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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) | 02:07 |
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nmz787 | abetusk: wow, watching the screencast now, the cross-browser-tab highlighting is really cool | 02:24 |
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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) | 05:43 |
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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 | 05:44 |
abetusk | I assume you're going to do some sort of "paint negative on the pcb, burn off with laser cutter, etch" procedure? | 05:46 |
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/) | 05:50 |
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 | 05:51 |
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kanzure | 70 MB pluto image http://www.nasa.gov/sites/default/files/thumbnails/image/crop_p_color2_enhanced_release.png | 07:29 |
kanzure | algal bloom in amazon river as seen from orbit https://d3jc3ahdjad7x7.cloudfront.net/4v7P8ScJia484c1r1ZVOBFEl1B7XCDrv.jpg | 07:36 |
kanzure | glowforge is apparently offloading motion planning to their remote servers for their laser cutter product https://news.ycombinator.com/item?id=10276091 | 07:40 |
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 | 07:41 |
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kanzure | http://arstechnica.com/science/2015/09/supermassive-black-holes-found-spiraling-in-at-seven-percent-light-speed/ | 08:00 |
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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* | 09:04 |
eudoxia | but i never actually saw the full list: http://lifeboat.com/ex/boards?background=white | 09:05 |
kanzure | oh look there's fenn | 09:05 |
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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 | 09:06 |
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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 | 09:17 |
kanzure | hplusroadmap should have an antiboard of advisors | 09:18 |
kanzure | (see pm) | 09:19 |
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 | 09:21 |
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 | 09:22 |
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/ | 09:25 |
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) | 09:26 |
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 | 09:27 |
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 | 09:28 |
CaptHindsight | one of the Duke references went into that | 09:29 |
CaptHindsight | mainly making the larger fragments | 09:29 |
CaptHindsight | they have managed a patent bottleneck | 09:30 |
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 | 09:31 |
CaptHindsight | give them the plans, sit back and watch the price fall | 09:32 |
kanzure | "polymerase chain assembly" not sure how they physically isolated those reactoins | 09:33 |
kanzure | er, "polymerase cycle assembly" | 09:33 |
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 | 09:34 |
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 | 09:35 |
CaptHindsight | the problem is finding partners and not getting sucked into anything military | 09:36 |
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 | 09:38 |
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 | 09:40 |
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. | 09:41 |
kanzure | and also, it's not really one-pot if you have to sequence everything | 09:42 |
CaptHindsight | it starts as one pot | 09:42 |
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" | 09:43 |
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? | 09:44 |
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 | 09:45 |
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) | 09:46 |
kanzure | oops i mean "cycling ligase reaction" | 09:47 |
kanzure | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107329 | 09:48 |
kanzure | or "cycled ligation assembly" gah.. | 09:48 |
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 | 09:49 |
kanzure | https://www.dnalc.org/view/15487-DNA-ligation-3D-animation-with-no-audio.html | 09:52 |
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CaptHindsight | has anyone copied the proteins that cells use to repair breaks in DNA? | 09:58 |
CaptHindsight | or are they just starting to be discovered | 09:59 |
CaptHindsight | they mend single and double breaks | 09:59 |
CaptHindsight | and they are really really small | 10:00 |
CaptHindsight | have to make the tiny tiny tool shop first | 10:01 |
kanzure | there are many dna repair proteins | 10:07 |
kanzure | https://en.wikipedia.org/wiki/DNA_repair#DNA_repair_mechanisms | 10:07 |
kanzure | dna ligases are often numbered because organisms often have more than one variant of dna ligase to work with | 10:08 |
CaptHindsight | I read several papers on the proteins but none get into it at the molecular level | 10:14 |
CaptHindsight | it's more like "SALL14 makes this protein and it repairs breaks" | 10:15 |
CaptHindsight | https://en.wikipedia.org/wiki/BRCA1#Function_and_mechanism | 10:16 |
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/ | 10:17 |
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 | 10:18 |
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 | 10:45 |
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 | 10:46 |
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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 | 12:39 |
kanzure | i think the tdt ideas came from cathal garvey anyway | 12:43 |
kanzure | and cathal probably got them from.. who knows. | 12:44 |
kanzure | https://equipmentshare.com/ "an online caterpillar renting exchange site" well.. okay. | 12:49 |
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kanzure | "generate boring reports from data and turn them into press releases to ddos everyone" https://www.narrativescience.com/ | 12:50 |
kanzure | that's a clever way to frontrun all the press releases | 12:51 |
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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. | 12:51 |
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 | 12:52 |
kanzure | narratives aren't even necessary; just use templates. | 12:53 |
kanzure | there was also a weirdo company doing something like papermate for quarterly filings. i forget who though. | 12:54 |
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kanzure | surface tension of water on the space station https://www.youtube.com/watch?v=9jB7rOC5kG8 | 13:29 |
kanzure | http://benchling.engineering/crispr-aws-lambda/ | 13:36 |
kanzure | vineet gopal? ok | 13:37 |
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 | 13:55 |
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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 | 14:40 |
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nmz787 | abetusk: is there a class for the art_entry object that is thrown around a lot in bleepsixSchematic.js ? | 15:20 |
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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. | 16:09 |
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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? | 17:07 |
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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. | 17:17 |
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kanzure | gada contacted me re: gada prize | 17:41 |
maaku | kanzure: :( | 17:45 |
kanzure | seems that gada grand prize timeline is approaching | 17:48 |
kanzure | wonder if humanity+ has kept the money | 17:48 |
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kanzure | maaku: any sort of materials that i should prepare for your chemicals person? | 18:21 |
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maaku | kanzure: not sure. still need to get ahold of him | 18:28 |
maaku | interacted with him before on a mars mission planning project, but he's probably compatible with h+ goals | 18:29 |
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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 | 19:27 |
dpk | what's this? indoctrination planning? | 19:52 |
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maaku | dpk: there are many out there that just haven't been exposed to extropian ideas | 22:10 |
maaku | some of whom could be really useful... | 22:11 |
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JayDugger | Good morning, everyone. | 22:30 |
maaku | Good evening JayDugger | 22:31 |
fenn | http://youtu.be/CCDIuZUfETc building a rope bridge with quadcopters | 22:32 |
fenn | so many terrible top level domains now | 22:33 |
maaku | kanzure: what sorts of chemistry things? | 22:58 |
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--- Log closed Sat Sep 26 00:00:15 2015 |
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