--- Log opened Thu Jul 19 00:00:15 2018
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01:47 < fenn> nanotech related: https://www.chemistryworld.com/news/most-complex-reaction-ever-triggered-by-atomic-manipulation-makes-molecular-wire/3009210.article
02:48 < maaku> does anyone know of algorithms for searching shape-space, e.g. indexing 3d forms (or better, scalar fields) for the purpose of later comparing a reference against a database?
02:48 < fenn> you want something like a hash? or just a distance metric?
02:49 < maaku> a distance metric
02:49 < maaku> e.g. an R-tree or kd-tree can be used to index points by subdivision of space, for the purpose of accelerating a nearest neighbor search. query a test point and you get an ordered list of the nearest points to it
02:50 < maaku> I want something where you insert either shapes or scalar fields, and later present a test shape/field and get a list of elements sorted by similarity
02:53 < maaku> e.g. have a database of biomolecules and metabolic pathways, and the query value is the DFT field representing the "shape" of a drug. the result of the query is a list of biomolecules and reaction pathways affected by the drug within <threshold> energy
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02:54 < maaku> my google scholar skills aren't helping me find anything.
02:54 < maaku> (hit and run question; I need to get some zzz's)
02:57 < fenn> wikipedia says the jaccard coefficient is used in chemoinformatics; it's the boolean intersection divided by the boolean union
03:00 < fenn> you could build a tree of bounding volumes to search efficiently
03:04 < fenn> dimensions being x,y,z and dx,dy,dz
03:05 < fenn> i suppose you could also add average electronegativity and hydrophobicity for the volume
03:07 < fenn> then you do nearest neighbor search on the bounding volumes (which are now considered points for the purposes of the nearest neighbor algorithm)
03:08 < fenn> i just made up this algorithm, there are probably better solutions
03:14 < fenn> charge, not electronegativity
03:15 < fenn> aka electrostatic potential
03:15 < fenn> i think a bounding volume hierarchy is equivalent to a haar wavelet transform; it may be better to use a gaussian wavelet transform instead
03:19 < fenn> instead of discrete volume boundaries you would use an overlapping window function (i.e. a gaussian window)
03:28 < fenn> ugh there are 44 different similarity metrics being used in chemoinformatics
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03:30 < kanzure> all yer shapes can be represented as graphs
03:30 < kanzure> then you can do graph similarity metric blah blah blah
03:30 < fenn> that doesn't work for comparing the DFT fields
03:31 < kanzure> simple, they are "attributes" on the graph! </sarcasm>
03:31 < fenn> yeah, try solving the problem by using numbers
03:32  * fenn is helpful
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04:38 < archels> .title http://www.teleopto.com/
04:38 < yoleaux> Teleopto :: Home
04:38 < archels> "Wireless Optogenetic Stimulator"
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06:04 < kanzure> hmm why wouldn't a phone work? the receiver could do a wifi chip or something.
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07:14 < kanzure> farmerwampum: be greeted
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07:19 < kanzure> .tw https://twitter.com/neurowitz/status/1019236264611123201
07:19 < yoleaux> Scalable data storage is a problem. New awards from NSF, along with the ongoing DARPA Molecular Informatics program, are working to solve fundamental scientific problems at the interface between polymer storage media and semiconductor tech. https://twitter.com/NSF/status/1019221794711064578 (@neurowitz)
07:19 < kanzure> .tw https://twitter.com/NSF/status/1019221794711064578
07:19 < yoleaux> NSF announces new awards in semiconductor #syntheticbiology. Could the entire contents of the Library of Congress soon fit on a device the size of your fingernail? http://bit.ly/SemiSynBio https://pbs.twimg.com/media/DiUAukLX4AI5ev2.jpg (@NSF)
07:20 < solene> those would be for long-term storage or cold-storage I assume
07:20 < kanzure> for now just cold storage like tape with slow read+write
07:21 < kanzure> nmz787 argues that he can make it work at speeds similar to solid state devices
07:21 < kanzure> er, flash memory read/write speeds
07:21 < kanzure> solene: http://diyhpl.us/~bryan/dna-data-storage-workshop-summary-report.draft.2017-10-26.pdf
07:22 < solene> I wonder what would be the case around this storage for regular user. Like the floppy was a disk inside a square case
07:22 < solene> disc
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07:23 < kanzure> https://nsf.gov/news/news_summ.jsp?cntn_id=295968&org=NSF&from=news
07:23 < kanzure> "To address a worldwide need for data storage that far outstrips today's capabilities, federal agencies and a technology research consortium are investing $12 million in new research through the Semiconductor Synthetic Biology for Information Processing and Storage Technologies (SemiSynBio) program. The goal is to create storage systems that integrate synthetic biology with semiconductor ...
07:23 < kanzure> ...technology."
07:24 < kanzure> oh wait, i think these are the projects that nmz787 was asked to review
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08:13 < kanzure> about that recent "crispr-cas9 causes undesired errors!!!" paper: https://news.ycombinator.com/item?id=17566871
08:13 < kanzure> "The root cause here is the DNA double-strand break induced by Cas9, and the ensuing DNA repair processes that occassionally produces large deletions (the paper reports two thirds or 32/48 were less than 50 bp and 21% or 10/48 were greater than 250 bp). This has been largely known by the DNA repair community for 20+ years."
08:13 < kanzure> "(1) The paper's main finding has been known by the DNA repair community, (2) relying on DNA double-strand breaks for genome editing has been known to be non-ideal in the long-term, and (3) current ex vivo therapies are unaffected since we can screen cells after editing."
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09:24 < bluebear_> kanzure: so, as usual, lots of ruckus around relatively little... as I expected. Thanks a lot for sharing this info!
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10:21 < kanzure> http://www.businessinsider.com/designer-babes-made-by-editing-embryos-ethics-2018-7
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13:21 < nmz787> kanzure: I wonder if ligase tethered to cas-9 would help in some way... or instead of ligase (or in addition?) also tether on the repair enzyme... some mega-fusion enzyme
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14:15 < maaku> fenn: cheminformatics may have been the keyword I was missing.
14:16 < maaku> kanzure: my intuition is that treating a polygon as a graph isn't going to work very well. the structure of the resulting graph (vertex-edge relationships and connectivity) is inconsequential
14:17 < maaku> that said, maybe if the polygons were generated by the same algorithm there might be latent intoformation encoded well enough to be useful
14:19 < maaku> but what I'm expecting instead is something that transforms a shape into a point in a high dimensional vector space, such that if the distance between two points is small, the two shapes are more likely to "fit"
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14:26 < kanzure> lookup shape graphs or shape grammars?
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18:03 < kanzure> hmm.
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18:43 < kanzure> .title https://www.nature.com/articles/d41586-018-05711-y
18:43 < yoleaux> A record-breaking microscope
18:44 < kanzure> .wik ptychography
18:44 < yoleaux> "Ptychography (/tɪˈtʃoʊɡræfi/ ti-CHOH-graf-ee; πτυχο-γραφία, from πτυχή = fold + γραφή = writing/scripture)  is a technique invented by Walter Hoppe that aims to solve the diffraction-pattern phase problem by interfering adjacent Bragg reflections coherently and thereby determine their relative phase. In the original formulation, Hoppe  …" — https://en.wikipedia.org/wiki/Ptychography
18:45 < fenn> just say electron diffraction ffs
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--- Log closed Fri Jul 20 00:00:16 2018