" http://www.glenresearch.com/GlenReports/GR22-18.html18:40
kanzuredepurination http://www.glenresearch.com/GlenReports/GR22-19.html18:40
kanzurechemical phosphorylation http://www.glenresearch.com/GlenReports/GR23-17.html18:41
kanzure"2-Amino-dA is very susceptible to depurination if electron withdrawing protecting groups, for example acyl protection groups, are used. To stabilize the glycosidic bond, strongly electron donating formamidine protecting groups are used in this monomer. We surmise that the N2 formamidine group can activate the N3, which attacks the 3' carbon to displace the phosphonium iodide intermediate, leading to chain scission." ...18:42
kanzure... http://www.glenresearch.com/GlenReports/GR23-28.html18:42
kanzure"Ubiqitous reagent for deprotection" http://www.glenresearch.com/GlenReports/GR26-14.html18:45
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kanzure"Reversible photoswitching of DNA function with azobenzene-tethered DNA" http://www.glenresearch.com/GlenReports/GR27-11.html18:46
kanzure"30% ammonium hydroxide/propylamine/water 2:1:1 (v/v/v) for deprotection" http://www.glenresearch.com/GlenReports/GR27-13.html18:47
kanzure"However, methylamine does have a downside, in that it is used as a reagent in the illicit production of methamphetamine.2 As a result, it is a DEA-regulated substance and in California additional regulatory hurdles have been implemented on the purchase and use of methylamine solutions and salts, making it difficult to procure quickly or easily.3 As a result, we investigated alternative alkylamines that are not under the DEA's list of ...18:47
kanzure... regulated chemicals for our Californian customers. The best candidate we found was propylamine. Propylamine is a liquid at room temperature, boiling at 48 °C, and is miscible with water. However, we found that adding it directly to 30% ammonium hydroxide led to significant degassing of ammonia from the solution. To avoid this, water was added to the solution yielding the final formulation of APA as 30% ammonium ...18:47
kanzure... hydroxide/propylamine/water 2:1:1 (v/v/v)."18:47
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juri_http://www.sciencemag.org/content/349/6249/677.full23:19
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