--- Log opened Fri Sep 25 00:00:06 2015
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02:07 < nmz787> abetusk: does the g-code output of meowcad have dwell time or some sort of thickness/trace-width specified? I just got a laser etcher that I would like to feed with CAD designs, using the thinnest possible linewidths (I am just getting started with this cutter still need to figure out how to drive it via g-code)
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02:24 < nmz787> abetusk: wow, watching the screencast now, the cross-browser-tab highlighting is really cool
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05:43 < abetusk> nmz787, thanks, the cross tab highlighting thing was actually not that bad to implement and adds a lot.  I think there's a lot of little nicities in MeowCAD (if you look past all the rough edges)
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05:44 < abetusk> in terms of g-code, no dwell time.  The thickness and trace widths come from the design files.  I imagine you won't always want the thinnest possible line and probably want to adjust for the kerf (that's what it's called, right?) based on knowledge you have of your cutter
05:46 < abetusk> I assume you're going to do some sort of "paint negative on the pcb, burn off with laser cutter, etch" procedure?
05:50 < abetusk> sorry, the gcode produces outlines of the traces and whatever else, without filling in the rest of the space.  To produce the gcode, I use a tool I made called gbl2ngc (https://github.com/abetusk/gbl2ngc) but I think one of the standard ones that people use is pcb2gcode (http://sourceforge.net/projects/pcb2gcode/)
05:51 < abetusk> gbl2ngc can be used to "fill in" the negative space but you'll have to run it at the command line.  pcb2gcode is much more mature but it's raster based and not vector based, which is why I created gbl2ngc
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07:29 < kanzure> 70 MB pluto image http://www.nasa.gov/sites/default/files/thumbnails/image/crop_p_color2_enhanced_release.png
07:36 < kanzure> algal bloom in amazon river as seen from orbit https://d3jc3ahdjad7x7.cloudfront.net/4v7P8ScJia484c1r1ZVOBFEl1B7XCDrv.jpg
07:40 < kanzure> glowforge is apparently offloading motion planning to their remote servers for their laser cutter product https://news.ycombinator.com/item?id=10276091
07:41 < kanzure> er i guess they don't need realtime motion planning, because otherwise i don't see how a server could provide realtime feedback fast enough
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08:00 < kanzure> http://arstechnica.com/science/2015/09/supermassive-black-holes-found-spiraling-in-at-seven-percent-light-speed/
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09:04 < eudoxia> i know it's a running joke here that at least 20% of the world population is on the Lifeboat Foundation bard
09:04 < eudoxia> board*
09:05 < eudoxia> but i never actually saw the full list: http://lifeboat.com/ex/boards?background=white
09:05 < kanzure> oh look there's fenn
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09:06 < maaku> joke? it's true
09:06 < maaku> :P
09:06 < eudoxia> apparently some people belong to multiple boards, because gotta pad these numbers
09:06 < kanzure> maaku too
09:06 < maaku> yeah waste of time that was
09:06 < kanzure> hehe
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09:17 < maaku> I got myself taken off all the mailing lists, but I suppose they still want to credit me as an advisory board member
09:17 < maaku> not sure what the goal of the permissive lifeboat board is
09:18 < kanzure> hplusroadmap should have an antiboard of advisors
09:19 < kanzure> (see pm)
09:21 < CaptHindsight> kanzure: are you aware of any DNA synthesis projects more recent than the work at Duke that is publishing info?
09:21 < kanzure> that are publishing info? eh not really.
09:21 < kanzure> george church often has various dna synthesis projects
09:22 < kanzure> this is a good review: http://diyhpl.us/~bryan/papers2/DNA/Large-scale%20de%20novo%20DNA%20synthesis:%20technologies%20and%20applications%20-%20Church%20-%202014.pdf
09:22 < CaptHindsight> I hear of others but they are tight lipped about details
09:25 < kanzure> there's also the molecularassemblies people who are doing tdt-related stuff
09:25 < kanzure> as described in some random patent
09:25 < CaptHindsight> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112592/
09:26 < kanzure> .title
09:26 < yoleaux> Gene Assembly from Chip-Synthesized Oligonucleotides
09:26 < kanzure> search for "tdt" here http://gnusha.org/logs/2015-07-20.log
09:26 < kanzure> customarray is doing the electrode-based microarray synthesis approach, but they don't do ligation or assembly into larger fragments (similarly, azcobiotech sells a customarray product or an equivalent product? i dunno)
09:27 < CaptHindsight> the Duke project had assemblies into the few thousands
09:27 < kanzure> here's an old description of a tdt approach to dna synthesis (theoretical):
09:27 < kanzure> http://diyhpl.us/wiki/dna/synthesis/tdt/
09:27 < kanzure> http://2014.igem.org/Team:Cooper_Union/TdT_project
09:27 < CaptHindsight> of base pairs
09:27 < kanzure> http://2014.igem.org/Team:Rutgers
09:28 < kanzure> cooper union tdt approach was also mentioned here https://groups.google.com/forum/#!searchin/enzymaticsynthesis/tdt/enzymaticsynthesis/DApMjXx8gS4/CmKEK9-vJlwJ
09:28 < kanzure> the trick is to combine highly parallel synthesis with highly parallel ligation into larger fragments
09:29 < CaptHindsight> one of the Duke references went into that
09:29 < CaptHindsight> mainly making the larger fragments
09:30 < CaptHindsight> they have managed a patent bottleneck
09:31 < kanzure> this one? http://www.rsc.org/images/loc/2013/PDFs/Papers/638_0077.pdf
09:31 < kanzure> or the pcr subpool assembly thingy? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139991/
09:31 < CaptHindsight> looks like I'll have to do this all myself, maybe in China
09:32 < CaptHindsight> give them the plans, sit back and watch the price fall
09:33 < kanzure> "polymerase chain assembly" not sure how they physically isolated those reactoins
09:33 < kanzure> er, "polymerase cycle assembly"
09:34 < kanzure> "nicking strand displacement and polymerase cycle assembly".. yes but the physical layout part is more interesting.
09:34 < kanzure> https://www.scienceopen.com/document_file/765df1c9-75e0-484b-b0dd-5264beec0b09/PubMedCentral/765df1c9-75e0-484b-b0dd-5264beec0b09.pdf
09:35 < CaptHindsight> I still want to make inkjet heads in China
09:35 < kanzure> "20bp barcode primer pairs"
09:35 < CaptHindsight> they currently only make thermal heads
09:36 < CaptHindsight> the problem is finding partners and not getting sucked into anything military
09:38 < kanzure> "The shotgun method is based on the hypothesis that a pool of oligonucleotides can be synthesized in one pot to produce randomly assembled products" huh
09:40 < kanzure> i think the second set of oligonucleotides, using the other restriction digest sequence, are used for hybridization reasons? but why have a second set of restriction digest sequences anyway. so they must be doing something else here.
09:40 < kanzure> (this is their "shotgun synthesis" method)
09:40 < CaptHindsight> list of things to make: lower cost piezo printheads, FIB mills and "printers", SEM and atomic force scopes and manipulators
09:41 < CaptHindsight> if you can rapidly sequence then the shotgun approach makes sense
09:41 < kanzure> or er, "shotgun assembly"
09:41 < kanzure> no it doesn't.. you don't want to have to sequence while assembling.
09:42 < kanzure> and also, it's not really one-pot if you have to sequence everything
09:42 < CaptHindsight> it starts as one pot
09:43 < CaptHindsight> it's like getting your car as a bag-o-parts
09:43 < kanzure> here's someone citing that method.. http://diyhpl.us/~nmz787/pdf/Next_generation_1536-well_oligonucleotide_synthesizer_with_on-the-fly_dispense.pdf
09:43 < CaptHindsight> "some assembly required"
09:44 < kanzure> anyway, if this is just "use the other oligos for hybridization" then i think we've seen better descriptions of similar techniques before.
09:44 < CaptHindsight> whats the goal?
09:45 < CaptHindsight> obviously being able to synthesize 3B bp in 1 second would be nice
09:45 < kanzure> dna synthesis and assembly of 10 kbp fragments, without maintaining 1000 machines that each synthesize 100 bp at a time over 3 hours or w/e
09:45 < CaptHindsight> heh, beat me to it
09:46 < kanzure> 3 billion would be nice, yes
09:46 < CaptHindsight> 10k's covers most of it
09:46 < kanzure> "ligase cycling reaction" looked promising (check the logs)
09:47 < kanzure> oops i mean "cycling ligase reaction"
09:48 < kanzure> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107329
09:48 < kanzure> or "cycled ligation assembly" gah..
09:49 < kanzure> actually, any of the logs mentioning ligase, i guess https://www.google.com/search?num=100&safe=off&q="ligase"+site%3Agnusha.org%2Flogs
09:52 < kanzure> https://www.dnalc.org/view/15487-DNA-ligation-3D-animation-with-no-audio.html
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09:58 < CaptHindsight> has anyone copied the proteins that cells use to repair breaks in DNA?
09:59 < CaptHindsight> or are they just starting to be discovered
09:59 < CaptHindsight> they mend single and double breaks
10:00 < CaptHindsight> and they are really really small
10:01 < CaptHindsight> have to make the tiny tiny tool shop first
10:07 < kanzure> there are many dna repair proteins
10:07 < kanzure> https://en.wikipedia.org/wiki/DNA_repair#DNA_repair_mechanisms
10:08 < kanzure> dna ligases are often numbered because organisms often have more than one variant of dna ligase to work with
10:14 < CaptHindsight> I read several papers on the proteins but none get into it at the molecular level
10:15 < CaptHindsight> it's more like "SALL14 makes this protein and it repairs breaks"
10:16 < CaptHindsight> https://en.wikipedia.org/wiki/BRCA1#Function_and_mechanism
10:17 < CaptHindsight> https://en.wikipedia.org/wiki/Homologous_recombination
10:17 < kanzure> polymerase is a pretty-well studied dna binding and dna polymerizing enzyme http://diyhpl.us/~bryan/papers2/polymerase/
10:18 < CaptHindsight> https://en.wikipedia.org/wiki/Non-homologous_end_joining
10:18 < kanzure> "Evolved and rationally-designed polymerases" http://diyhpl.us/~bryan/papers2/polymerase/The%20evolution%20of%20DNA%20polymerases%20with%20novel%20activities.pdf.evolved-or-rationally-designed-polymerases.png
10:18 < kanzure> still an awesome list
10:45 < kanzure> as you increase the number of different oligos in your pool, you increase the chance that a wrong overlap will happen despite dna hybridization
10:45 < kanzure> especially if there are similar sequences
10:46 < kanzure> to increase the number of unique overlapping sequences you need to increase the length of these wings, which is problematic because you only have so many nucleotides to work with anyway before your phosphoramidite synthesis protocol causes crippling poor yields/results
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12:39 < nmz787> kanzure: that molecularassemblies group seems to be some of the only people I would consider doing anything interesting these days in the synthesis realm... but that patent definitely came out after we talked about tdt methods here/on-forums... but I guess it's a first-to-file world now
12:43 < kanzure> i think the tdt ideas came from cathal garvey anyway
12:44 < kanzure> and cathal probably got them from.. who knows.
12:49 < kanzure> https://equipmentshare.com/ "an online caterpillar renting exchange site" well.. okay.
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12:50 < kanzure> "generate boring reports from data and turn them into press releases to ddos everyone" https://www.narrativescience.com/
12:51 < kanzure> that's a clever way to frontrun all the press releases
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12:51 < cpopell3> >We are helping companies operationalize data storytelling with Quill, our advanced natural language generation (NLG) platform. By automatically transforming data into narratives, our artificial intelligence software dramatically reduces the time and energy people spend analyzing, interpreting and explaining data.
12:52 < cpopell3> I'm not seeing a clear link to a sample
12:52 < cpopell3> oh
12:52 < cpopell3> this...is not revolutionary
12:52 < cpopell3> bleh
12:52 < cpopell3> http://www.businessinsider.com/narrative-science-quill-gamechanger-2014-7
12:53 < kanzure> narratives aren't even necessary; just use templates.
12:54 < kanzure> there was also a weirdo company doing something like papermate for quarterly filings. i forget who though.
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13:29 < kanzure> surface tension of water on the space station https://www.youtube.com/watch?v=9jB7rOC5kG8
13:36 < kanzure> http://benchling.engineering/crispr-aws-lambda/
13:37 < kanzure> vineet gopal? ok
13:55 < cpopell3> I did some surface tension shit for my master's thesis
13:55 < cpopell3> for ultra-small droplet
13:55 < cpopell3> e.g. Surface energy >> Kinetic energy
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14:40 < nmz787> cpopell3: huh, so is that why in fluid dynamics there is the no-slip condition boundary? basically the point where the kinetics of the flow are overpowered by the wall interaction...hmm, seems logical
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15:20 < nmz787> abetusk: is there a class for the art_entry object that is thrown around a lot in bleepsixSchematic.js  ?
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16:09 < abetusk> nmz787, no, no class, it's an object.  The object it not really documented but it follows closely the KiCAD .sch format, just in JSON form.
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17:07 < maaku> kanzure: earlier you posted this : https://www.reddit.com/r/chemistry/comments/3gx7kg/seeking_collaborators_for_a_selffunded/
17:07 < maaku> you talked to these people?
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17:17 < kanzure> peacock spider http://i.ytimg.com/vi/d_yYC5r8xMI/maxresdefault.jpg
17:17 < kanzure> maaku: yes i talked to those people
17:17 < kanzure> maaku: "oh well that's just engineering and it's boring..." but strangely, one of them was very pro-sens foundation. just anti-engineering/hardware/doing things.
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17:41 < kanzure> gada contacted me re: gada prize
17:45 < maaku> kanzure: :(
17:48 < kanzure> seems that gada grand prize timeline is approaching
17:48 < kanzure> wonder if humanity+ has kept the money
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18:21 < kanzure> maaku: any sort of materials that i should prepare for your chemicals person?
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18:28 < maaku> kanzure: not sure. still need to get ahold of him
18:29 < maaku> interacted with him before on a mars mission planning project, but he's probably compatible with h+ goals
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19:27 < maaku> kanzure: he's a kid (just graduating college I think) who wants to personally explore / colonize / terraform Mars. he needs to be gently convinced that this will not happen in his lifetime, and the solution to that is to extend lifetimes
19:27 < maaku> but he's pretty smart and a total chemistry nerd, so he'd be a good addition
19:52 < dpk> what's this? indoctrination planning?
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22:10 < maaku> dpk: there are many out there that just haven't been exposed to extropian ideas
22:11 < maaku> some of whom could be really useful...
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22:30 < JayDugger> Good morning, everyone.
22:31 < maaku> Good evening JayDugger
22:32 < fenn> http://youtu.be/CCDIuZUfETc building a rope bridge with quadcopters
22:33 < fenn> so many terrible top level domains now
22:58 < maaku> kanzure: what sorts of chemistry things?
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--- Log closed Sat Sep 26 00:00:15 2015