--- Log opened Sat Nov 21 00:00:31 2015
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00:38 < archels> .title http://advances.sciencemag.org/content/1/10/e1501136
00:38 < yoleaux> Electronic plants | Science Advances
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05:10 < kanzure> http://gnusha.org/logs/archives/hplusroadmap-2015-11-21.tar.gz af63bce07bf33da0d894edffa5fec5f7481670d58f23665620602c5d5cee8224
05:34 < kanzure> what's with the file corruption in 2008-03-25.log ?
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06:33 < kanzure> perhaps the data corruption fairies got to that file before i could
06:35 < kanzure> doh, it's a tar file
06:35 < kanzure> nobody has noticed all these years?
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07:12 < kanzure> updating 2010-07-05.log to include 2010-07-05.initial.log, old hash was 01e681a1562a6541ce25b88318c81c68fbf3a70192745f555232fe9294a51417 new hash is 3fba336e9e7dcb42fb4f8e44d0b150c2f53b3184c6bb7e479dbc47751455b96a
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07:35 < kanzure> file *.log reports that some of the logs are "UTF-8 Unicode text, with very long lines" while others are "Python"
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07:42 < kanzure> hplusroadmap-2015-11-21.tar.gz 9fea9fbf68626ce5842b75f12653550f4c8eb7d6a4d668cb805435f9481ada91 not af63bce07bf33da0d894edffa5fec5f7481670d58f23665620602c5d5cee8224
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08:35 < pasky> my logs start on 2010-10-31 but are quite complete, if you have any gaps
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10:33 < kanzure> .title http://biorxiv.org/content/early/2015/11/20/032417
10:33 < yoleaux> Genome-wide analysis of over 106,000 individuals identifies 9 neuroticism-associated loci | bioRxiv
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11:02 < kanzure> http://gnusha.org/logs/graphs/300-days-anycolor-heatmap-cropped.png
11:03 < kanzure> image is a heatmap visualization of text mass from 300 days of early hplusroadmap logs (horizontal axis is HH:MM vertical axis is log day)
11:03 < cluckj> neat
11:05 < cluckj> did you/can you do that with specific words?
11:07 < kanzure> can you be more particular?
11:09 < cluckj> like "bitcoin" or "microfluidics" or "FDA"?
11:10 < kanzure> oops i think that was random sort, here is fixed version http://gnusha.org/logs/graphs/300-days-anycolor-heatmap-cropped-sorted.png
11:10 < kanzure> yeah i could do something with particular words, but not sure what strategy to use?
11:10 < kanzure> rate of mention of "microfluidics" is not too high!
11:10 < kanzure> so not sure what visualization to show for that
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11:12 < cluckj> try the same heatmap thing
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11:14 < kanzure> i'm not sure what to do there? you mean set to 0 every line that does not mention "microfluidics"?
11:14 < cluckj> yeah
11:15 < kanzure> that would be basically everything, though
11:15 < cluckj> hmm
11:16 < cluckj> yes?
11:16 < kanzure> so it would just be blue with like 1 red pixel every 20 days or something
11:16 < cluckj> heatmaps are good for finding intersections between things that you haven't noticed before
11:17 < cluckj> so like microfluidics + cheese, or something of that nature
11:17 < kanzure> ok, sounds like you want something like, "same graph structure, but highlight any HH:MM with a special color when a word out of some_list is found"
11:18 < kanzure> but what happens if more than one word is found in same HH:MM segment?
11:18 < kanzure> (from the same list)
11:19 < kanzure> also: why is there so much vertical correlation in this image?
11:19 < kanzure> time-of-day correlation makes sense because some people have a temporally-decided schedule. but i'm not sure that should correlate vertically with line length/text density...
11:21 < cluckj> do HH:MM:SS?
11:22 < fenn> you're probably parsing the time wrong
11:22 < fenn> like it's actually MM:SS being plotted maybe
11:23 < fenn> that would be a really surprising temporal regularity if it were true
11:23 < fenn> "tune in to ##hplusroadmap on the hour every hour"
11:23 < kanzure> there's no :SS data
11:23 < cluckj> haha
11:24 < fenn> or maybe you're parsing 0-60 out of 100
11:25 < kanzure> out of 100?
11:25 < fenn> it's not regular enough for that, nevermind
11:26 < kanzure> https://gist.github.com/kanzure/110ecb73abc3a9f9c28b
11:26 < fenn> merry textmas
11:28 < cluckj> you mean textmass
11:29 < kanzure> i see ~35 vertical columns at the bottom of that last .png
11:29 < kanzure> kinda hard to count because they sorta blur together. maybe 25-35.
11:29 < kanzure> maybe there's a bias towards 10 minute intervals
11:32 < kanzure> "2:20pm oh boy, this is an especially hplusroadmappy time to send a message"
11:34 < cluckj> could be an artifact of pixel sizing?
11:34 < kanzure> and why are there multiple days in a row where all vertical columns break
11:35 < fenn> shouldn't this be sorted? data.append(some_day.values())
11:36 < kanzure> some_day is dictionary of HH:MM -> int
11:36 < fenn> sorted by key
11:36 < fenn> dicts are arbitrarily ordered based on whatever python feels like
11:37 < kanzure> applying extra sorting
11:38 < cluckj> oh
11:38 < cluckj> isn't one of the axes a log scale?
11:38 < fenn> no
11:38 < fenn> "log" means the text file
11:39 < cluckj> duh
11:39 < kanzure> old: http://gnusha.org/logs/graphs/300-days-anycolor-heatmap-cropped-sorted.png
11:39  * cluckj facepalm
11:39 < kanzure> new: http://gnusha.org/logs/graphs/300-days-anycolor-heatmap-cropped-really-sorted.png
11:39 < fenn> that looks better
11:39 < fenn> see if you can find daylight savings shifts :P
11:40 < kanzure> wasn't able to generate this graph for all 2555 days because computer hates me
11:40 < cluckj> haha
11:42 < cluckj> haha at fenn, not your jerk computer
11:42 < fenn> maybe you should plot pixel brightness on a logarithmic scale, because there are a few walls of text that throw off the entire color scale
11:43 < kanzure> not sure how to do that
11:44 < fenn> plt.pcolor(math.log(data)) ?
11:46 < kanzure> 730 days http://gnusha.org/logs/graphs/hplusroadmap-textmass-heatmap-2013-11-22-to-2015-11-21.png
11:49 < kanzure> math.log ValueError: math domain error
11:50 < kanzure> oh, 0
11:50 < fenn> um, numpy.log ?
11:52 < kanzure> http://gnusha.org/logs/graphs/hplusroadmap-textmass-heatmap-2013-11-22-to-2015-11-21-logarithmic-color-scale.png
11:53 < fenn> woah
11:55 < fenn> oh it's not one pixel line per day
11:56 < kanzure> matplotlib is weird
11:56 < kanzure> i'm not tied to it
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12:01 < kanzure> updated http://gnusha.org/logs/graphs/textmass.py
12:16 < kanzure> cluckj: any other plotting ideas?
12:19 < cluckj> not specifically
12:20 < cluckj> you might want to do a "times mentioned" search
12:20 < cluckj> like one of those word cloud things
12:21 < kuudes> if you have percentages or similar fractions, I have found it useful to take first succession rule of them which removes 0% and 100% and centers it, and then take logit out of it
12:23 < cluckj> kanzure, what I look for when I do discourse analysis (qualitatively) is intersections of words/concepts that are surprising or unconnected, then try to figure out how they are related to one another
12:23 < cluckj> so if there are a bunch if lines that contain "X" and "Y," but it's not clear how they are related to one another, you have a novel connection that you can explore
12:24 < cluckj> let me see if I can find the map I did for DIYbio
12:30 < cluckj> :( no luck
12:36 < kanzure> maybe i'll do 30-day-wide graph with coloration of which days a term was mentioned. then regenerate graph for a different word to search. but not sure what value to expect from this sorta graph.
12:40 < kuudes> so, that is two years per each minute to a dot? I suppose ##hplusroadmap has drifted to earlier times? and people irc more on summer vacation than they do otherwise and also on winter vacation so I guess there are reasonable amount of students on the channel
12:53 < cluckj> yes
12:55 < kanzure> http://gnusha.org/logs/graphs/hplusroadmap-textmass-heatmap-2008-to-2015-logarithmic-color-scale.png
13:02 < kanzure> fenn: i was thinking of doing a full-read of the logs, but want to do pre-work correctly.
13:03 < kanzure> fenn: in particular i was thinking i should write down all the things i should expect to find, so that when i am done i can fix whatever didn't meet my expectations
13:03 < kanzure> was also thinking of making bookmarks to particular timestamps, or dumping certain kinds of material into certain wiki pages (but i don't know which types to focus on, haven't thought about this yet)
13:05 < kanzure> i could write down signal-noise ratio estimates for different segments of text. or write down weights for whatever tags i bookmark different sections with.
13:07 < kanzure> oh i wanted to write down a "technology index" since we seem to mention stuff that everyone else tends to forget about
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13:10 < cluckj> sorry for not being more of a help
13:11 < kanzure> an index of diagrams and figures from papers we have read (or at least, the diagrams and figures that we have mentioned) would be fun
13:11 < cluckj> I am in deadline hell for a couple weeks
13:13 < cluckj> intro/conclusion/abstract due monday, then by 12/4 the whole thing needs to be immaculately copy edited and turned in
13:14 < kanzure> what happened to being done before defending?
13:14 < cluckj> I was, these are revisions
13:14 < kanzure> brutal
13:15 < cluckj> yeah
13:15 < cluckj> they're "easy" revisions, relatively speaking
13:16 < cluckj> honestly if they had given me anything that I couldn't complete in time to graduate in december, I would have called it quits
13:20 < kanzure> i should also extract a list of recommended scifi
13:21 < kanzure> written summaries?
13:24 < cluckj> I'm doing those right now
13:24 < cluckj> I hadn't updated them for the final draft, so I had to do them over again as part of a new introduction
13:25 < cluckj> luckily for me I had to summarize everything in the defense presentation
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13:33 < cluckj> oh crap I need to copyright and CC license this before then too
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14:46 < kanzure> "So maybe this will lead to open source Jurassic Park style dinosaur code on GitHub that you can write to DNA and breed?" although funny is somewhat sad; programmers are always going to be very disappointed when they learn about biology, i think.
14:46 < kanzure> from https://news.ycombinator.com/item?id=10604522
14:46 < cluckj> lol
14:47 < cluckj> "wait, synbio is just like legos and programming?? that's so easy"
14:48 < cluckj> the engineering metaphors are goofy and reductive
14:48 < cluckj> but they get people who wouldn't otherwise be interested in biology into it
14:50 < kanzure> yeah but that's a recipe for producing really really angry users
14:50 < kanzure> "WHAT DO YOU MEAN it's nothing like legos?"
14:51 < kanzure> visual phenotype of software is pixel-controllable (sometimes), but by comparison there's no direct 1:1 between genotype and phenotype
15:00 < fenn> the heatmap should have a pixel dimension of 1440x2550ish
15:05 < kanzure> right
15:24 < kanzure> http://gnusha.org/bitcoin-wizards/graphs/bitcoin-wizards-textmass-2014-10-19-to-2015-11-21.png
15:24 < kanzure> the vertical line on the left turns out handy for calibration
15:27 < kanzure> wait.. a blue background doesn't make sense.
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16:08 < kanzure> compare these two:
16:08 < kanzure> http://gnusha.org/logs/graphs/hplusroadmap-textmass-heatmap-2008-to-2015-logarithmic-color-scale.png
16:08 < kanzure> http://gnusha.org/logs/graphs/hplusroadmap-textmass-heatmap-2008-to-2015-pypng.png
16:09 < kanzure> vertical order was flipped for pypng version, but other things seem wrong to me
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16:23 < kuudes> why is there the drift to earlier time? is this because of mismatch in day length, say 1441 minutes per day or something, or is there a real effect?
16:36 < fenn> pypng is 1438 pixels wide and has three bands alternating transparent-gray then clear then transparent-gray which drift down and right 20 degrees, (or just dimming of those pixels?) also the image is sorta but not exactly repeated 3 times in the horizontal direction and the overall dimensions are off by a factor of about 3 (units 7yr 1438*917min = 2.79)
16:38 < fenn> great, and now i am seeing ghostly skull images in the data
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16:52 < kanzure> http://gnusha.org/bitcoin-wizards/graphs/bitcoin-wizards-textmass-2014-10-19-to-2015-11-21-better.png
16:54 < kanzure> http://gnusha.org/logs/graphs/hplusroadmap-textmass-heatmap-2008-to-2015-pypng-better.png
16:58 < kanzure> since andy-logbot is calibrated correctly in the -wizards version i'm gonna guess that the other graph is also correct now
17:04 < fenn> looks right
17:05 < fenn> good work, you are not a "data scientist"
17:05 < fenn> now*
17:05 < fenn> heh
17:09 < kanzure> only true once i can factor out the bias for your 2 week time jumps
17:13 < kanzure> graph would be more useful if i could query by tags and tag scores.. e.g. "microfluidics OR neuroscience" (and have some magic hypernym stuff going on in the background thanks to the glorious wordnet) and then color by cumulative score.
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17:17 < cluckj> yes
17:17 < cluckj> that might give you some interesting intersections of topics
17:23 < kanzure> http://diyhpl.us/~bryan/irc/extropians/irclogs/lesswrong-irc-logs-textmass-2010-09-10-to-2015-09-21.png
17:24 < cluckj> I'm seeing a ghastly ayn rand face there
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17:31 < kanzure> i think that last one is more accurately described as a graph of freenode downtime
17:39 < cluckj> almost at 2000 words for the day
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17:43 < kanzure> oops wrong filename
17:43 < kanzure> http://diyhpl.us/~bryan/irc/extropians/irclogs/lesswrong-irc-logs-textmass-2010-09-10-to-2015-11-21.png
17:44 < kanzure> http://diyhpl.us/~bryan/irc/irc-log-graphs/electronics-irc-logs-textmass-2010-08-03-to-2015-11-21.png
17:47 < kanzure> http://diyhpl.us/~bryan/irc/irc-log-graphs/reprap-irc-logs-textmass-2010-08-03-to-2015-11-21.png
17:52 < kanzure> heh reprap logs are larger than python, javascript, nodejs, linux, electronics, jqurey, rubyonrails, git, bitcoin logs. (lesswrong comes in behind dogecoin and bitcoin logs.)
17:59 < kanzure> http://diyhpl.us/~bryan/irc/irc-log-graphs/bitcoin-irc-logs-textmass-2010-11-16-to-2015-11-21.log
18:01 < kanzure> http://diyhpl.us/~bryan/irc/irc-log-graphs/bitcoin-dev-irc-logs-textmass-2013-03-12-to-2015-11-21.png
18:11 < kanzure> http://diyhpl.us/~bryan/irc/irc-log-graphs/swhack-irc-logs-textmass-2013-01-15-to-2015-11-21.png
18:11 < kanzure> swhack visualization is somewhat unique
18:20 < kanzure> ugh i should do this for email
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18:45 < drethelin> kanzure are there any good transfection forums out there
18:45 < drethelin> that it would be usefull for me to make a post on advertising fugene
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19:00 < kanzure> protocol-online? but really, adwords dude
19:00 < kanzure> adsense i mean
19:02 < drethelin> yeah I know
19:02 < drethelin> dad is being weird about wanting to try various things before that
19:03 < drethelin> http://www.protocol-online.org/forums/topic/35058-free-samples-of-fugene-hd/
19:03 < kanzure> find some magic articles on hubspot, pick a few things to show him
19:04 < kanzure> lifecycle drip-line emails, stuff about funnels, evergreen content, the usual....
19:07 < kanzure> tell him to do a deal with indiebio, genspace, biotechnbeyond, counter culture labs, etc.
19:07 < kanzure> or p212121
19:07 < drethelin> he wants to try to do some stuff with competitor URLs first
19:08 < drethelin> but he told me I could post to forums :/
19:08 < kanzure> absolutely nothing beats a good marketing funnel
19:10 < drethelin> sure
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