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| ldlework | kanzure: you still use paperbot? | 01:03 |
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| nmz787_ | github STL diffs are pretty nice: https://github.com/nmz787/python-brlcad-tcl/commit/5e57bef2f8acac4e5609e526759c5503ec129088 | 01:29 |
| nmz787_ | .title | 01:29 |
| yoleaux | Added first implementation of 'connection points' which consist of a … · nmz787/python-brlcad-tcl@5e57bef · GitHub | 01:29 |
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| wrldpcmbl | Per the earlier discussion: Peter Rothman who just completed a thyroid regeneration trial is looking for something new to jump into. He's all about self-experimentation. | 05:51 |
| wrldpcmbl | Thyroid? Maybe thymus. | 05:53 |
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| kanzure | ldlework: paperbot is currently not in use at the moment. | 06:51 |
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| Regex__ | http://medicalxpress.com/news/2016-08-revolutionary-method-brain-single-neuron-resolution.html | 08:03 |
| kanzure | tsk tsk, link to the source, not the journalist garbage | 08:15 |
| kanzure | oh it's mapseq. well in that case, read the channel logs. | 08:16 |
| __mz_o | may you relink the paper. grep didn't provide the link | 08:20 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/High-throughput%20mapping%20of%20single%20neuron%20projections%20by%20sequencing%20of%20barcoded%20RNA%20-%202016.pdf | 08:21 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Rosetta%20brains:%20A%20strategy%20for%20molecularly-annotated%20connectomics%20-%20Marblestone%20-%20Church%20-%20Boyden%20-%202014.pdf | 08:21 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/On%20optical%20detection%20of%20densely%20labeled%20synapses%20in%20neuropil%20and%20mapping%20connectivity%20with%20combinatorially%20multiplexed%20fluorescent%20synaptic%20markers%20-%20Mishchenko%20-%202010.pdf | 08:21 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20of%20complete%20connectivity%20matrix%20for%20connectomics%20by%20sampling%20neural%20connectivity%20with%20fluorescent%20synaptic%20markers%20-%20Mishchenko%20-%202011.pdf | 08:21 |
| kanzure | "Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4327781/ | 08:22 |
| kanzure | http://gnusha.org/logs/2016-07-14.log | 08:22 |
| kanzure | http://gnusha.org/logs/2016-07-13.log | 08:23 |
| __mz_o | thank you | 08:25 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Conneconomics:%20The%20economics%20of%20large-scale%20neural%20connectomics%20-%20Marblestone.pdf | 08:27 |
| __mz_o | also I see its apache, but what is powering the wiki? | 08:27 |
| __mz_o | is it just a git repo? | 08:27 |
| kanzure | while you guys are here, please also read: | 08:27 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Designing%20scalable%20biological%20interfaces%20-%20Marblestone.pdf | 08:27 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20and%20simulation%20of%20neocortical%20microcircuitry.pdf | 08:28 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/Whole-body%20and%20whole-organ%20clearing%20and%20imaging%20techniques%20with%20single-cell%20resolution:%20toward%20organism-level%20systems%20biology%20in%20mammals%20-%20Susaki%20-%202016.pdf | 08:28 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Physical%20principles%20for%20scalable%20neural%20recording%20-%20Marblestone.pdf | 08:28 |
| kanzure | "Continuous genetic recording with self-targeting CRISPR-Cas in human cells" http://biorxiv.org/content/early/2016/05/20/053058 | 08:28 |
| kanzure | "Molecular recordings by directed CRISPR spacer acquisition" http://diyhpl.us/~bryan/papers2/bio/Molecular%20recordings%20by%20directed%20CRISPR%20spacer%20acquisition%20-%20Church%20-%202016.pdf | 08:29 |
| kanzure | __mz_o: wiki is built using ikiwiki, it's essentially a git repository and text-to-html compiler thingy | 08:29 |
| kanzure | instructions for pushing updates are on http://diyhpl.us/wiki/ or you can use https://github.com/kanzure/diyhpluswiki | 08:30 |
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| kanzure | online llvm-based c++ repl http://fiddle.jyt.io/ | 10:38 |
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| ldlework | kanzure: has it bit rotted or do you expect it to work | 12:17 |
| kanzure | it works. | 12:18 |
| ldlework | why don't you use it anymore | 12:18 |
| kanzure | zotero setup is sort of annoying. that might have som bitrot. | 12:18 |
| ldlework | kanzure: have you considered producing a docker image? | 12:18 |
| ldlework | also sorry for the questions randomly | 12:19 |
| kanzure | unfortunately if i was to run a docker container my sysadmin would murder me | 12:19 |
| ldlework | I found it on github | 12:19 |
| ldlework | kanzure: oh yeah? | 12:19 |
| kanzure | yeah he's great. | 12:19 |
| kanzure | always looking out for people, 'n such | 12:19 |
| ldlework | lol can't tell whether you're being sarcastic :) | 12:20 |
| ldlework | This is a wierd channel, I never heard of it before | 12:20 |
| kanzure | there's a little bit of sarcasm but also reality is a blend of everything | 12:20 |
| ldlework | What is "hplusroadmap" supposed to mean | 12:21 |
| kanzure | hplusroadmap is described here- http://diyhpl.us/wiki/hplusroadmap | 12:21 |
| ldlework | Neat. | 12:22 |
| ldlework | Is neuroscience a welcome topic? | 12:23 |
| ldlework | I'm guessing so. | 12:23 |
| kanzure | yep | 12:23 |
| kanzure | here's some stuff http://diyhpl.us/~bryan/papers2/neuro/ | 12:23 |
| ldlework | kanzure: have you heard of the Attention Schema Theory by Graziano? | 12:23 |
| ldlework | I wonder if you could tell me how to feel about it | 12:24 |
| kanzure | yes that was mentioned in this one: | 12:24 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/Delegation%20to%20automaticity:%20the%20driving%20force%20for%20cognitive%20evolution%3f.pdf | 12:24 |
| kanzure | it was recently mentioned here https://news.ycombinator.com/item?id=11853151 | 12:25 |
| ldlework | kanzure: I read Graziano's paper directly, but I'm not expert. Just wondering what others think. | 12:25 |
| kanzure | anyway, i don't really care about consciousness and i think it's a bad idea | 12:26 |
| ldlework | Well, I'm not super interested in the subject experience bit either | 12:26 |
| kanzure | like the question about "subjective experience" is just totally meaningless to me. why should i care whether it's subjective or not? | 12:26 |
| ldlework | I just think its really cool to think that you have attention, an emergent process of signal competition | 12:27 |
| kanzure | i strongly doubt that i have attention | 12:27 |
| ldlework | and then you have another system that "learns" the behavior of this system | 12:27 |
| ldlework | erm... | 12:27 |
| kanzure | or self-awareness. in fact most girls agree with this assessment :). | 12:27 |
| ldlework | hehe | 12:27 |
| ldlework | I like the idea that, since various parts of your brain cannot "query" a process that the brain builds up a model of its behavior, so that other parts of the brain can know what's being attended to | 12:28 |
| kanzure | there was one about some pile of neurons that compute saliency or something, | 12:28 |
| ldlework | I find a lot of enjoyment at sort of just ... I don't know taking in how elegant things can be | 12:28 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/The%20expected%20value%20of%20control:%20an%20integrative%20theory%20of%20anterior%20cingulate%20cortex%20function.pdf | 12:29 |
| kanzure | oh that's called navel gazing | 12:29 |
| ldlework | yeah that | 12:29 |
| ldlework | if you want to equate wonderment with narrowmindedness I suppose :) | 12:30 |
| kanzure | paperbot needs a component written to query across multiple ezproxy servers, or to fetch from scihub instead of only submitting to scihub | 12:32 |
| ldlework | kanzure: if you are interested in improving paperbot I might be motivated to try to build a nice image for it | 12:33 |
| ldlework | There are some other channels on freenode that could benefit from a thing like paperbot (if I understand its function correctly) | 12:33 |
| kanzure | i am sure others would appreciate that kind of pull requet | 12:39 |
| kanzure | .. pull request | 12:39 |
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| abstractmonkey | 2/ | 13:56 |
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| chris_99 | does anyone think 3d printers could come down a lot more in price, i've not really seen a price graph per year | 14:57 |
| kanzure | "The people I know who are trying it have a version where each benzene ring can attach to a different cysteine - so it just rips it apart depending on its isomer. The trouble is designing the cysteines such that they can form both connections to the azo benzene since it is somewhat geometrically constrained." | 14:57 |
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| kanzure | thesnark: *poke* | 16:03 |
| thesnark | hey kanzyre | 16:04 |
| thesnark | erm | 16:04 |
| thesnark | kaz | 16:04 |
| thesnark | fuck | 16:04 |
| thesnark | kanzure | 16:04 |
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| kanzure | molecular assemblies seems to have requested that the content of their patent application be withdrawn or something? not sure what's going on there | 16:14 |
| kanzure | https://patentimages.storage.googleapis.com/pdfs/US9279149.pdf | 16:14 |
| kanzure | http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=9279149.PN.&OS=PN/9279149&RS=PN/9279149 | 16:14 |
| kanzure | content is available there^ | 16:14 |
| kanzure | "The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3' OH, i.e., as found in "natural" deoxyribose and ... | 16:14 |
| kanzure | ... ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems." | 16:14 |
| kanzure | ah here we go, http://pimg-fpiw.uspto.gov/fdd/49/791/092/0.pdf | 16:18 |
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| CaptHindsight | cleavable couplers/linkers | 17:48 |
| kanzure | there are many. | 17:49 |
| CaptHindsight | and they recycle the unused portions | 17:49 |
| CaptHindsight | at least you'll be able to buy or make these | 17:52 |
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| CaptHindsight | were the previous patents on cleavable linkers not broad enough? | 17:54 |
| kanzure | probably this is just a random land grab. "take previous efforts, apply to nucleotides". | 17:54 |
| CaptHindsight | seems like it | 17:55 |
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| kanzure | iirc these people have are related to something about oligonucleotide synthesis methods | 17:55 |
| kanzure | this was mentioned in the ancient backlogs; i don't remember the specifics. maybe it was something about the original abi machines? | 17:56 |
| CaptHindsight | http://www.molecularassemblies.com/team.html | 17:57 |
| kanzure | "before joining Applied Biosystems as the 9th employee ... There he hired and led the R&D group that commercialized phosphoramidite oligonucleotide synthesis and the Models 380A, 380B and 381 DNA synthesizers" | 17:57 |
| CaptHindsight | oligonucleotide synthesis for fun and profit | 17:57 |
| CaptHindsight | well profit anyway | 17:58 |
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| nmz787_ | did I mention that lightning terminator company said no to selling/working with a(another) DNA synthesis project? | 18:14 |
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| streety | I think so nmz787_ something along the lines of get back in touch later in case anything changes? | 18:46 |
| nmz787_ | ah, yeah | 18:50 |
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| fenn | what's this about lightning terminators? | 18:53 |
| fenn | "Lasergen’s key technology, Lightning Terminators™, provides unique photocleavable terminator chemistry with faster reaction kinetics and robust cleavage properties." | 18:55 |
| fenn | meh | 18:55 |
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| fenn | hello DumpsterDiver, been doing a bit of that myself lately | 18:56 |
| kanzure | for all you know they mean a different kind of dumpster | 18:56 |
| fenn | words, what are they? | 18:56 |
| fenn | more slippery than salmon, as soon as you look closely they turn into something else, it's like living in a dream | 18:57 |
| kanzure | were you the one that told me about librivox? | 19:01 |
| kanzure | or am i just confusing this with the something about libvorbis? | 19:01 |
| kanzure | -the | 19:01 |
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| fenn | seems like something that would have come up recently wrt labeled audio transcription training corpus | 19:03 |
| fenn | anyway it wasn't me | 19:03 |
| kanzure | no it was years ago | 19:04 |
| DumpsterDiver | Why punt a dildo. Not a bsd field position all things considered | 19:06 |
| fenn | gnusha.org/logs/2010-06-06.log:11:56 < fenn> fun to see people i know on here http://www.voxforge.org/home/downloads/metrics | 19:08 |
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| fenn | hmm p2p yak shaving/yak trading sounds like a good idea | 19:20 |
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| kanzure | yak genocide | 19:22 |
| fenn | yak derivatives | 19:23 |
| kanzure | thesnark: *poke* | 19:25 |
| kanzure | fenn: perhpas you could look at the current state of the polymerase draft and offer comments or reorganizing the outline? | 19:31 |
| fenn | sounds like work | 19:32 |
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| kanzure | er, yes, porobably | 19:36 |
| fenn | i seem to have misplaced the URL | 19:37 |
| fenn | btw how is the ultrasound thingy coming along? | 19:37 |
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| fenn | ah i found it in a PM | 19:45 |
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| maaku | Is there any basis for B12 as a energy/metabolism booster? | 20:10 |
| maaku | Well there is no UL so I guess it doesn't hurt | 20:23 |
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| kanzure | oh right, ultrasoud stuff | 21:03 |
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