--- Log opened Fri Aug 14 00:00:40 2015
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00:36 < nmz787> the 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-heights
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01:25 < nmz787> kanzure: that intel history link is pretty awesome, especially since I am working on test equipment development
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04:05 < kanzure> https://www.reddit.com/r/chemistry/comments/3gx7kg/seeking_collaborators_for_a_selffunded/
04:07 < gradstudentbot> No no no no! Use your key commands!
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07:36 < kanzure> greetings CyberelfJess
07:41 < fenn> who is trollzyme?
07:41 < fenn> or rather, why use a new account
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07:43 < kanzure> one-directional privacy
07:44 < fenn> "There are already DNA synthesizers on the market that work nicely" lol yeah right
07:45 < fenn> efficient market fallacy
07:45 < kanzure> praise unto the market
07:45 < kanzure> take the wheel, supply side jesus
07:49 < fenn> some 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.jpg
07:55 < kanzure> it's weird how you have to argue for every inch everywhere you go even if you're offering money
07:55 < kanzure> just once i'd rather not explain the entire philosophical context of everything ever
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08:09 < xtalmath> that clip just stays so incredible https://www.youtube.com/watch?v=H_nnZntSYjo
08:11 < kanzure> .title
08:11 < yoleaux> The Tianjin Explosion - Stabilized - YouTube
08:22 < JayDugger> Good morning, everyone.
08:24 < kanzure> are you guys done with your disaster porn yet
08:25 < xtalmath> its not disaster porn, its a reminder of how important safety precautions are
08:42  * fenn straps on a hard hat in case oakland explodes
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11:38 < kanzure> beep boop
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11:55 < chris_99> i'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 USB
11:56 < chris_99> i'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 everything
11:57 < kanzure> linuxcnc
11:57 < chris_99> so i just looked at their page, isn't it a full distro though?
11:57 < kanzure> i dunno if you can use linuxcnc without realtime mode, but my guess is probably, so just throw it in a virtual machine
11:59 < chris_99> i was wondering if theres not a core piece of their distro i could just install instead, or is it all heavily interlinked
12:01 < kanzure> i'm not the right person to ask, try fenn or CaptHindsight or #linuxcnc
12:02 < chris_99> ta, i'll try in their channel
12:02 < fenn> use grbl and arduino unless you specifically need the dev board
12:03 < chris_99> i don't have any arduinos
12:03 < fenn> USB is terrible for motion control and negates the benefit of linuxcnc
12:03 < fenn> also i don't think linuxcnc even works with any usb libraries because the devs hate it
12:03 < chris_99> ah heh
12:04 < fenn> actually that's not right, but it will be hard to set up something controlling motion via usb
12:04 < kanzure> ah i see
12:04 < kanzure> i was hoping that using linuxcnc would make up for the horribleness of usb
12:04 < fenn> no, it's the other way around
12:04 < fenn> usb is so terrible even linuxcnc can't fix it
12:04 < kanzure> some sort of net project karmic measurement
12:04 < kanzure> ah i see.
12:05 < chris_99> what other candidates are there that i could use on a laptop, i can only think of ethernet, but is that much better
12:06 < fenn> just buy an atmega328 for $5 sheesh
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12:06 < chris_99> i don't want to use arduinos though :P
12:09 < kanzure> fenn: did you hang out with t12 by any chance?
12:10 < fenn> no
12:14 < kanzure> got a reply about cambrian genomics.. at least they are topical.
12:14 < kanzure> having trouble figuring out why i know P212121.. he's not in my stalkmatrix, but i know about p212121.com?
12:23 < xtalmath> fenn: you propose connecting an arduino through something else than USB to the computer?
12:24 < fenn> the arduino would be running the timing-sensitive motion control software
12:24 < kanzure> obviously you should use gsm https://www.usenix.org/system/files/conference/usenixsecurity15/sec15-paper-guri-update.pdf
12:24 < chris_99> heh is that the gsmem paper
12:24 < xtalmath> chris_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 < gradstudentbot> When is he back from sabbatical?
12:25 < fenn> it's stepper motors so open loop
12:25 < kanzure> yes that is the gsmem paper
12:25 < xtalmath> fenn: what is the application? direct write or viewing slides?
12:25 < chris_99> oh it's to image chips
12:25 < fenn> fuck if i know
12:26  * fenn goes away and stews
12:26 < xtalmath> chris_99: then I can't imagine the setup you propose to be troublesome in the sense of needing tight path control
12:27 < xtalmath> chris_99: the important imaging will always happen when the stage is stationary?
12:28 < chris_99> yeah
12:28 < xtalmath> then why sweat about such an issue?
12:29 < xtalmath> or your question was more general? if so, I don't have enough experience/data to see if your components are suitable for your steppers...
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12:30 < chris_99> i'm also wondering for other cnc stuff too, just asking in #linuxcnc re. I/O mechanism
12:31 < nmz787_w> kanzure: wiley error dump showing some python stuff http://pastebin.com/pnVzq91p
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12:31 < nmz787_w> kanzure: 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=7a2594f665c25453d028c5a73dba9b33359563c8
12:32 < nmz787_w> kanzure: coming from this accessible link http://onlinelibrary.wiley.com/doi/10.1002/anie.201501779/suppinfo
12:32 < kanzure> thank you
12:33 < kanzure> mod_python haha
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12:33 < kanzure> that pdf loads for me
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12:49 < nmz787_w> kanzure: anything interesting in the PDF, still doesn't work here
12:53 < nmz787_w> i'm guessing nothing too interesting... since the main paper doesn't seem to indicate any kind of DNA work
12:53 < nmz787_w> interesting to me
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14:39 < justanotheruser> okay, what happens today
15:02 < kanzure> "oh that sounds like an engineering problem"
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15:04 < kanzure> "just call glenn research's tech support line, they will tell you all the details"
15:05 < kanzure> er, glen research's
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17:03 < jrayhawk> what's funny about mod_python
17:06 < kanzure> really you should be using mod_wsgi
17:06 < jrayhawk> why
17:07 < jrayhawk> unlike most web developers, i can actually read apache documentation and not run the damned thing in prefork
17:07 < jrayhawk> not that there's clear benefits either way
17:08 < jrayhawk> either way on mod_wsgi vs. mod_python
17:08 < jrayhawk> mod_wsgi gets more scheduling pressure, mod_python gets interpreter overhead
17:08 < kanzure> hm..
17:13 < jrayhawk> the scheduling pressure is extra funny when apache starts bouncing between minsparethreads and maxrequestworkers/threadlimit on wsgi
17:13 < jrayhawk> or the prefork equivalent
17:14 < jrayhawk> so 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 apache
17:14 < jrayhawk> so then they switch to nginx
17:18 < jrayhawk> i will say doing privilege separation without wsgi is pretty horrible
17:18 < jrayhawk> possible, but horrible
17:21 < kanzure> surely it's not an apache configuration issue
17:24 < jrayhawk> apache makes sane privilege separation incredibly hard
17:25 < jrayhawk> nginx "solves" this problem by just not supporting dynamic execution
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17:33 < jrayhawk> which i guess is a good thing in an Apple sort of design philosophy paradigm
17:35 < gradstudentbot> Should this be on ice?
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18:05 < kanzure> http://www.glenresearch.com/Reference/oligohouses.html
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18:15 < kanzure> http://www.glenresearch.com/Reference/background.html
18:16 < 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 ...
18:17 < 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."
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18:19 < kanzure> "Ultrafast DNA synthesis - 10 minute deprotection" (december 1993) http://www.glenresearch.com/GlenReports/GR6-22.html
18:23 < kanzure> "Non-enzymatic ligation of single-stranded and duplex DNA" http://www.glenresearch.com/GlenReports/GR10-18.html
18:24 < kanzure> an announcement about the mermade synthesizer http://www.glenresearch.com/GlenReports/GR12-14.html
18:24 < kanzure> "which chemical phosphorylation reagent?" http://www.glenresearch.com/GlenReports/GR12-16.html
18:25 < kanzure> "A rapid method for atomic mutagenesis of nucleic acids" http://www.glenresearch.com/GlenReports/GR13-12.html
18:25 < kanzure> 96-well 30-mer synthesizer http://www.glenresearch.com/GlenReports/GR13-14.html (polyplex synthesizer / genemachines)
18:26 < kanzure> "Trityl groups in the 3rd millenium" http://www.glenresearch.com/GlenReports/GR13-13.html <--- this looks good
18:27 < kanzure> photocleavable biotin http://www.glenresearch.com/GlenReports/GR14-14.html
18:27 < kanzure> preparation of methyl triester linkages http://www.glenresearch.com/GlenReports/GR14-16.html
18:28 < kanzure> immobilizing oligos to gold surfaces using thiol anchors http://www.glenresearch.com/GlenReports/GR16-12.html
18:29 < kanzure> "Unicap phosphoramidite, an alternative to acetic anhydride capping" http://www.glenresearch.com/GlenReports/GR17-13.html
18:31 < 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.html
18:32 < kanzure> "Precautions during packaging of phosphoramidites and transfers into alternate vials" http://www.glenresearch.com/GlenReports/GR19-13.html
18:33 < kanzure> hmm looks like they do a lot of work with ellington
18:34 < kanzure> preventing impurities http://www.glenresearch.com/GlenReports/GR19-18.html
18:34 < kanzure> synthesis and deprotection of synthetic RNA http://www.glenresearch.com/GlenReports/GR19-22.html
18:34 < kanzure> tetrazole and other activators http://www.glenresearch.com/GlenReports/GR19-29.html
18:36 < kanzure> phosphonoacetate oligonucleotides with enhanced nuclease resistance http://www.glenresearch.com/GlenReports/GR20-21.html and http://www.glenresearch.com/GlenReports/GR20-2CONT.html
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18:36 < kanzure> optimal deprotection strategies http://www.glenresearch.com/GlenReports/GR20-24.html
18:38 < kanzure> avoiding trityl loss during oligonucleotide synthesis http://www.glenresearch.com/GlenReports/GR21-19.html
18:38 < kanzure> azobenzene phosphoramidite http://www.glenresearch.com/GlenReports/GR21-27.html (cute)
18:39 < kanzure> "Synthesis of long oligonucleotides" http://www.glenresearch.com/GlenReports/GR21-211.html
18:40 < kanzure> "Alternatives to ammonium hydroxide for deprotection" http://www.glenresearch.com/GlenReports/GR22-18.html
18:40 < kanzure> depurination http://www.glenresearch.com/GlenReports/GR22-19.html
18:41 < kanzure> chemical phosphorylation http://www.glenresearch.com/GlenReports/GR23-17.html
18:42 < 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.html
18:45 < kanzure> "Ubiqitous reagent for deprotection" http://www.glenresearch.com/GlenReports/GR26-14.html
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18:46 < kanzure> "Reversible photoswitching of DNA function with azobenzene-tethered DNA" http://www.glenresearch.com/GlenReports/GR27-11.html
18:47 < kanzure> "30% ammonium hydroxide/propylamine/water 2:1:1 (v/v/v) for deprotection" http://www.glenresearch.com/GlenReports/GR27-13.html
18:47 < 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)."
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23:19 < juri_> http://www.sciencemag.org/content/349/6249/677.full
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--- Log closed Sat Aug 15 00:00:41 2015