--- Log opened Sun Mar 25 00:00:29 2018 00:01 -!- jtimon [~quassel@142.29.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 00:02 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Read error: Connection reset by peer] 00:03 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 00:08 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Ping timeout: 276 seconds] 00:58 -!- aeiousomething [~aeiousome@124.123.14.99] has joined ##hplusroadmap 01:22 -!- jtimon [~quassel@142.29.134.37.dynamic.jazztel.es] has quit [Ping timeout: 246 seconds] 01:28 -!- aeiousomething [~aeiousome@124.123.14.99] has quit [Ping timeout: 240 seconds] 01:46 -!- schindler [uid149928@gateway/web/irccloud.com/x-vhtthaensdljxiax] has joined ##hplusroadmap 01:47 < schindler> Hey folks, just wondering if anyone here has worked on python BRL-CAD? 01:48 < schindler> I'm planning to work with BRL-CAD this summer and wanted to revamp the python bindings and needed some help doing the same. 04:08 -!- aeiousomething [~aeiousome@27.59.187.235] has joined ##hplusroadmap 04:58 -!- redlegion [~redlegion@gateway/tor-sasl/redlegion] has quit [Ping timeout: 268 seconds] 04:59 -!- redlegion [~redlegion@gateway/tor-sasl/redlegion] has joined ##hplusroadmap 05:00 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 05:37 -!- aeiousomething [~aeiousome@27.59.187.235] has quit [Read error: Connection reset by peer] 06:29 < kanzure> schindler: i think nmz787 has done so 06:32 < schindler> @nmz787 Any documentation or code you could redirect me to? 06:34 < kanzure> schindler: https://github.com/nmz787/python-brlcad-tcl 06:38 < kanzure> i'm not really sure why he made this. ctypes is cool. 06:40 -!- emeraldgreen [~user@70.ip-145-239-90.eu] has joined ##hplusroadmap 06:40 -!- emeraldgreen [~user@70.ip-145-239-90.eu] has quit [Client Quit] 06:41 -!- emeraldgreen [~user@70.ip-145-239-90.eu] has joined ##hplusroadmap 07:43 < schindler> yea, so far even I've not found any issues with ctypes 07:46 -!- jtimon [~quassel@142.29.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 08:16 < kanzure> schindler: you should probably go and read the recent commits to ctypesgen (there's only like <50 commits) to see what was going on 08:16 < kanzure> schindler: it has some platform-specific code in a few places (which might help with your osx problem) 08:18 < schindler> Sure thing! 08:21 < kanzure> schindler: and this thing, https://github.com/kanzure/python-brlcad/blob/master/brlcad/install/post_install.py 08:22 < schindler> Thanks kanzure! All this is going to help a ton. I'll get back if I'm stuck somewhere 08:27 < archels> .g dna clock 08:27 < yoleaux> http://ipv6.google.com/sorry/index?continue=http://www.google.com/search%3F%26q%3Ddna%2520clock%26btnI%3D&q=EhAqAQT4AgFyMAAAAAAACGrnGOn_3tUFIhkA8aeDS_HozUSdXZv1sU2yfq1ulcUGyPzuMgFy 08:28 < archels> hmmm. via https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345458/ 08:29 < archels> "We chose repetitive microsatellite DNA that mutates (unlike point mutations) only as a result of cellular replication, providing us with a natural ‘cell-cycle counter’." 08:31 < kanzure> that would be useful with the cas9-based cell lineage tracing techniques 08:31 < kanzure> or er, cell lineage barcoding things 09:18 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 09:24 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 09:45 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 09:46 < kanzure> re: continuous ribosomal synthesis of proteins and nanoparticles. one immediately viable application would be the construction of proteins for debugging cellular state. you can make all kinds of sensors and reporter particles. and you need to rapidly iterate on which reporter particles you make so that you can follow the rabbit hole to figure out what the problem is. 09:48 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Client Quit] 09:50 < kanzure> unclear to me if anyone has used phosphoramidite chemistry with "enzymatic protecting groups" e.g. use of pencillin G acylase to remove a protecting group see page 6 section E http://diyhpl.us/~bryan/papers2/DNA/Enzymatic%20protecting%20group%20techniques.pdf 09:54 < kanzure> .tw https://twitter.com/cybergibbons/status/977823576702234627 09:54 < yoleaux> Cool repair of a damaged FPGA chip in a console https://wiki.arcadeotaku.com/w/Sega_Naomi_Repair_Logs https://pbs.twimg.com/media/DZHtWYSX0AA_bUY.jpg (@cybergibbons) 09:55 < kanzure> good stuff on oocyte science things http://www.rbmojournal.com/issues#decade=loi_decade_200 09:58 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 10:00 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 10:09 < nmz787> kanzure: schindler made that because kanzure's ctypes bindings didn't cause me anything but troubles 10:11 < nmz787> schindler: figured TCL interface won't be deprecated or broken as quickly as ctypes bindings 10:13 < kanzure> what trouble did you have? 10:15 < schindler> kanzure, nmz787 can I share the link to the tcl bindings (https://github.com/nmz787/python-brlcad-tcl) on the wiki page for python BRL-CAD? 10:15 < schindler> Also yea, what problems exactly? 10:16 < schindler> kanzure: Why did you make python bindings in the first place? What's wrong with just using c code? 10:19 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 260 seconds] 10:19 < nmz787> kanzure: it just didn't want to work with the latest SVN build... I don't know, something about function names changing or something, not really sure, it was like 5 years ago or something 10:19 < nmz787> schindler: sure, share away 10:20 < nmz787> schindler: I've mentioned it a few times on the BRLCAD mailing list, never really got any hits... there've been a bunch of people saying they were interested in Python stuff for google summer of code type projects... I would post my repo link, but no one ever replied, so I guess they never went any further with their project idea(s) 10:21 < nmz787> schindler: my goal was to enable people to get shit done, not deal with pointers and data-type casting pains 10:21 < nmz787> schindler: that's very important when you're targetting scientists, especially biologists 10:22 < kanzure> schindler: honestly i don't remember why i made python bindings (btw someone else worked on them for a while after me). i like rapid iteration i guess, and i don't like tcl that much? 10:24 < schindler> nmz787: sounds like you've got valid reasons to move to tcl 10:25 < schindler> kanzure, nmz787: do you think we could drop the earlier python BRL-CAD and create a new one building upon the TCL bindings? 10:26 < schindler> nmz787: Hate to sound selfish, but yea I'm planning to take this up as a GSoC project. Would you be up for mentoring? :D 10:26 < nmz787> schindler: my package doesn't care what version the binary is 10:27 < nmz787> and I don't really feel like learning TCL... honestly writing the conversions is the most TCL I've written 10:27 < nmz787> I kinda was using that as my only excuse to 'learn' TCL 10:28 < nmz787> schindler: not sure how much I can mentor... but I would support however I could 10:28 < schindler> I think ctypes also doesn't care what the version of the binary is 10:28 < nmz787> at this point my biggest pain point is the lack of an easy to use 3D editor GUI 10:28 < schindler> Ah! 10:28 < nmz787> I was most recenttly working something up, but it's super laggy 10:28 < schindler> What were you build it with? 10:29 < nmz787> I think it was Python Tkinter :P 10:29 < nmz787> there was also some C/C++ Qt program that someone posted a few months ago to the mailing list 10:29 < schindler> I think tkinter tends to lag if you've got rapid refreshes (IIRC from some article I read) 10:30 < nmz787> but their approach was essentially the same as my Python Tkinter approach: render an image of your model, then show the image in an image-widget 10:30 < nmz787> super laggy 10:30 < nmz787> (render it with system/command-line calls to the existing BRLCAD tools to generate an image of a model) 10:30 < schindler> It'd be real fun to actually solve this :P 10:31 < nmz787> https://sourceforge.net/p/brlcad/mailman/message/36182970/ 10:34 < nmz787> https://sourceforge.net/p/brlcad/mailman/message/36207551/ 10:34 < schindler> "but obviously I 10:34 < schindler> > could probably /somehow/ use the actual C++ GUI stuff BRL-CAD already 10:34 < schindler> > has" 10:34 < schindler> Could we not use Cython for this? I'm just making a wild guess here 10:34 < nmz787> hmm, apparently I've been posting on the users forum... I wonder if I'd get more response posting on the devel forum 10:35 < nmz787> I forgot I was subscribed to them both... they all just go to a BRLCAD filter in my email box 10:35 < nmz787> schindler: brlcad isn't C 10:35 < nmz787> it's C++ 10:36 < schindler> Wait, Cython doesn't support C++. 10:36 < schindler> Oh shoot! 10:36 < nmz787> not sure, wiki says it does 10:36 < schindler> Not completely though 10:36 < kanzure> python-brlcad-tcl doesn't use tcl bindings 10:37 < schindler> Do you have any ideas on what we could experiment with to do away with the lag if a gui were to be made? 10:37 < nmz787> kanzure: right, it generates TCL data files, then feeds them into the existing BRLCAD TCL processors 10:38 -!- gabbar1947 [uid205515@gateway/web/irccloud.com/x-qyaiemumamruzpfa] has joined ##hplusroadmap 10:38 < kanzure> python-brlcad can be modified to run an interactive visualization tool from brlcad i think 10:38 < kanzure> requires some sort of eventloop to be added 10:38 < nmz787> schindler: it would seem to have to be C++ code, compiled with the BRLCAD code, to do all the rendering in the same process, then it could be more-quickly drawn to a frame-buffer 10:39 < kanzure> that's false nmz787 10:39 < nmz787> ? 10:39 < nmz787> you want to do IPC? 10:39 < kanzure> heh no 10:39 < nmz787> interprocess comms? 10:39 < kanzure> ctypes is already using the same process 10:39 < nmz787> sure, how does that falsify "C++ code, compiled with the BRLCAD code" 10:40 < kanzure> "it would seem to have to be [x] to do all the rendering in the same process" i am saying that your statement is too limiting (interactive rendering in the same process does not require C/C++) 10:40 < nmz787> schindler: simple experiment I was doing was simply opening a model in the GUI, rotate... you'll see/feel the lag 10:40 < kanzure> which gui 10:41 < nmz787> but the BRLCAD code is all C++ 10:41 < nmz787> so you either have to manage to compile a library 10:41 < nmz787> which seemed to be fraught with issues 10:41 < nmz787> or compile with your GUI 10:41 < nmz787> link 10:41 < nmz787> etc 10:41 < kanzure> huh? have you done this before or are you just guessing? 10:42 < kanzure> do you remember pythonocc's interactive visualizer? 10:42 < nmz787> I've compiled Python extensions, and C++ libraries to use to link to other compiled things 10:42 < nmz787> yes 10:42 < nmz787> no, don't remember that GUI 10:43 < kanzure> .title https://www.youtube.com/watch?v=swUPSa2zyrY 10:43 < yoleaux> Node-OCC Demonstration - YouTube 10:44 < kanzure> this ain't the python one, but it's a nicer video anyway. 10:44 < nmz787> what's your point though? 10:45 < schindler> " C++ code, compiled with the BRLCAD code" : I'm still confused how you would do this nmz787 10:45 < kanzure> only limiting factor is whether brlcad has a real-time rendering mode, nmz787 10:45 < nmz787> schindler: another point I should make, I wanted to hook my GUI up so it generated Python code (even if it was too verbose, that could be refactored by a human later) 10:47 < nmz787> schindler: you just code up a Qt GUI layout, then include the BRLCAD header files, then you have to setup your BRLCAD objects, and link your GUI buttons to perform BRLCAD object operations, code the image display stuff, taking the render buffer and moving it to the framebuffer 10:49 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 10:49 < schindler> Yea, sounds reasonably doable! 10:50 < nmz787> they have a starter project here... I wasn't able to get that branch to compile though when I last tried: https://sourceforge.net/p/brlcad/code/HEAD/tree/brlcad/branches/qtged/src/qged/ 10:50 < schindler> I didn't get that part about the GUI generating the python code? Could you elaborate a bit on that? 10:51 < gabbar1947> *** grabs popcorn *** 10:52 -!- augur [~augur@2600:380:8451:6226:1de2:87e6:9b22:cb65] has joined ##hplusroadmap 10:53 < nmz787> like if I want to make a new box object in the GUI, I would click a box icon, then in a 3D landscape image/view I would click a grid point where I wanted the first corner of the box... then move the mouse and click a second grid point, and that would be my box... then the code would take those two points and just plug-n-chug... it would generate the Python code which says 'make a box with these two 10:53 < nmz787> corner points', shove that in the 'current project' text file, send the Python to get converted to TCL, send that TCL to BRLCAD interpreter to be modelled, then render model, then display rendering in GUI 10:54 < nmz787> (in my world where I am still using TCL as an intermediary to stay away from low-level programming woes) 10:59 < nmz787> if there was a way to load un-modified BRLCAD libraries into Python using ctypes, that might be enough to then shove TCL at, and pull out a rendered image buffer 10:59 < nmz787> I guess someone has to try it 11:00 < nmz787> kanzure seems like the more knowledgable person to talk on that 11:05 < kanzure> actually i forget whether python-brlcad required modified brlcad libraries 11:10 < nmz787> well it doesn't work out of the box, at least not for me "ImportError: /usr/brlcad/dev-7.25.0/lib/libwdb.so not found." 11:15 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Quit: WeeChat 2.0] 11:16 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 11:17 < nmz787> exporting BRLCAD_PATH doesn't have any effect either 11:18 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 11:18 < nmz787> omg tons of hard-coded paths, and none of them appear to check the BRLCAD_PATH env var 11:18 < nmz787> hmm, maybe I need to uninstall and reinstall 11:19 < nmz787> and that fails too 11:19 < nmz787> (setup.py itself) 11:20 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 11:44 -!- aeiousomething [~aeiousome@124.123.14.99] has joined ##hplusroadmap 12:07 -!- aeiousomething [~aeiousome@124.123.14.99] has quit [Ping timeout: 276 seconds] 12:12 -!- fluke`` [~user@193.165.236.4] has quit [Ping timeout: 240 seconds] 13:11 -!- augur [~augur@2600:380:8451:6226:1de2:87e6:9b22:cb65] has quit [Remote host closed the connection] 13:15 -!- JayDugger1 [~jwdugger@47.185.249.138] has joined ##hplusroadmap 13:17 -!- JayDugger [~jwdugger@47.185.249.138] has quit [Ping timeout: 256 seconds] 13:35 -!- augur [~augur@2600:380:846c:b2c1:397c:c9e6:15b6:a0a6] has joined ##hplusroadmap 13:50 -!- JayDugger1 [~jwdugger@47.185.249.138] has quit [Quit: Leaving.] 14:37 -!- gabbar1947 [uid205515@gateway/web/irccloud.com/x-qyaiemumamruzpfa] has quit [Quit: Connection closed for inactivity] 14:38 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-iehjpsbpwyutxkxc] has joined ##hplusroadmap 14:49 -!- augur [~augur@2600:380:846c:b2c1:397c:c9e6:15b6:a0a6] has quit [Remote host closed the connection] 14:53 -!- aeiousomething [~aeiousome@124.123.14.99] has joined ##hplusroadmap 15:01 -!- emeraldgreen [~user@70.ip-145-239-90.eu] has quit [Quit: Leaving.] 15:20 -!- aeiousomething [~aeiousome@124.123.14.99] has quit [Ping timeout: 263 seconds] 15:22 -!- aeiousomething [~aeiousome@124.123.14.99] has joined ##hplusroadmap 15:36 < superkuh> Hah. sci-bay already had to close. 15:36 < superkuh> Lasted about 2 days after being popularized on a hackernews thread. 16:27 -!- gabbar1947 [uid205515@gateway/web/irccloud.com/x-fozdhbhnnnuqxwsh] has joined ##hplusroadmap 16:28 -!- heath [~heath@unaffiliated/ybit] has quit [Ping timeout: 264 seconds] 16:28 -!- heath [~heath@unaffiliated/ybit] has joined ##hplusroadmap 16:29 -!- rancyd_ [stryfe@gateway/shell/firrre/x-jomsnjoixzwjvvkv] has quit [Ping timeout: 245 seconds] 16:31 -!- rancyd [stryfe@gateway/shell/firrre/x-tybmcodlcmpnsttp] has quit [Ping timeout: 276 seconds] 16:34 -!- rancyd [stryfe@gateway/shell/firrre/x-tlitixrmzaqzrxcl] has joined ##hplusroadmap 16:50 < kanzure> nmz787: did you install brlcad? 17:24 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-iehjpsbpwyutxkxc] has quit [Quit: Connection closed for inactivity] 17:35 < kanzure> https://www.coindesk.com/bitcoins-next-year-tech-development-coming-focus/ 17:41 -!- solarnetone [~scott@rrcs-67-79-182-237.se.biz.rr.com] has quit [Ping timeout: 276 seconds] 17:54 -!- solarnetone [~scott@rrcs-67-79-182-237.se.biz.rr.com] has joined ##hplusroadmap 18:05 -!- schindler [uid149928@gateway/web/irccloud.com/x-vhtthaensdljxiax] has quit [Quit: Connection closed for inactivity] 18:06 -!- drewbot_ [~cinch@54.92.225.106] has quit [Remote host closed the connection] 18:59 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 19:03 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 19:06 -!- gabbar1947 [uid205515@gateway/web/irccloud.com/x-fozdhbhnnnuqxwsh] has quit [Quit: Connection closed for inactivity] 19:11 -!- ebowden_ [~ebowden@128.250.0.194] has quit [Remote host closed the connection] 19:21 -!- ebowden [~ebowden@128.250.0.194] has joined ##hplusroadmap 19:23 -!- ebowden [~ebowden@128.250.0.194] has quit [Remote host closed the connection] 19:23 -!- ebowden [~ebowden@128.250.0.194] has joined ##hplusroadmap 19:28 -!- ebowden [~ebowden@128.250.0.194] has quit [Ping timeout: 248 seconds] 19:31 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 276 seconds] 19:49 -!- ebowden [~ebowden@128.250.0.194] has joined ##hplusroadmap 19:49 -!- ebowden [~ebowden@128.250.0.194] has quit [Remote host closed the connection] 19:51 -!- ebowden [~ebowden@128.250.0.194] has joined ##hplusroadmap 19:57 -!- ebowden [~ebowden@128.250.0.194] has quit [Remote host closed the connection] 20:05 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has joined ##hplusroadmap 20:09 < kanzure> blooort 20:21 -!- solarnetone [~scott@rrcs-67-79-182-237.se.biz.rr.com] has quit [Read error: No route to host] 20:30 -!- rancyd [stryfe@gateway/shell/firrre/x-tlitixrmzaqzrxcl] has quit [Ping timeout: 276 seconds] 20:30 < kanzure> "A bit-encoding based new data structure for time and memory efficient handling of spike times in an electrophysiological setup" https://link.springer.com/article/10.1007%2Fs12021-018-9367-z 20:31 -!- drewbot [~cinch@54.167.51.167] has joined ##hplusroadmap 20:35 -!- rancyd [stryfe@gateway/shell/firrre/x-shuywkjqixbekxmp] has joined ##hplusroadmap 20:44 < heath> https://github.com/aqlaboratory/proteinnet "Standardized data set for machine learning of protein structure 20:45 < heath> "Much like ImageNet helped spur the development of new computer vision techniques, ProteinNet aims to facilitate ML research on protein structure by providing a standardized data set, and standardized training / validation / test splits, that any group can use with minimal effort to get started." 20:57 -!- ebowden [~ebowden@128.250.0.194] has joined ##hplusroadmap 21:01 -!- ebowden [~ebowden@128.250.0.194] has quit [Ping timeout: 256 seconds] 21:04 -!- jtimon [~quassel@142.29.134.37.dynamic.jazztel.es] has quit [Ping timeout: 260 seconds] 21:08 -!- CandleGlow [~CandleGlo@unaffiliated/candleglow] has quit [Quit: ...and all my responses they stay the same.] 21:11 -!- schindler [uid149928@gateway/web/irccloud.com/x-zntbsvmrvairsigq] has joined ##hplusroadmap 21:31 -!- ebowden [~ebowden@128.250.0.220] has joined ##hplusroadmap 21:33 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Quit: ORGANS IN MAINS] 21:41 -!- ebowden_ [~ebowden@128.250.0.200] has joined ##hplusroadmap 21:44 -!- ebowden [~ebowden@128.250.0.220] has quit [Ping timeout: 240 seconds] 21:47 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 22:03 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 22:30 -!- aeiousomething [~aeiousome@124.123.14.99] has quit [Ping timeout: 276 seconds] 22:47 -!- yashgaroth [~yashgarot@2606:6000:c308:f700:bdaf:2b60:4c7b:3d44] has quit [Quit: Leaving] 22:57 -!- augur [~augur@2600:380:8710:e401:a1e9:480e:9188:dfc4] has joined ##hplusroadmap 23:01 -!- augur [~augur@2600:380:8710:e401:a1e9:480e:9188:dfc4] has quit [Remote host closed the connection] 23:05 -!- augur [~augur@2600:380:873e:ad18:7134:6e5f:cb6c:6523] has joined ##hplusroadmap 23:17 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 23:22 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 248 seconds] 23:24 -!- augur [~augur@2600:380:873e:ad18:7134:6e5f:cb6c:6523] has quit [Remote host closed the connection] 23:33 -!- jtimon [~quassel@142.29.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 23:40 -!- gabbar1947 [uid205515@gateway/web/irccloud.com/x-udsnondwbsuokyuh] has joined ##hplusroadmap --- Log closed Mon Mar 26 00:00:29 2018