| --- Log opened Sun Apr 24 00:00:55 2016 | ||
| 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 | 01:29 |
|---|---|---|
| nmz787 | not sure how easy your tool is to modify to do a sort of flood-fill of those areas | 01:30 |
| abetusk | nmz787, it has a fill already, horizontal, vertical and 'zen garden'. | 01:33 |
| 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 | 01:36 |
| 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) | 01:50 |
| nmz787 | I am messing with plotting the gerbers with python and wxpython | 01:52 |
| nmz787 | it looks like I just got something close to good: http://paste.pound-python.org/show/A2jFQYXOp3t7mSaFqVwi/ | 01:53 |
| nmz787 | http://imgur.com/R4uuNx3 | 01:55 |
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| nmz787 | ok, well now to try your thing | 01:57 |
| nmz787 | hmm, I am getting "PARSE ERROR: coordinate format exceeded at line 29" where line 29 is the first XY line: X179350499Y-122082495D02* | 02:01 |
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| nmz787 | abetusk: got it to work by changing pos = max_buf-2; to pos = max_buf-1; in gerber_interpret.c :/ | 02:39 |
| nmz787 | though I wonder if my leading 0's weren't added | 02:40 |
| nmz787 | abetusk: seems the other important piece of that parsing setup is this prior line: %FSLAX46Y46*% | 02:58 |
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| 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. | 03:43 |
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| 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 | 08:47 |
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| archels_ | http://www.neuroscientistnews.com/research-news/first-gene-therapy-successful-against-human-aging | 09:33 |
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| 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 | 10:44 |
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| nmz787 | sup | 11:24 |
| yoleaux | 10:43Z <chris_99> 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 | 11:24 |
| chris_99 | yeah, i'm gonna look into the filter approach it mentions too | 11:25 |
| 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 | 11:26 |
| 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 | 11:27 |
| 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 | 11:28 |
| 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 | 11:29 |
| 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 | 11:30 |
| 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 | 11:31 |
| 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 | 11:32 |
| 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 | 11:33 |
| 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) | 11:34 |
| chris_99 | sorry, i mean, if i wanted to attempt to distinguish between plants, i'd need a more powerful PSU? | 11:35 |
| 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 | 11:36 |
| 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 | 11:37 |
| 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 | 11:38 |
| 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 | 11:39 |
| nmz787 | https://www.thermofisher.com/order/catalog/product/4322288 | 11:40 |
| chris_99 | eek, that's expensive | 11:40 |
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| 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 | 11:40 |
| 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? | 11:41 |
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| 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 | 11:42 |
| 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? | 11:43 |
| 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 | 11:45 |
| chris_99 | aha cheers, that makes sense | 11:46 |
| 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 | 11:47 |
| 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 | 11:48 |
| nmz787 | but people just say its some different cultivar, not species | 11:49 |
| 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 | 11:51 |
| kanzure | .title https://youtube.com/watch?v=-lgYYz3y_hY | 11:57 |
| yoleaux | Lightning Network as a Directed Graph: Single-Funded Channel Network Topology - YouTube | 11:57 |
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| kanzure | "neural network to colorize grayscale images" https://github.com/pavelgonchar/colornet | 12:09 |
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| kanzure | .title https://news.ycombinator.com/item?id=11559684 | 15:20 |
| yoleaux | Telomere lengthening via gene therapy in a human individual | Hacker News | 15:20 |
| 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.... | 15:21 |
| 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 |
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| kanzure | https://www.edge.org/conversation/george_church-the-augmented-human-being | 15:25 |
| maaku | kanzure perhaps this is protein design vs protein prediction. Avoid the things you don't know how to fold. | 15:37 |
| kanzure | oh. | 15:38 |
| 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. | 16:00 |
| kanzure | http://arep.med.harvard.edu/webpage-%20science%20info%20-%20lab%20members/Bobby/Bobby%20Dhadwar.htm | 16:01 |
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| 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 | 16:09 |
| 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 | 16:15 |
| chris_99 | heh, sorry to be specific i'm talking about dry leaves | 16:16 |
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| 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 | 16:41 |
| 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) | 16:42 |
| 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 | 16:43 |
| 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 | 16:44 |
| 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 | 16:45 |
| nmz787 | (when checking a little ruler pattern with a cheap digital plastic micrometer) | 16:46 |
| 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/ | 16:47 |
| nmz787 | chris_99: I got this to upgrade to next: http://www.diyouware.com/node/116 | 16:49 |
| nmz787 | which is detailed a bit more here http://www.diyouware.com/node/164 | 16:50 |
| nmz787 | .title http://www.diyouware.com/node/161 | 16:51 |
| yoleaux | Hacking the PHR-803T | Diyouware.com | 16:51 |
| chris_99 | nice, looks fun | 16:51 |
| chris_99 | planning on using for uv pcbs or something | 16:52 |
| nmz787 | that would be nice to do | 16:52 |
| nmz787 | i've got copper clad and some photoresist | 16:53 |
| nmz787 | ultimately I want to try microfluidics | 16:53 |
| chris_99 | i'm confused, you mean to use the laser to etch plastic for that? | 16:55 |
| 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 | 16:56 |
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| 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 | 21:08 |
| 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 | 21:11 |
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| nmz787 | abetusk: cool I will check out how you fix diffs from what I did | 23:39 |
| 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 | 23:41 |
| nmz787 | pushed something to the laser earlier and it seemed pretty OK | 23:42 |
| 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 | 23:43 |
| --- Log closed Mon Apr 25 00:00:56 2016 | ||
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