--- Log opened Mon May 30 00:00:15 2016
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03:38 < kanzure> hmph
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03:52 < esmerelda> Up late I see
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03:53 < esmerelda> So apparently pelvic bone actually changes shape before and then reverses after menopause
03:53 < esmerelda> So apparently bone remodeling post puberty does happen
03:54 < esmerelda> I'd like to remodel some bones
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03:58 < kanzure> http://www.nature.com/news/two-hundred-terabyte-maths-proof-is-largest-ever-1.19990
04:04 < esmerelda> Why does this seem like an existential crisis to mathematicians?
04:04 < esmerelda> Computers are just another level of abstraction for them
04:05 < esmerelda> Programs are information-theoretically equivalent to expanded proofs
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05:30 < maaku> eh this one is super sensational
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05:31 < maaku> basically someone else had already shown that if it held tue for numbers <=7,825 then it holds true for all numbers by induction
05:32 < maaku> so they just exhaustively checked each set of colorings for the numbers <=7,825.
05:33 < maaku> I'm guessing that the 200TB proof is just each of these checks appended together, although it's a asmall program that did it
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05:49 < kanzure> :frowns: so there's no 200 tb coq proof?
05:52 < maaku> well there is, but it's literally "Coq proof of possible coloring #1, Coq proof of possible coloring #2, ..."
06:10 < kanzure> why are you awake
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06:38 < maaku> good question
06:38  * maaku sleep
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07:34 < kanzure> does anyone have that old pic of a shotgun or rifle used to blast pellets at petri dishes for transformation reasons
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09:55 < nmz787> abetusk: 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.patch
09:57 < nmz787> compiled with: gcc -I ../../../brlcad-svn-trunk/src/other/tcl/generic/ -I /usr/brlcad/include/brlcad -L /usr/brlcad/lib/ gcode.c -lbu -lrt
09:57 < nmz787> also see http://brlcad.org/w/images/6/66/Converting_Geometry.pdf      section "2.3 Converters Currently Available in BRL-CAD"
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10:21 < abetusk> nmz787, need help?
10:24 < nmz787> well I don't have much time before I have to leave and go do some heat-seal bagging
10:24 < nmz787> My plan was to convert that C code into Python
10:25 < nmz787> but if I could get the C working with little effort, then maybe I'd call it a day and forget about it
10:25 < abetusk> alright.  Is the brlcad python stuff in a useable enough state for anyone to download and start playing with it?
10:25 < abetusk> yeah, seems pretty straight forward, assuming it works the way I think it does
10:25 < nmz787> hmm, it should be pretty OK
10:25 < abetusk> set up some callbacks for 'hits' and 'misses', fill in an array that represents the bitmap
10:26 < nmz787> it basically just appends strings to a list, saves that list to a text file, then shoves that file to BRLCAD as a TCL script
10:26 < abetusk> compile it with debugging on, run it with valgrind and it should tell you exactly where it crashed
10:26 < nmz787> mmm
10:27 < nmz787> as far as that C code, I simply installed BRLCAD packages in ubuntu, and was able to compile with that one-liner I pasted earlier
10:27 < nmz787> oh, 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 installed
10:28 < abetusk> they updated their landing page
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10:28 < nmz787> I wonder if there is some intermediate format that I could pass to your gbl2ngc program
10:28 < nmz787> since that really seems to do a nice job on the vector-perimeters and infill
10:29 < abetusk> "nice"...still pretty rough I think
10:29 < abetusk> but yeah, it takes in gerbers...
10:30 < nmz787> apparently shooting rays is the stanadard method for interrogating 3D geometry
10:30 < nmz787> in BRLCAD
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10:31 < nmz787> if we had IRC bitcoin based kudos... I would totally send you some abetusk ;)
10:31 < abetusk> I'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 scene
10:31 < abetusk> ha, maybe I should set it up
10:33 < nmz787> well 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 pixel
10:34 < abetusk> that's interesting.  Can you get the underlying 3d geometry as a bag of triangles or something a list of polygons?
10:34 < nmz787> yeah
10:34 < nmz787> BOT is the bag of triangles export
10:34 < nmz787> and I guess STL might count as something
10:35 < nmz787> not sure of list of polygons otherwise
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10:36 < abetusk> ok, 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 holes
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10:39 < nmz787> hmm, I have read a few times on the primitive of CCW but never really fully grasped it
10:40 < abetusk> if brlcad gives you other options, then great but I'm trying to construct it with the bag of triangles and ray shooting primitives
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10:40 < nmz787> I mean using counterclockwise/clockwise as a primitive geometric operation
10:40 < abetusk> clipperlib 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).
10:42 < nmz787> this is what I've read and not fully internalized yet: https://www.toptal.com/python/computational-geometry-in-python-from-theory-to-implementation#introducing-ccw
10:43 < abetusk> that picture is horrible
10:44 < abetusk> http://www.angusj.com/delphi/clipper/documentation/Docs/Units/ClipperLib/Functions/Orientation.htm
10:45 < abetusk> http://www.angusj.com/delphi/clipper/documentation/Docs/Units/ClipperLib/Functions/SimplifyPolygon.htm
10:46 < abetusk> sorry, maybe I should say, what don't you understand about it?
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10:49 < nmz787> mmm, 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)
10:50 < abetusk> you 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)
10:51 < nmz787> sure
10:51 < abetusk> if 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 around
10:51 < nmz787> seems this would be CCW
10:51 < abetusk> yeah
10:51 < nmz787> if (x,y)
10:52 < abetusk> and if the points were laid out as [[0,0], [5,5], [10,0]] ?
10:52 < nmz787> CW
10:52 < abetusk> so that's it.  Nothing magical
10:52 < nmz787> but now I've labelled them, but how does it help?
10:53 < abetusk> hm?  They're labeled from their order.  How does what help?
10:53 < nmz787> i mean what does labelling them afford us?
10:55 < nmz787> "A simple (but non-obvious) computational geometry algorithm for determining convexity is to check that every triplet of consecutive vertices is CCW."
10:56 < abetusk> I'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.
10:58 < abetusk> http://debian.fmi.uni-sofia.bg/~sergei/cgsr/docs/clockwise.htm
10:59 < abetusk> please don't read that post anymore.  It seems really misleading and bad
10:59 < nmz787> hmm, but isn't a list already ordered?
10:59 < nmz787> haha, ok
10:59 < nmz787> I also won't send it to anyone else then
10:59 < abetusk> sure.  I give you an ordered list of points making up the boundary of a polygon.  Tell me whether the polygon is clockwise or counterclockwise
11:01 < abetusk> that 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 < nmz787> I see that, which gives you concave vs convex
11:01 < kanzure> http://www.theonion.com/article/voyager-probe-badly-damaged-after-smashing-end-uni-52996
11:02 < abetusk> if it's mixed, then you can't tell.  If it's concave then it will tell you the orientation
11:02 < abetusk> I think.  I think his statement is at best misleading and at worst flat out wrong
11:03 < abetusk> the article he links to (which I linked to above) does a good job of explaining.
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12:07 < archels_> kanzure: speaking of infinite torture, The Age of Em is finally coming out this week
12:08 < kanzure> i saw googe had indexed the book's contents the other day.. its chapters started showing up in search results.
12:10 < archels_> cute
12:10 < archels_> I wonder how quickly it's going to turn up on libgen
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12:31 < maaku> kanzure: 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...
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13:16 < kanzure> .title https://news.ycombinator.com/item?id=11802629
13:16 < yoleaux> The New Napster: How Sci-Hub Is Blowing Up the Academic Publishing Industry | Hacker News
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16:50 < kanzure> instead of using microwells for the inkjet dna synthesizer, peter clark suggests using stencil templates (also with micro cutouts or whatever).
16:51 < 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."
16:54 < kanzure> i understand his flow idea (sounds like my flooding idea) but not the centrifugation part
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17:02 < yashgaroth> yeah you can't centrifuge dna or protein if it's in solution, I mean you can if you want but they're not gonna sediment
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20:02 < xentrac_> I've never understood why not, yashgaroth; shouldn't solvated complexes have a slightly different density than the bulk solvent?
20:03 < 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?
20:04 < xentrac_> I know I'm pretty naïve about chemistry and thermodynamics
20:05 < yashgaroth> as 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 separate
20:08 < xentrac_> oh, yeah, I didn't mean they'd come out of solution
20:10 < yashgaroth> it's mostly for the prior discussion of centrifuging the template array, written by a mathematician
20:11 < yashgaroth> even with any additives you'd like, centrifuging/separating DNA that small would require g forces that would wreck whatever material the array was built from
20:12 < xentrac_> I was thinking that maybe you could end up with concentrated dissolved DNA in one end of the well
20:13 < yashgaroth> yes, 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 activity
20:18 < xentrac_> heh
20:18 < xentrac_> also, sorry I didn't see you said "sediment" earlier
20:19 < 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 molecules
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20:31 < yashgaroth> I 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-productive
20:33 < jcorgan> what types of solvent are we talking about?
20:36 < yashgaroth> alcohol precipitation of DNA is traditional, I'm sure there are others but no one uses them
20:37 < jcorgan> so, i'm not familiar with DNA precipitation, but, if i read correctly above, you have DNA completely solvated, right?
20:38 < yashgaroth> in aqueous buffers, yes
20:38 < jcorgan> and your goal is to selectively precipitate different fractions of it, or is it all at once
20:39 < jcorgan> (sorry, have only been lightly skimming the conversation)
20:39 < yashgaroth> I suppose you could do it selectively, not sure if there's a relation between % alcohol and DNA size for precipitation though
20:40 < jcorgan> ok, so i'm speculating here, but
20:40 < yashgaroth> all at once, though
20:40 < jcorgan> oh, that's easier
20:40 < jcorgan> call the solvent A
20:41 < jcorgan> find a solvent B with two properties--1) it is miscible with A, and 2) the solute is completely insoluble in B
20:41 < jcorgan> then you can start adding B in incremental amounts until the solvent system can no longer sustain the solute and it precipitates
20:42 < jcorgan> there might even be a range of concentration that provides selective "crashing out"
20:42 < yashgaroth> yes that's how it usually works, B doesn't need to be a solvent necessarily but yes
20:44 < jcorgan> ah, 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 there
20:45 < yashgaroth> yeah the selective precipitation is popular, best example is proteins in ammonium sulfate but dna/alcohol is the other one
20:45 < xentrac_> yeah, microliters of ethanol are definitely practical for at-home use, unlike ultracentrifuges
20:54 < jcorgan> it will take me awhile to catch up to what is obvious in this group of people
20:56 < yashgaroth> I have my small domain of biology and very little else, I wouldn't worry
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21:21 < maaku> .title https://arxiv.org/abs/1605.08695
21:21 < yoleaux> [1605.08695] TensorFlow: A system for large-scale machine learning
21:21 < maaku> new tensorflow paper out of google brain
21:22 < jcorgan> data-flow based systems FTW
21:23 < jcorgan> but any indication of the delta between this paper and the earlier TF one?
21:27 < jcorgan> also, might be stating the obvious, but the Keras library provides a really usable abstraction layer atop TF
21:35 < nmz787> you could just use electrophoresis and dialysis tubing/agrose/PAGE gel
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21:54 < yashgaroth> I assume that's to do with our prior discussion and not tensorflow, but applying those to 4000 wells is tricky
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--- Log closed Tue May 31 00:00:16 2016