2015-09-25.log

--- Log opened Fri Sep 25 00:00:06 2015
--- Day changed Fri Sep 25 2015
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nmz787abetusk: 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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nmz787abetusk: wow, watching the screencast now, the cross-browser-tab highlighting is really cool02:24
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abetusknmz787, 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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abetuskin 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 cutter05:44
abetuskI assume you're going to do some sort of "paint negative on the pcb, burn off with laser cutter, etch" procedure?05:46
abetusksorry, 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
abetuskgbl2ngc 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 gbl2ngc05:51
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kanzure70 MB pluto image http://www.nasa.gov/sites/default/files/thumbnails/image/crop_p_color2_enhanced_release.png07:29
kanzurealgal bloom in amazon river as seen from orbit https://d3jc3ahdjad7x7.cloudfront.net/4v7P8ScJia484c1r1ZVOBFEl1B7XCDrv.jpg07:36
kanzureglowforge is apparently offloading motion planning to their remote servers for their laser cutter product https://news.ycombinator.com/item?id=1027609107:40
kanzureer i guess they don't need realtime motion planning, because otherwise i don't see how a server could provide realtime feedback fast enough07:41
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kanzurehttp://arstechnica.com/science/2015/09/supermassive-black-holes-found-spiraling-in-at-seven-percent-light-speed/08:00
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eudoxiai know it's a running joke here that at least 20% of the world population is on the Lifeboat Foundation bard09:04
eudoxiaboard*09:04
eudoxiabut i never actually saw the full list: http://lifeboat.com/ex/boards?background=white09:05
kanzureoh look there's fenn09:05
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maakujoke? it's true09:06
maaku:P09:06
eudoxiaapparently some people belong to multiple boards, because gotta pad these numbers09:06
kanzuremaaku too09:06
maakuyeah waste of time that was09:06
kanzurehehe09:06
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maakuI got myself taken off all the mailing lists, but I suppose they still want to credit me as an advisory board member09:17
maakunot sure what the goal of the permissive lifeboat board is09:17
kanzurehplusroadmap should have an antiboard of advisors09:18
kanzure(see pm)09:19
CaptHindsightkanzure: are you aware of any DNA synthesis projects more recent than the work at Duke that is publishing info?09:21
kanzurethat are publishing info? eh not really.09:21
kanzuregeorge church often has various dna synthesis projects09:21
kanzurethis is a good review: http://diyhpl.us/~bryan/papers2/DNA/Large-scale%20de%20novo%20DNA%20synthesis:%20technologies%20and%20applications%20-%20Church%20-%202014.pdf09:22
CaptHindsightI hear of others but they are tight lipped about details09:22
kanzurethere's also the molecularassemblies people who are doing tdt-related stuff09:25
kanzureas described in some random patent09:25
CaptHindsighthttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112592/09:25
kanzure.title09:26
yoleauxGene Assembly from Chip-Synthesized Oligonucleotides09:26
kanzuresearch for "tdt" here http://gnusha.org/logs/2015-07-20.log09:26
kanzurecustomarray 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
CaptHindsightthe Duke project had assemblies into the few thousands09:27
kanzurehere's an old description of a tdt approach to dna synthesis (theoretical):09:27
kanzurehttp://diyhpl.us/wiki/dna/synthesis/tdt/09:27
kanzurehttp://2014.igem.org/Team:Cooper_Union/TdT_project09:27
CaptHindsightof base pairs09:27
kanzurehttp://2014.igem.org/Team:Rutgers09:27
kanzurecooper union tdt approach was also mentioned here https://groups.google.com/forum/#!searchin/enzymaticsynthesis/tdt/enzymaticsynthesis/DApMjXx8gS4/CmKEK9-vJlwJ09:28
kanzurethe trick is to combine highly parallel synthesis with highly parallel ligation into larger fragments09:28
CaptHindsightone of the Duke references went into that09:29
CaptHindsightmainly making the larger fragments09:29
CaptHindsightthey have managed a patent bottleneck09:30
kanzurethis one? http://www.rsc.org/images/loc/2013/PDFs/Papers/638_0077.pdf09:31
kanzureor the pcr subpool assembly thingy? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139991/09:31
CaptHindsightlooks like I'll have to do this all myself, maybe in China09:31
CaptHindsightgive them the plans, sit back and watch the price fall09:32
kanzure"polymerase chain assembly" not sure how they physically isolated those reactoins09:33
kanzureer, "polymerase cycle assembly"09:33
kanzure"nicking strand displacement and polymerase cycle assembly".. yes but the physical layout part is more interesting.09:34
kanzurehttps://www.scienceopen.com/document_file/765df1c9-75e0-484b-b0dd-5264beec0b09/PubMedCentral/765df1c9-75e0-484b-b0dd-5264beec0b09.pdf09:34
CaptHindsightI still want to make inkjet heads in China09:35
kanzure"20bp barcode primer pairs"09:35
CaptHindsightthey currently only make thermal heads09:35
CaptHindsightthe problem is finding partners and not getting sucked into anything military09:36
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" huh09:38
kanzurei 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
CaptHindsightlist of things to make: lower cost piezo printheads, FIB mills and "printers", SEM and atomic force scopes and manipulators09:40
CaptHindsightif you can rapidly sequence then the shotgun approach makes sense09:41
kanzureor er, "shotgun assembly"09:41
kanzureno it doesn't.. you don't want to have to sequence while assembling.09:41
kanzureand also, it's not really one-pot if you have to sequence everything09:42
CaptHindsightit starts as one pot09:42
CaptHindsightit's like getting your car as a bag-o-parts09:43
kanzurehere's someone citing that method.. http://diyhpl.us/~nmz787/pdf/Next_generation_1536-well_oligonucleotide_synthesizer_with_on-the-fly_dispense.pdf09:43
CaptHindsight"some assembly required"09:43
kanzureanyway, if this is just "use the other oligos for hybridization" then i think we've seen better descriptions of similar techniques before.09:44
CaptHindsightwhats the goal?09:44
CaptHindsightobviously being able to synthesize 3B bp in 1 second would be nice09:45
kanzuredna synthesis and assembly of 10 kbp fragments, without maintaining 1000 machines that each synthesize 100 bp at a time over 3 hours or w/e09:45
CaptHindsightheh, beat me to it09:45
kanzure3 billion would be nice, yes09:46
CaptHindsight10k's covers most of it09:46
kanzure"ligase cycling reaction" looked promising (check the logs)09:46
kanzureoops i mean "cycling ligase reaction"09:47
kanzurehttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.010732909:48
kanzureor "cycled ligation assembly" gah..09:48
kanzureactually, any of the logs mentioning ligase, i guess https://www.google.com/search?num=100&safe=off&q="ligase"+site%3Agnusha.org%2Flogs09:49
kanzurehttps://www.dnalc.org/view/15487-DNA-ligation-3D-animation-with-no-audio.html09:52
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CaptHindsighthas anyone copied the proteins that cells use to repair breaks in DNA?09:58
CaptHindsightor are they just starting to be discovered09:59
CaptHindsightthey mend single and double breaks09:59
CaptHindsightand they are really really small10:00
CaptHindsighthave to make the tiny tiny tool shop first10:01
kanzurethere are many dna repair proteins10:07
kanzurehttps://en.wikipedia.org/wiki/DNA_repair#DNA_repair_mechanisms10:07
kanzuredna ligases are often numbered because organisms often have more than one variant of dna ligase to work with10:08
CaptHindsightI read several papers on the proteins but none get into it at the molecular level10:14
CaptHindsightit's more like "SALL14 makes this protein and it repairs breaks"10:15
CaptHindsighthttps://en.wikipedia.org/wiki/BRCA1#Function_and_mechanism10:16
CaptHindsighthttps://en.wikipedia.org/wiki/Homologous_recombination10:17
kanzurepolymerase is a pretty-well studied dna binding and dna polymerizing enzyme http://diyhpl.us/~bryan/papers2/polymerase/10:17
CaptHindsighthttps://en.wikipedia.org/wiki/Non-homologous_end_joining10:18
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.png10:18
kanzurestill an awesome list10:18
kanzureas you increase the number of different oligos in your pool, you increase the chance that a wrong overlap will happen despite dna hybridization10:45
kanzureespecially if there are similar sequences10:45
kanzureto 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/results10:46
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nmz787kanzure: 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 now12:39
kanzurei think the tdt ideas came from cathal garvey anyway12:43
kanzureand cathal probably got them from.. who knows.12:44
kanzurehttps://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
kanzurethat's a clever way to frontrun all the press releases12:51
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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
cpopell3I'm not seeing a clear link to a sample12:52
cpopell3oh12:52
cpopell3this...is not revolutionary12:52
cpopell3bleh12:52
cpopell3http://www.businessinsider.com/narrative-science-quill-gamechanger-2014-712:52
kanzurenarratives aren't even necessary; just use templates.12:53
kanzurethere was also a weirdo company doing something like papermate for quarterly filings. i forget who though.12:54
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kanzuresurface tension of water on the space station https://www.youtube.com/watch?v=9jB7rOC5kG813:29
kanzurehttp://benchling.engineering/crispr-aws-lambda/13:36
kanzurevineet gopal? ok13:37
cpopell3I did some surface tension shit for my master's thesis13:55
cpopell3for ultra-small droplet13:55
cpopell3e.g. Surface energy >> Kinetic energy13:55
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nmz787cpopell3: 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 logical14:40
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nmz787abetusk: is there a class for the art_entry object that is thrown around a lot in bleepsixSchematic.js  ?15:20
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abetusknmz787, 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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maakukanzure: earlier you posted this : https://www.reddit.com/r/chemistry/comments/3gx7kg/seeking_collaborators_for_a_selffunded/17:07
maakuyou talked to these people?17:07
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kanzurepeacock spider http://i.ytimg.com/vi/d_yYC5r8xMI/maxresdefault.jpg17:17
kanzuremaaku: yes i talked to those people17:17
kanzuremaaku: "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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kanzuregada contacted me re: gada prize17:41
maakukanzure: :(17:45
kanzureseems that gada grand prize timeline is approaching17:48
kanzurewonder if humanity+ has kept the money17:48
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kanzuremaaku: any sort of materials that i should prepare for your chemicals person?18:21
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maakukanzure: not sure. still need to get ahold of him18:28
maakuinteracted with him before on a mars mission planning project, but he's probably compatible with h+ goals18:29
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maakukanzure: 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 lifetimes19:27
maakubut he's pretty smart and a total chemistry nerd, so he'd be a good addition19:27
dpkwhat's this? indoctrination planning?19:52
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maakudpk: there are many out there that just haven't been exposed to extropian ideas22:10
maakusome of whom could be really useful...22:11
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JayDuggerGood morning, everyone.22:30
maakuGood evening JayDugger22:31
fennhttp://youtu.be/CCDIuZUfETc building a rope bridge with quadcopters22:32
fennso many terrible top level domains now22:33
maakukanzure: what sorts of chemistry things?22:58
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--- Log closed Sat Sep 26 00:00:15 2015

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