2016-05-30.log

--- Log opened Mon May 30 00:00:15 2016
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kanzurehmph03:38
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esmereldaUp late I see03:52
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esmereldaSo apparently pelvic bone actually changes shape before and then reverses after menopause03:53
esmereldaSo apparently bone remodeling post puberty does happen03:53
esmereldaI'd like to remodel some bones03:54
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kanzurehttp://www.nature.com/news/two-hundred-terabyte-maths-proof-is-largest-ever-1.1999003:58
esmereldaWhy does this seem like an existential crisis to mathematicians?04:04
esmereldaComputers are just another level of abstraction for them04:04
esmereldaPrograms are information-theoretically equivalent to expanded proofs04:05
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maakueh this one is super sensational05:30
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maakubasically someone else had already shown that if it held tue for numbers <=7,825 then it holds true for all numbers by induction05:31
maakuso they just exhaustively checked each set of colorings for the numbers <=7,825.05:32
maakuI'm guessing that the 200TB proof is just each of these checks appended together, although it's a asmall program that did it05:33
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kanzure:frowns: so there's no 200 tb coq proof?05:49
maakuwell there is, but it's literally "Coq proof of possible coloring #1, Coq proof of possible coloring #2, ..."05:52
kanzurewhy are you awake06:10
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maakugood question06:38
* maaku sleep06:38
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kanzuredoes anyone have that old pic of a shotgun or rifle used to blast pellets at petri dishes for transformation reasons07:34
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nmz787abetusk: this is some C code that is seg-faulting on me at the moment... but was offered as a good example of how to use the BRLCAD API (which is largely accessible via command-line tools) to generate rastered g-code: http://brlcad.org/~sean/tmp/g-gcode.patch09:55
nmz787compiled with: gcc -I ../../../brlcad-svn-trunk/src/other/tcl/generic/ -I /usr/brlcad/include/brlcad -L /usr/brlcad/lib/ gcode.c -lbu -lrt09:57
nmz787also see http://brlcad.org/w/images/6/66/Converting_Geometry.pdf      section "2.3 Converters Currently Available in BRL-CAD"09:57
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abetusknmz787, need help?10:21
nmz787well I don't have much time before I have to leave and go do some heat-seal bagging10:24
nmz787My plan was to convert that C code into Python10:24
nmz787but if I could get the C working with little effort, then maybe I'd call it a day and forget about it10:25
abetuskalright.  Is the brlcad python stuff in a useable enough state for anyone to download and start playing with it?10:25
abetuskyeah, seems pretty straight forward, assuming it works the way I think it does10:25
nmz787hmm, it should be pretty OK10:25
abetuskset up some callbacks for 'hits' and 'misses', fill in an array that represents the bitmap10:25
nmz787it basically just appends strings to a list, saves that list to a text file, then shoves that file to BRLCAD as a TCL script10:26
abetuskcompile it with debugging on, run it with valgrind and it should tell you exactly where it crashed10:26
nmz787mmm10:26
nmz787as far as that C code, I simply installed BRLCAD packages in ubuntu, and was able to compile with that one-liner I pasted earlier10:27
nmz787oh, I guess I have included a brlcad-svn repo header... not sure if I would be able to use only the stuff that the ubuntu package installed10:27
abetuskthey updated their landing page10:28
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nmz787I wonder if there is some intermediate format that I could pass to your gbl2ngc program10:28
nmz787since that really seems to do a nice job on the vector-perimeters and infill10:28
abetusk"nice"...still pretty rough I think10:29
abetuskbut yeah, it takes in gerbers...10:29
nmz787apparently shooting rays is the stanadard method for interrogating 3D geometry10:30
nmz787in BRLCAD10:30
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nmz787if we had IRC bitcoin based kudos... I would totally send you some abetusk ;)10:31
abetuskI'm not that familiar with 3d modelers, especially at this level.  I would have though it would be possible to intersect 2d or 3d geometry with your scene10:31
abetuskha, maybe I should set it up10:31
nmz787well you can do a boolean operation with a thin planar rectangle, doing a union will give you a slice of your model... then with that you can view it from top-down, and shoot rays in a raster fashion... finding when the rays 'hit' confirms a pixel10:33
abetuskthat's interesting.  Can you get the underlying 3d geometry as a bag of triangles or something a list of polygons?10:34
nmz787yeah10:34
nmz787BOT is the bag of triangles export10:34
nmz787and I guess STL might count as something10:34
nmz787not sure of list of polygons otherwise10:35
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abetuskok, so how about this:  Intersect with a thin rectangle, get the bag of triangles and only consider lines that sit at the top of the thin triangle.  Test for clockwise or counterclockwise line segments by shooting rays at an epsilon distance to the left and right of each line.  Then stitch up the lines and you have your polygons with holes10:36
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nmz787hmm, I have read a few times on the primitive of CCW but never really fully grasped it10:39
abetuskif brlcad gives you other options, then great but I'm trying to construct it with the bag of triangles and ray shooting primitives10:40
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nmz787I mean using counterclockwise/clockwise as a primitive geometric operation10:40
abetuskclipperlib represents geometry as polygons and polygons with holes, where the outer boundary is in one orientation (clockwise, say) and the holes are in the other (counter clockwise, say).10:40
nmz787this is what I've read and not fully internalized yet: https://www.toptal.com/python/computational-geometry-in-python-from-theory-to-implementation#introducing-ccw10:42
abetuskthat picture is horrible10:43
abetuskhttp://www.angusj.com/delphi/clipper/documentation/Docs/Units/ClipperLib/Functions/Orientation.htm10:44
abetuskhttp://www.angusj.com/delphi/clipper/documentation/Docs/Units/ClipperLib/Functions/SimplifyPolygon.htm10:45
abetusksorry, maybe I should say, what don't you understand about it?10:46
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nmz787mmm, I guess it just doesn't "click" I've read it a few times over the last year or year-and-a-half and still just doesn't really "click" (and I work on geometry calculations for PCB schematics and layout design... so it better sink in soon enough or I will be a sitting duck at work)10:49
abetuskyou have a list of x,y points, say [[0,0], [10,0], [5,5]].  Assuming the last point connects with the first, it makes a triangle (in 2d)10:50
nmz787sure10:51
abetuskif you were sitting in the middle of the triangle and watched an ant traverse the boundary from the first point to the last (then back to the first point) you'd be spinning around10:51
nmz787seems this would be CCW10:51
abetuskyeah10:51
nmz787if (x,y)10:51
abetuskand if the points were laid out as [[0,0], [5,5], [10,0]] ?10:52
nmz787CW10:52
abetuskso that's it.  Nothing magical10:52
nmz787but now I've labelled them, but how does it help?10:52
abetuskhm?  They're labeled from their order.  How does what help?10:53
nmz787i mean what does labelling them afford us?10:53
nmz787"A simple (but non-obvious) computational geometry algorithm for determining convexity is to check that every triplet of consecutive vertices is CCW."10:55
abetuskI'm having a little trouble understanding where you're coming from.  Usually polygons are defined as a list of ordered (x,y) points, indicating the edge boundary.  The triangle above is really three edges, [[0,0], [5,5]], [[0,0],[10,0]] and [[5,5],[10,0]] but in order to make a polygon you need to know an ordering of those edges.  You can see how it gets more complex for more edges.10:56
abetuskhttp://debian.fmi.uni-sofia.bg/~sergei/cgsr/docs/clockwise.htm10:58
abetuskplease don't read that post anymore.  It seems really misleading and bad10:59
nmz787hmm, but isn't a list already ordered?10:59
nmz787haha, ok10:59
nmz787I also won't send it to anyone else then10:59
abetusksure.  I give you an ordered list of points making up the boundary of a polygon.  Tell me whether the polygon is clockwise or counterclockwise10:59
abetuskthat post was talking about the cross product.  Take the cross product of consecutive points and if they all have positive sign (say) it's one orientation, if they all have negative sign it's the other orientation.11:01
nmz787I see that, which gives you concave vs convex11:01
kanzurehttp://www.theonion.com/article/voyager-probe-badly-damaged-after-smashing-end-uni-5299611:01
abetuskif it's mixed, then you can't tell.  If it's concave then it will tell you the orientation11:02
abetuskI think.  I think his statement is at best misleading and at worst flat out wrong11:02
abetuskthe article he links to (which I linked to above) does a good job of explaining.11:03
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archels_kanzure: speaking of infinite torture, The Age of Em is finally coming out this week12:07
kanzurei saw googe had indexed the book's contents the other day.. its chapters started showing up in search results.12:08
archels_cute12:10
archels_I wonder how quickly it's going to turn up on libgen12:10
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maakukanzure: one more reason for draining the channel -- archeological artifacts more than a few cm under the surface of the seafloor are preserved in the anaerobic environment...12:31
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kanzure.title https://news.ycombinator.com/item?id=1180262913:16
yoleauxThe New Napster: How Sci-Hub Is Blowing Up the Academic Publishing Industry | Hacker News13:16
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kanzureinstead of using microwells for the inkjet dna synthesizer, peter clark suggests using stencil templates (also with micro cutouts or whatever).16:50
kanzure... "if you design the template cleverly you can actually centrifuge dna in it. You need one with 2 sets of joined wells. One that forms over the glass slide and one set joined to the first that the solution can simply flow into when you tip the slide - template assembly on its side. That should help with automation."16:51
kanzurei understand his flow idea (sounds like my flooding idea) but not the centrifugation part16:54
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yashgarothyeah you can't centrifuge dna or protein if it's in solution, I mean you can if you want but they're not gonna sediment17:02
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xentrac_I've never understood why not, yashgaroth; shouldn't solvated complexes have a slightly different density than the bulk solvent?20:02
xentrac_and if not, couldn't you just saturate the solution with barium iodide or something in order to change the density of the solvated complexes that aren't solvating your protein?20:03
xentrac_I know I'm pretty naïve about chemistry and thermodynamics20:04
yashgarothas am I; if they're soluble then they won't pellet at g forces achievable in the lab...sure if you use strong salts or solvents or a density gradient they'll separate20:05
xentrac_oh, yeah, I didn't mean they'd come out of solution20:08
yashgarothit's mostly for the prior discussion of centrifuging the template array, written by a mathematician20:10
yashgarotheven with any additives you'd like, centrifuging/separating DNA that small would require g forces that would wreck whatever material the array was built from20:11
xentrac_I was thinking that maybe you could end up with concentrated dissolved DNA in one end of the well20:12
yashgarothyes, but good luck removing the upper layer without pulling out all the DNA; even if you're just trying to speed up reactions by doing so, the necessary solvents would wreck enzyme activity20:13
xentrac_heh20:18
xentrac_also, sorry I didn't see you said "sediment" earlier20:18
xentrac_obviously you're correct; you're not going to be able to overcome electrostatic attraction between polar moieties and adjacent water molecules with the masses of the molecules20:19
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yashgarothI mean there may well be an engineering solution to it, but considering the goal is ultra-low-cost, at-home use, something like a custom ultracentrifuge rotor seems a little counter-productive20:31
jcorganwhat types of solvent are we talking about?20:33
yashgarothalcohol precipitation of DNA is traditional, I'm sure there are others but no one uses them20:36
jcorganso, i'm not familiar with DNA precipitation, but, if i read correctly above, you have DNA completely solvated, right?20:37
yashgarothin aqueous buffers, yes20:38
jcorganand your goal is to selectively precipitate different fractions of it, or is it all at once20:38
jcorgan(sorry, have only been lightly skimming the conversation)20:39
yashgarothI suppose you could do it selectively, not sure if there's a relation between % alcohol and DNA size for precipitation though20:39
jcorganok, so i'm speculating here, but20:40
yashgarothall at once, though20:40
jcorganoh, that's easier20:40
jcorgancall the solvent A20:40
jcorganfind a solvent B with two properties--1) it is miscible with A, and 2) the solute is completely insoluble in B20:41
jcorganthen you can start adding B in incremental amounts until the solvent system can no longer sustain the solute and it precipitates20:41
jcorganthere might even be a range of concentration that provides selective "crashing out"20:42
yashgarothyes that's how it usually works, B doesn't need to be a solvent necessarily but yes20:42
jcorganah, ok, i'm really unfamiliar with the area you guys are discussing but it's a common technique elsewhere, so shouldn't be surprised it's also used there20:44
yashgarothyeah the selective precipitation is popular, best example is proteins in ammonium sulfate but dna/alcohol is the other one20:45
xentrac_yeah, microliters of ethanol are definitely practical for at-home use, unlike ultracentrifuges20:45
jcorganit will take me awhile to catch up to what is obvious in this group of people20:54
yashgarothI have my small domain of biology and very little else, I wouldn't worry20:56
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maaku.title https://arxiv.org/abs/1605.0869521:21
yoleaux[1605.08695] TensorFlow: A system for large-scale machine learning21:21
maakunew tensorflow paper out of google brain21:21
jcorgandata-flow based systems FTW21:22
jcorganbut any indication of the delta between this paper and the earlier TF one?21:23
jcorganalso, might be stating the obvious, but the Keras library provides a really usable abstraction layer atop TF21:27
nmz787you could just use electrophoresis and dialysis tubing/agrose/PAGE gel21:35
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yashgarothI assume that's to do with our prior discussion and not tensorflow, but applying those to 4000 wells is tricky21:54
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