2014-08-23.log

--- Log opened Sat Aug 23 00:00:43 2014
nmz787juri_: do you have to be anoxic to prevent it from turning into alumina? (II would think the next layer wouldn't bind very well if it already had an oxide skin)00:00
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nmz787http://upload.wikimedia.org/wikipedia/commons/6/6f/Photon_Mean_Free_Path.png00:56
nmz787'Mean free path for photons in energy range from 1 keV to 20 MeV for Elements Z = 1 to 100. Based on data from.[5] The discontinuities are due to low density of gas elements. Six bands correspond to neighborhoods of six noble gases'00:56
nmz787so that's why they make lases with those gasses00:56
nmz787:)00:56
nmz787lasers00:56
nmz787.wik mean free path00:57
yoleaux"In physics, the mean free path is the average distance travelled by a moving particle (such as an atom, a molecule, a photon) between successive impacts (collisions),  which modify its direction or energy or other particle properties." — http://en.wikipedia.org/wiki/Mean_free_path00:57
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nmz787.wik mcbj01:35
yoleaux"A break junction is an electronic device which consists of two metal wires separated by a very thin gap, on the order of the inter-atomic spacing (less than a nanometer). This can be done by physically pulling the wires apart or through chemical etching or electromigration." — http://en.wikipedia.org/wiki/Break_junction01:36
nmz787paperbot: http://www.nature.com/srep/2012/120710/srep00501/full/srep00501.html01:36
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fsrep0050101:36
nmz787(that may be open)01:36
nmz787.title01:36
nmz787.title http://www.nature.com/srep/2012/120710/srep00501/full/srep00501.html01:36
yoleauxSingle-Molecule Electrical Random Resequencing of DNA and RNA01:36
yoleauxnmz787: Sorry, that command (.title) crashed.01:36
nmz787"Single base molecules on a DNA molecule in a solution are identified via a tunnelling current that passes between nanoelectrodes. Nanogaps of 0.8 nm were fabricated using a nano-MCBJ. A constant DC voltage of 0.4 V was applied between the nanoelectrodes, and electrical signals were measured at a sampling rate of 10 KHz."01:37
nmz787daaaannnnnnnggggg01:37
ebowden_Oh, heard of that a few months ago, I think.01:39
nmz787"The fabrication procedures for MCBJs are described elsewhere.29 First, we coated a phosphor bronze substrate with a thin polyimide layer for electrical insulation. A gold nanojunction was then fabricated using electron beam lithography and a subsequent lift-off process. The junction was then exposed to isotropic reactive ion etching using CF4/O2 gas to remove the underlying polyimide and obtain a free-standing gold nanobridge. The MCBJ sample ...01:40
nmz787... was mounted in a three-point bend configuration. The substrate was then bent and the junction broken mechanically to form a pair of gold nanoelectrodes. The junction conductance was monitored using a Keithley 6487 picoammeter (Keithley) under a DC bias voltage of 0.1 V. A 10-k resistor was connected in series during this process to protect the junction from overcurrent-induced electromigration failure. Special care was taken while adjusting ...01:40
nmz787... the electrode gap size by a self-breaking technique."01:41
nmz787that actually doesn't sound terribly hard01:41
nmz787heh, I was just reading about femtoampere design last night01:42
ebowden_So, how fast can this take the measurements?01:44
nmz787huh http://www.quantumbiosystems.com/get/index.html?lang=en01:45
nmz787"Raw quantum sequencing data are freely available for scientific and research use, allowing you, for example, to develop your own algorithms and software for quantum sequencing."01:46
nmz787All data in this site belong to Quantum Biosystems. These pre-publication data are preliminary and may contain errors. The goal of our policy is that early release should enable the progress of science. The data is published under a Creative Commons licence Attribution-NonCommercial 3.0 (CC-BY-NC 3.0)01:46
nmz787ebowden_: probably very fast01:46
ebowden_Do they make any claims on speed in this paper?01:47
ebowden_(Sequencing speed)01:48
nmz787looks like the use the term ms01:48
nmz787but i am tired01:48
nmz787i think they're saying at least 2 ms per base01:49
nmz787but the junction is only 0.8nm wide, so you can parallelize the hell out of this, assuming you come up with a good fab technique01:49
nmz787'the characteristic dwell time for single bases was 0.8 ms, as shown in Fig. 2e'01:50
nmz787supplement http://www.nature.com/srep/2012/120710/srep00501/extref/srep00501-s1.doc01:51
nmz787whoa bunnie is on their team01:52
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ebowden_Who's bunnie?01:55
caterna well known hardware hacker01:56
caternhttp://en.wikipedia.org/wiki/Andrew_Huang01:56
ebowden_Huh.01:56
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ebowden_Was this sequencer the first to work in that manner?01:57
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nmz787ebowden_: probably not02:05
nmz787nano-whatever has been all the rage for years now02:05
nmz787the fab technique for that was pretty cool is all I thought02:06
nmz787nothing like the protein pores some use02:06
nmz787or annealing-based porous silicon filter things02:06
nmz787sorta like TEM grids02:07
nmz787(i may have just thought TEM grid like things would be good for separating proteins from DNA, I mightn't of seen it in a paper)02:08
nmz787prob some that use carbon nanotubes or something02:08
nmz787just look at some of the reference names on that paper02:08
altersidwell, now its nano no mo', quantum here I cum02:08
altersidnice for bunnie, they look like they have some serious brainpower02:10
nmz787huh, so with ParahSailin's 2 billion 18mer human genome fragment comment earlier02:10
nmz7872000000000 milliseconds to days is 23.148102:10
nmz787so parallelizing would be pretty quick02:11
nmz787even if it was macro scale02:11
nmz787parallelizing02:11
nmz787i.e. that fab just replicated on an assembly line02:11
nmz787rather than on-chip density scaling02:11
nmz787or per-chip02:11
* nmz787 sleeps02:14
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dpkpaperbot: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=497646302:34
paperbothttp://libgen.org/scimag/get.php?doi=10.1109%2FDCC.2009.4202:34
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kanzurehttps://www.crowdsupply.com/xipiter/usbcondom06:58
ParahSailinalso 547233228 unique 15mers, so about 50% of the space07:09
kanzure"Also the big problem for BSD with original advertising clause is that legally they had to list a dozen authors for some of the drivers, back when people would contribute under license terms that said "Use or marketing of this software must include the statement: "Driver written by Jonathan Cline jcline@ieee.org". That is one reason they added the "no advertising" clause to BSD later."07:15
abetuskkanzure, online as in this room or somewhere else?07:37
kanzureemail07:38
abetuskI emailed him yesterday07:38
kanzurehe didn't reply? what a slacker07:39
kanzurehe replied to something i sent him last nght07:39
kanzure*night07:39
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juri_nmz787: this is casting, not printing. ;)11:16
jrayhawk.title http://www.youtube.com/watch?v=yOon17suyaI11:26
yoleauxResistance Training, Brain Structure, and Brain Function11:26
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pi-paperbot: http://www.ncbi.nlm.nih.gov/pubmed/1239511012:32
nmz787pi-: thanks! now where's that bottle of ashwaganda i bought years ago?12:40
pi-:)12:41
kanzure.title12:42
yoleauxAxon- or dendrite-predominant outgrowth induced ... [Neuroreport. 2002]12:42
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nmz787first part of a 3-part series... very very good... http://edn.com/design/analog/4368681/Design-femtoampere-circuits-with-low-leakage-part-one13:04
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nmz787http://jeb.biologists.org/content/217/11/1833.113:58
nmz787.title13:58
yoleauxParasitic fig wasps bore with zinc-tipped drill bit13:58
nmz787video here http://www.popularmechanics.com/science/environment/found-the-first-metal-plated-syringe-in-a-living-creature-16838120?click=pm_latest13:58
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kanzure"Plastic bag was bore with zinc trapped yelling bit"13:59
kanzure"what?"13:59
kanzure"how did they know my brain wallet passphrase?"14:00
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nmz787http://www.popularmechanics.com/science/environment/the-first-gear-discovered-in-nature-1591643314:03
kanzurecc gene_hacker14:04
nmz787.title http://www.sciencemag.org/content/341/6151/125414:04
yoleauxInteracting Gears Synchronize Propulsive Leg Movements in a Jumping Insect14:04
nmz787'Even stranger is that the issus doesn't keep these gears throughout its life cycle. As the adolescent insect grows, it molts half a dozen times, upgrading its exoskeleton (gears included) for larger and larger versions. But after its final molt into adulthood—poof, the gears are gone. The adult syncs its legs by friction like all the other planthoppers. "I'm gobsmacked," says Sutton. "We have a hypothesis as to why this is the case, but ...14:04
nmz787... we can't tell you for sure." Their idea: If one of the gear teeth were to slip and break in an adult (the researchers observed this in adolescent bugs), its jumping ability would be hindered forever. With no more molts, it would have no chance to grow more gears. And with every bound, "the whole system might slip, accelerating damage to the rest of the gear teeth," Sutton says. "Just like if your car has a gear train missing a tooth. Every ...14:05
nmz787... time you get to that missing tooth, the gear train jerks."'14:05
nshwow14:19
nshneat14:19
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nshpaperbot, http://link.springer.com/content/pdf/10.1007%2F978-3-642-31912-9_16.pdf16:57
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/8988e3727afbb40b32e0bc01c09db62f.txt16:57
nshpaperbot, http://link.springer.com/chapter/10.1007/978-3-642-31912-9_1616:58
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/53662cbd47d8822c90cf548181ad2810.txt16:58
kanzurehttp://nordicapis.com/legos-api-strategy-resourcing-developers-building-business-case/17:15
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nmz787pfft, fiction19:20
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kanzuregene_hacker: insect gear thing http://www.sciencemag.org/content/341/6151/125419:22
gene_hackerseen it already19:22
gene_hackerbe interesting to see if it's actually superior to the involute profile as far as wear goes19:23
gene_hackerhey do you know someone made a universal constructor?(for a universe consisting of plastic blocks)19:24
kanzureminecraft?19:25
gene_hackerhttp://www.sciencedirect.com/science/article/pii/S092188901300146219:25
kanzure.title19:25
yoleauxAn architecture for universal construction via modular robotic components19:25
gene_hackerwait did someone do it in minecraft now too?19:25
kanzureprobably?19:25
gene_hackerno real life19:25
kanzurensh_: ping?19:26
kanzureor maybe jrayhawk would be better for that q19:26
kanzurepaperbot: http://www.sciencedirect.com/science/article/pii/S092188901300146219:26
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/8af183b63698e909c84b816158831deb.txt19:26
gene_hackerunfortunately, it's not viable19:26
gene_hackerit makes too many errors for unassisted replication19:26
jrayhawki doubt it19:27
jrayhawkat least, not without a lot of cheat mods19:27
gene_hackeryou can just email the author of the paper...19:27
gene_hackerI think they have components up on github too19:27
kanzureusually paperbot works :(19:27
gene_hackerhttps://github.com/mattmoses/MJMCS19:28
gene_hackerhere's components19:28
gene_hackererrr... nothing appears to be there19:29
gene_hackerrecently talked with one of the authors19:29
kanzurei was introduced to matt by tihamer toth-fejel19:30
kanzurei think tihamer worked at nanorex (nanoengineer)19:30
gene_hackernah one of the other guys19:32
gene_hackerapparently progress is slow because everyone wants to fund human co-robots19:32
kanzuregross19:33
kanzurebtw what was the conference?19:33
gene_hackerUC wasn't shown though19:33
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nmz787http://diyhpl.us/~nmz787/pdf/An_architecture_for_universal_construction_via_modular_robotic_components.pdf20:32
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kanzurehttp://grabcad.com/library/shock-free-high-speed-intermittent-gearing-121:15
kanzuredpk: ping21:20
nmz787dpk: https://github.com/kanzure/paperbot/blob/master/modules/papers.py#L10821:20
nmz787or thereabouts21:20
nmz787seems like DRY is being violated, and it could be wrapped in a for loop21:21
kanzureDRY is most definitely being violated21:21
nmz787so we could put the URL into some proxy URL as a substring21:21
nmz787if successful paper download fails21:21
kanzureyou would probably do this: requests.get("http://sciencedirect.com/", proxies={"http": "http://localhost:84841"}) and localhost:84841 would be responsible for doing ezproxy things21:24
kanzureif you feel like deleting huge chunks of paperbot code go right ahead21:25
nmz787http://docs.python-requests.org/en/latest/user/advanced/#proxies21:27
nmz787doesn't seem like you can give that a list though21:27
nmz787so you'd still need a for loop21:27
nmz787starting with http:http (or proxies=None)21:28
nmz787whatever the correct API is21:28
kanzurelocalhost:84841 would have the list itself21:29
kanzurebecause you only have access to one ezproxy server or whatever21:29
kanzureinstead of trying that entire list where 99% are inaccessible21:29
nmz787i commonly use 321:32
nmz787but i may not be the only proxy host on there21:32
nmz787what if some other person wants to be a proxy, not having a list means it isn't a one-line addition to the list file21:32
nmz787or maybe if not a list, a dict with a priority associated with each proxy URL21:33
nmz787would my proxy need a callback too, in case the returned pdf_url failed?21:34
nmz787since my proxy would itself have multiple urls to try21:35
kanzureif they want to add one it can be an extra file in a directory that gets scanned for configs21:35
kanzureproxy should just proxy http requests and return back the content from the remote server21:35
kanzurepaperbot is responsible for parsing or saving pdf21:36
kanzure*parsing html or saving pdf21:36
nmz787but often a proxy i have creds to fails21:36
nmz787and i need to try the next21:36
nmz787so would I have a separate socket for each?21:36
nmz787and thus paperbot's list of proxies would have 3 listings for me21:37
nmz787(since I have 3 proxies)21:37
kanzureproxy server can return an integer as an http header to paperbot in the http response21:37
kanzurepaperbot will look at the http header and then determine whether or not to send another request21:37
kanzurethe next request can include an incoming http header that says to try the next one21:37
kanzureproxy looks at incoming http request header and thinks real hard about it21:37
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nmz787ok21:38
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nmz787kanzure: this example look OK? http://mitmproxy.org/doc/scripting/libmproxy.html21:47
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kanzureyup21:52
kanzurethat's what i've used in the past21:52
kanzurei was using libmproxy to do http caching21:53
kanzurewith some rather deep http request/response modification because i wasn't thinking straight at the time..21:53
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kanzure.tell fenn http://en.wikipedia.org/wiki/Project_Habakkuk22:42
yoleauxkanzure: I'll pass your message to fenn.22:42
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--- Log closed Sun Aug 24 00:00:44 2014

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