--- Log opened Sun Apr 24 00:00:55 2016 01:29 < nmz787> abetusk: actually, I think I want vector for the isolation routes (since they define the edges of my actual desired traces), then raster the area in-between 01:30 < nmz787> not sure how easy your tool is to modify to do a sort of flood-fill of those areas 01:33 < abetusk> nmz787, it has a fill already, horizontal, vertical and 'zen garden'. 01:36 < abetusk> One of the gerber to gcode tools I remember having a good following...it was open source and worked but it created the gcode by first converting the gerbers to an image, then converting the image to gcode. The end effect was that the gcode had many small 'steps', going up then left, say, instead of straight diagonal. They were small enough to not make a significant difference for most things (they were the size of pixels) but 01:36 < abetusk> I wanted a tool that was closer to vectorizing the gerbers, so I created gbl2ngc 01:50 < nmz787> so it has an option to output the vectors along with fill in the same g file? 01:50 < nmz787> (I haven't looked yet) 01:52 < nmz787> I am messing with plotting the gerbers with python and wxpython 01:53 < nmz787> it looks like I just got something close to good: http://paste.pound-python.org/show/A2jFQYXOp3t7mSaFqVwi/ 01:55 < nmz787> http://imgur.com/R4uuNx3 01:56 -!- Quashie_ [~boingredd@45.42.8.151] has quit [Ping timeout: 244 seconds] 01:57 < nmz787> ok, well now to try your thing 02:01 < nmz787> hmm, I am getting "PARSE ERROR: coordinate format exceeded at line 29" where line 29 is the first XY line: X179350499Y-122082495D02* 02:39 -!- pompolic [~A@unaffiliated/pompolic] has joined ##hplusroadmap 02:39 < nmz787> abetusk: got it to work by changing pos = max_buf-2; to pos = max_buf-1; in gerber_interpret.c :/ 02:40 < nmz787> though I wonder if my leading 0's weren't added 02:58 < nmz787> abetusk: seems the other important piece of that parsing setup is this prior line: %FSLAX46Y46*% 03:38 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 03:43 < chris_99> .tell nmz787 http://www.asdlib.org/learningModules/AtomicEmission/S-Order_overlap.html -- I found what I was wondering about the other day, it's called 'order overlap' that URL has ways to cope with it 03:43 < yoleaux> chris_99: I'll pass your message to nmz787. 04:00 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-tztkjjkvlesfiuvd] has quit [Quit: Connection closed for inactivity] 05:09 -!- jcluck is now known as cluckj 05:36 -!- Gurkenglas [Gurkenglas@dslb-178-000-178-156.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 246 seconds] 05:42 -!- Gurkenglas [Gurkenglas@dslb-178-000-178-156.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 06:38 -!- nildicit [~nildicit@unaffiliated/nildicit] has quit [Ping timeout: 252 seconds] 07:14 -!- gluytium [~gluytium@li394-234.members.linode.com] has quit [Quit: ZNC 1.6.1+deb1 - http://znc.in] 07:20 -!- gluytium [gluytium@2600:3c03::f03c:91ff:fe55:c675] has joined ##hplusroadmap 07:24 -!- jaboja [~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 07:38 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 244 seconds] 07:51 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-qknvoohijlkvtbed] has joined ##hplusroadmap 08:35 -!- jaboja [~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 08:43 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 250 seconds] 08:47 < chris_99> does anyone know if you could possibly identify different species of the same plant via electrophoresis on it's leaves, after extracting its DNA 09:04 -!- ArturSha1 [~ArturShai@31.29.29.38] has joined ##hplusroadmap 09:12 -!- Gurkenglas [Gurkenglas@dslb-178-000-178-156.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 252 seconds] 09:32 -!- Gurkenglas [Gurkenglas@dslb-178-000-178-156.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 09:33 < archels_> http://www.neuroscientistnews.com/research-news/first-gene-therapy-successful-against-human-aging 10:24 -!- sandeepkr__ [~sandeep@111.235.64.4] has quit [Remote host closed the connection] 10:39 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 10:44 < archels_> .title http://www.nature.com/nrc/journal/v13/n9/abs/nrc3566.html 10:44 < yoleaux> Fluorescence-guided surgery with live molecular navigation [mdash] a new cutting edge : Nature Reviews Cancer : Nature Publishing Group 10:51 -!- ArturSha1 [~ArturShai@31.29.29.38] has quit [Ping timeout: 268 seconds] 10:59 -!- jaboja [~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 11:06 -!- nildicit [~nildicit@gateway/vpn/privateinternetaccess/nildicit] has joined ##hplusroadmap 11:08 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 260 seconds] 11:12 -!- jaboja [~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 11:16 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 11:18 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Read error: Connection reset by peer] 11:19 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 11:24 < nmz787> sup 11:24 < yoleaux> 10:43Z nmz787: http://www.asdlib.org/learningModules/AtomicEmission/S-Order_overlap.html -- I found what I was wondering about the other day, it's called 'order overlap' that URL has ways to cope with it 11:24 < nmz787> chris_99: ah, cool,yeah I've seen spectrometers with cascaded gratings to slowly pull out the orders 11:25 < chris_99> yeah, i'm gonna look into the filter approach it mentions too 11:26 < nmz787> chris_99: DNA barcoding is either done with primers for barcode-regions (regions that pick up random non-selected for mutation, which can be used as trackers)... or is done with something like STR analysis or RFLP 11:26 < nmz787> https://en.wikipedia.org/wiki/STR_analysis 11:26 < nmz787> https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism 11:27 < nmz787> but you basically need an enzyme for them to break them up (tho the latter can probably be sonic with sonication that is very predictable/repeatable) 11:27 < nmz787> and also an enzyme to amplify the signal (PCR) 11:27 < chris_99> and then after that you can do electrophoresis? or..? 11:27 < nmz787> yeah, capillary electrophoresis would be my recommendataion 11:28 < nmz787> with a detector at the end (photodiode measuring absorbance of the crosssection of the electrphoresis gel) 11:28 < nmz787> that way you get really good signal to noise, use less gel and DNA, automated data collection 11:29 < nmz787> I wonder if a cell phone camera could be coerced into being a good-enough detector 11:29 < nmz787> you might be able to do some cross-sectional impedance measurement too... I am not sure 11:29 < chris_99> interesting, i'll read some more info about the photodiode idea, i'd not heard of that before 11:30 < nmz787> I know it works along the length of DNA... so you might be able to at least get a DNA present/not-present 11:30 < nmz787> oh yeah, that's standard capillay gel electrphoresis setup for sanger sequencers going back probably 30 years 11:30 < nmz787> well, no 11:30 < nmz787> 15 at least 11:31 < nmz787> 10 at least, probably 15 11:31 < chris_99> even the photodiode part? 11:31 < nmz787> yeah 11:31 < chris_99> oh didn't realise that 11:31 < nmz787> prior to ~15 years ago I think they used mega-gels 11:31 < nmz787> which I have a power-supply from/for 11:32 < nmz787> http://s.hswstatic.com/gif/dna-profiling-1.jpg 11:32 < chris_99> i've got an electrophoresis psu too, which i've thus far only used for nixies 11:32 < nmz787> http://www.achievement.org/achievers/lan0/large/lan0-006.jpg 11:32 < nmz787> does it go up to like 3kV? 11:32 < chris_99> no, it goes to 400V 11:33 < nmz787> yeah, that is for student-size gels 11:33 < nmz787> or standard-fare these days for lab stuff 11:33 < nmz787> maybe 10cm long at most 11:33 < nmz787> these sequencing gels are like 40cm long 11:33 < nmz787> if not 50 or 60cm 11:34 < chris_99> oh so it wouldn't be powerful enough 11:34 < chris_99> ? 11:34 < nmz787> (were) 11:34 < nmz787> yeah, the volts/cm is the field strength 11:34 < nmz787> which is the key term in the electrophoresis mobility equation 11:34 < nmz787> (as well as in electroporation) 11:34 < nmz787> (along with some decay terms in that) 11:35 < chris_99> sorry, i mean, if i wanted to attempt to distinguish between plants, i'd need a more powerful PSU? 11:36 < nmz787> you'd have to experiment 11:36 < nmz787> but if you did, it would be an easy upgrade at the point when you realize you need it 11:36 < chris_99> mm, are the things like STR analysis hard to do though, for an amateur, or expensive even 11:37 < nmz787> a problem with direct/crude DNA extract and then i.e. sonication could be that the fragments resulting could have a spread/histogram of lengths like a chirp-function 11:37 < nmz787> which would not be unique 11:38 < nmz787> so you usually use enzymes that cut at specific sites 11:38 < nmz787> I think the FBI or police or whatever have like 10 or so enzyme sites they use 11:39 < chris_99> ah, so with sonication, it's randomly fragmenting the DNA if i'm understanding right? 11:39 < nmz787> or in the case of STR, I think they're primers 11:39 < nmz787> to start the PCR reaction at 11:39 < nmz787> yeah 11:40 < nmz787> https://www.thermofisher.com/order/catalog/product/4322288 11:40 < chris_99> eek, that's expensive 11:40 -!- Orpheon [~Orpheon@46.140.52.182] has quit [Read error: Connection reset by peer] 11:40 < nmz787> it's no harder than cooking some pudding or something that is very delicate and you need to monitor closely so... well I guess if a pudding was delicate it might crack, and that would be undesirable for fancy parties 11:41 < nmz787> well, $20 per reaction, cheap for law enforcement 11:41 < chris_99> mmm true 11:41 < nmz787> CODIS-approved 11:41 < nmz787> .wik codis 11:41 < yoleaux> "Combined DNA Index System (CODIS) is the FBI's program of support for criminal justice DNA databases as well as the software used to run these databases." — https://en.wikipedia.org/wiki/Codis 11:41 < chris_99> so that's only for human DNA isn't it, you'd need different enzymes for plants i assume? 11:42 -!- Orpheon [~Orpheon@46.140.52.182] has joined ##hplusroadmap 11:42 < nmz787> this seems like it could be useful it you can manage to get past the login https://www.coursehero.com/file/p2uikg/Advantages-of-RFLP-cheap-DNA-variation-codominant-Disadvantages-of-RFLP-labor/ 11:42 < nmz787> yeah, most likely 11:42 < nmz787> there is probably some non-randomness in sonication 11:43 < nmz787> like certain frequencies maybe (guessing) respond to certain nucleotide bond pairs 11:43 < chris_99> is there any reason you can't just apply electrophoresis without sonication etc, first? 11:45 < nmz787> the DNA will be so huge, other than the broken fragments resulting from your mishandling cellular contents while doing an extract (or pipetting from one place to another)... that it will just electrophorese as one clump... unless you use 11:45 < nmz787> .wik pulsed field electrophoresis 11:45 < yoleaux> "Pulsed field gel electrophoresis is a technique used for the separation of large deoxyribonucleic acid (DNA) molecules by applying to a gel matrix an electric field that periodically changes direction." — https://en.wikipedia.org/wiki/Pulsed-field_gel_electrophoresis 11:46 < chris_99> aha cheers, that makes sense 11:47 < nmz787> on its own, I guess it might tell you the mass of DNA per cell.... but I'm not sure if that is the way that assay is usually done 11:48 < nmz787> not sure how well DNA-length would be for species ID either 11:48 < nmz787> some cultivars of brassicas for example have chromosomes doubled 11:49 < nmz787> but people just say its some different cultivar, not species 11:51 < nmz787> I wonder if there is some method by which you make DNA loop on itself characteristically, like histone-size/level, and then when the DNA is all condensed... determine density using centrifugation 11:51 < nmz787> idk 11:51 < nmz787> you need to probe the contents of the DNA to do some kind of hash 11:57 < kanzure> .title https://youtube.com/watch?v=-lgYYz3y_hY 11:57 < yoleaux> Lightning Network as a Directed Graph: Single-Funded Channel Network Topology - YouTube 12:03 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 276 seconds] 12:03 -!- Betawolf [~matthew@xn--bta-yla.net] has left ##hplusroadmap [] 12:09 < kanzure> "neural network to colorize grayscale images" https://github.com/pavelgonchar/colornet 12:22 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 12:45 -!- justanot1eruser [~Justan@unaffiliated/justanotheruser] has 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[~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 15:20 < kanzure> .title https://news.ycombinator.com/item?id=11559684 15:20 < yoleaux> Telomere lengthening via gene therapy in a human individual | Hacker News 15:21 < kanzure> "In a longitudinal study testing telomere length in a large human cohort, 44% of people had longer telomeres than when they were 10 years younger (and 10 years is a lot of aging!) http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004191 So even if her telomeres did get longer, how confident can we be that is at all related to the gene therapy?" 15:21 < kanzure> haha.... 15:24 < kanzure> "Actually, protein design is fairly routine now. We used Exacycle, an idle-cycle computer at Google, to show that given reasonable amounts of computer time, design of proteins is a straightforward process. You don't need advanced supercomputers or even GPUs to solve this problem- just classic clusters- although GPUs (not supercomputers) speed up the rate significantly. The important reason why this works is that while "protein folding is ... 15:24 < kanzure> ... an NP-hard problem" is technically true for computer scientists, the more important fact is "we have approximations to the NP-hard problem that are good enough to finish in hours if you have a 600Kcores working on it"." 15:24 < kanzure> i thought there were still some folds that we haven't solved? what 15:24 -!- Quashie [~boingredd@45.42.8.151] has joined ##hplusroadmap 15:25 < kanzure> https://www.edge.org/conversation/george_church-the-augmented-human-being 15:37 < maaku> kanzure perhaps this is protein design vs protein prediction. Avoid the things you don't know how to fold. 15:38 < kanzure> oh. 16:00 < kanzure> "While I applaud the "boldness", and hope those probabilities won't be affected significantly to cause problems, I work everyday with binary code, made BY, FOR (and intentionally) humans, with all the manuals, blueprints, analytic tools, compiled WITH debugging info, etc etc etc and we STILL get it laughably wrong. I'm not touching self-modifying, tri-dimensional, billion year ad-hoc optimized spaghetti code with a 10 nano-foot pole ... 16:00 < kanzure> ... until at least the late 2020's" 16:00 < kanzure> hah. 16:01 < kanzure> http://arep.med.harvard.edu/webpage-%20science%20info%20-%20lab%20members/Bobby/Bobby%20Dhadwar.htm 16:06 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 250 seconds] 16:09 < kanzure> "note: each definite anticholinergic may increase the risk of cognitive impairment by 46% over 6 years." http://www.agingbraincare.org/uploads/products/ACB_scale_-_legal_size.pdf 16:15 < chris_99> Out of curiousity is it possible to grow a plant from a dried out tissue culture, i'm sceptical it would be possible? 16:15 < kanzure> do you consider seeds to be dry tissue 16:16 < chris_99> heh, sorry to be specific i'm talking about dry leaves 16:32 -!- c0rw1n is now known as c0rw|zZz 16:41 < nmz787> *bam* as kanzure pounces on seeds being composed of tissue 16:41 < nmz787> welp, the smoothed-PWM on the LM317 didn't work as planned :/ there is always some minimum voltage on the output (1.25V) and there is minimum load 16:42 < chris_99> whatcha doing 16:42 < nmz787> so I went back to the original laser driver config, sortof, with the exception of smoothed-PWMing the darlington-input (which results in a limited and non-linear power response) 16:43 < nmz787> chris_99: playing with this diyhpl.us/laser_etcher/NEJE_Laser_Etcher/ 16:43 < nmz787> i really should crop those pics at the top, and/or compress them or something 16:44 < chris_99> oh cool 16:44 < chris_99> is that the tiny laser etcher thing 16:44 < nmz787> yeah 16:44 < nmz787> towards the bottom you can see the rework i did like 2 weeks ago 16:44 < nmz787> http://diyhpl.us/laser_etcher/NEJE_Laser_Etcher/pwm_filter_lm317t_rework.jpg 16:45 < nmz787> butttt it didn't end up working... and also the grbl settings listed there didn't seem to match up when I got it working after re-reworking it today 16:45 < chris_99> darn 16:45 < nmz787> seems the right setting is 54 steps/mm 16:46 < nmz787> (when checking a little ruler pattern with a cheap digital plastic micrometer) 16:47 < nmz787> next i'm gonna try to laser some gerber-to-gcode i got to convert last night with abetusk's program 16:47 < nmz787> used this to visualize the gerber: http://jherrm.com/gcode-viewer/ 16:49 < nmz787> chris_99: I got this to upgrade to next: http://www.diyouware.com/node/116 16:50 < nmz787> which is detailed a bit more here http://www.diyouware.com/node/164 16:51 < nmz787> .title http://www.diyouware.com/node/161 16:51 < yoleaux> Hacking the PHR-803T | Diyouware.com 16:51 < chris_99> nice, looks fun 16:52 < chris_99> planning on using for uv pcbs or something 16:52 < nmz787> that would be nice to do 16:53 < nmz787> i've got copper clad and some photoresist 16:53 < nmz787> ultimately I want to try microfluidics 16:55 < chris_99> i'm confused, you mean to use the laser to etch plastic for that? 16:56 < nmz787> usually you expose photoresist, then cure it, then lay silicone on top, cure, peel, then bond silicone layer stack 16:56 < chris_99> ahh 17:00 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 17:55 -!- Aurelius_Laptop [~cpopell@c-73-129-20-70.hsd1.md.comcast.net] has quit [Ping timeout: 240 seconds] 18:30 -!- Gurkenglas [Gurkenglas@dslb-178-000-178-156.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 244 seconds] 19:08 -!- Orpheon [~Orpheon@46.140.52.182] has quit [Read error: Connection reset by peer] 19:27 -!- sandeepkr__ [~sandeep@111.235.64.4] has joined ##hplusroadmap 19:30 -!- sandeepkr_ [~sandeep@111.235.64.4] has quit [Ping timeout: 250 seconds] 19:52 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 19:52 -!- ArturSha1 [~ArturShai@37.218.135.148] has joined ##hplusroadmap 20:33 -!- wbraun [~wbraun@dhcp-18-189-12-176.dyn.MIT.EDU] has quit [Ping timeout: 260 seconds] 20:35 -!- wbraun [~wbraun@dhcp-18-189-42-40.dyn.mit.edu] has joined ##hplusroadmap 20:57 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-qywquqbvygykcsea] has joined ##hplusroadmap 21:08 < abetusk> nmz787, sorry about that, it was a bug on my end. I just pushed a fix that I hope fixes it but beware if you use it. If you'd be willing to give me your sample input file, I could use it as a test. 21:08 < abetusk> also beware that the metric and inches conversion might not work as you expect it to 21:11 < abetusk> In terms of visualization, sometimes you need to do a little pre-processing to get he web g-code viewer working. I've tweaked my own to be a little bit more liberal in the g-code it accepts and put it on one of my servers: http://mechaelephant.com/ngc_view . The file gets uploaded to my sever (over an unsecure line) so be warned 21:11 < abetusk> sorry for all the caveats...you can see the tool is not widely used. I got something working and haven't stress tested it 21:25 -!- Guest26370 [~dog@cpe-69-201-45-125.twcny.res.rr.com] has quit [Ping timeout: 268 seconds] 21:42 -!- drewbot [~cinch@ec2-54-205-12-128.compute-1.amazonaws.com] has quit [Remote host closed the connection] 21:42 -!- drewbot [~cinch@ec2-54-158-23-246.compute-1.amazonaws.com] has joined ##hplusroadmap 22:16 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has quit [Read error: Connection reset by peer] 22:16 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has joined ##hplusroadmap 22:23 -!- Guest26370 [~dog@cpe-69-201-45-125.twcny.res.rr.com] has joined ##hplusroadmap 22:50 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:39 < nmz787> abetusk: cool I will check out how you fix diffs from what I did 23:41 < nmz787> abetusk: as kicad exports in mM only, I am definitely not sure what the units outputted in the g-code is (it seems like it is the same number as in the gerber, but with a decimal inserted)... i had to change the Z commands to M commands anyway, and shifted everything to be in the positive quadrant starting at 0,0 23:41 < nmz787> but I did change the g command in the outputted file to set metric, rather than the set-inches it was commanding 23:42 < nmz787> pushed something to the laser earlier and it seemed pretty OK 23:43 < nmz787> the visualization of the zen garden looked like the first 'garden' trace is too far from the first isolation-routing trace... but Horizontal seems fine --- Log closed Mon Apr 25 00:00:56 2016