| --- Day changed Sat Jul 19 2008 | ||
| ybit | i've been chowing, yep, and it seems to prefer the uninstalled life | 00:08 |
|---|---|---|
| ybit | http://esw.w3.org/topic/HCLS/Banff2007Demo/HCLS/Banff2007Demo/HowToMakeOneForYourself | 00:08 |
| kanzure | gahh | 00:09 |
| ybit | didn't see this either? :P | 00:11 |
| ybit | krispy kreme is so evil | 00:12 |
| ybit | why do they have to flash the 'fresh' sign! | 00:12 |
| ybit | it's not fair they are situated three blocks from me | 00:13 |
| ybit | damn them! | 00:14 |
| ybit | ooh, now that's a nice link: http://sw.neurocommons.org/2007/kb-sources/ | 01:01 |
| ybit | don't start a flame-war with me kanzure ;) | 01:02 |
| ybit | the files on the page "HowToMakeOneForYourself" should be in the diybio repository | 01:03 |
| ybit | s/on/mentioned | 01:03 |
| ybit | for anyone following the guide, if you get sidetracked here: http://virtuoso.openlinksw.com/wiki/main/Main/VOSMake#Package%20Dependencies make sure to hit the back button! your app isn't complete | 01:04 |
| kanzure | your app isn't complete? | 01:06 |
| kanzure | ybit: don't know why that's a flame war | 01:06 |
| kanzure | I agree this should be in the repo | 01:06 |
| kanzure | let me go add it :) | 01:06 |
| ybit | that was just in case you decided to argue, since that's what you do ;P | 01:07 |
| kanzure | :( | 01:07 |
| kanzure | really? | 01:07 |
| ybit | lol | 01:07 |
| ybit | srsly, you've got to stop man | 01:07 |
| ybit | now i'm just messing with you | 01:08 |
| kanzure | stop what ? | 01:08 |
| ybit | i'll quit | 01:08 |
| * kanzure is confused | 01:08 | |
| kanzure | hm | 01:08 |
| ybit | grrr, if we were talking through SIP or mumble, then you'd understand i'm joking | 01:08 |
| kanzure | I wonder where I put the git repo on the server | 01:08 |
| kanzure | I know where the dot git file is | 01:09 |
| kanzure | but not the folder | 01:09 |
| kanzure | this is .. awkward :) | 01:09 |
| kanzure | I thought it might be http://heybryan.org/~bbishop/docs/ellingtonia/biotech/ | 01:09 |
| kanzure | but not so | 01:09 |
| kanzure | maybe it's local | 01:09 |
| kanzure | ooh | 01:09 |
| ybit | heh :) | 01:10 |
| kanzure | "fatal: not a git repository" | 01:12 |
| kanzure | then where the hell is it? | 01:12 |
| kanzure | it's not local, it's not on the server, | 01:12 |
| kanzure | am I missing something? | 01:12 |
| ybit | did you perform an "updatedb","locate <text here>"? | 01:13 |
| kanzure | found it :) | 01:14 |
| ybit | sweet | 01:15 |
| kanzure | I ran a git push, it asked me for the information to the latest heybryan.org IP (a good sign), and it says everything is up to date, but http://heybryan.org/gitweb.cgi says the last change was five weeks ago | 01:15 |
| kanzure | that doesn't sound right :) | 01:15 |
| kanzure | (I ran a "git add neuromaps/" first) | 01:15 |
| kanzure | oops | 01:16 |
| kanzure | it was 'git commit' that I wanted | 01:16 |
| kanzure | awesome, it worked | 01:17 |
| kanzure | http://heybryan.org/gitweb.cgi?p=biotech.git;a=summary | 01:17 |
| kanzure | http://heybryan.org/gitweb.cgi?p=biotech.git;a=tree;f=neuromaps;h=745b72a21840066e233407be49047545c6fc91d3;hb=55593693bc9b06731b2560f8252ec3849858202b | 01:17 |
| * kanzure does an awesomedance | 01:18 | |
| kanzure | I should throw in some perl while I'm at it | 01:19 |
| kanzure | but I'm embarrased that it doesn't work quite yet | 01:20 |
| kanzure | need to implement VBO | 01:20 |
| ybit | if you see query on your servery for port 8890 that's me | 01:23 |
| * ybit was trying to get back to my own server | 01:25 | |
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| ybit | http://www.utdallas.edu/~kilgard/lectures.htm | 04:20 |
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| ybit | kanzure, have you tried 'making one for yourself' | 06:12 |
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| ybit | hey jim | 06:13 |
| ybit | as i was saying, it's meant for a mac installation, some of the links are broken, and the directions aren't accurate | 06:14 |
| ybit | so what i might do (when i wake up) is skip most of the details and work with the data | 06:16 |
| ybit | ah, i have it running on me comp now | 06:27 |
| ybit | didn't even have to sleep on this one :) | 06:27 |
| ybit | http://bayimg.com/baJadaABp notice the location bar | 06:31 |
| ybit | it looks nice, but it's still broken | 06:34 |
| ybit | skdb, skos... | 06:51 |
| ybit | http://www.w3.org/2004/02/skos/ | 06:51 |
| ybit | not quite the same | 06:51 |
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| -!- You're now known as fenn | 09:28 | |
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| jm | is the mailing list still working? | 14:07 |
| jm | i didn't receive anything for a week | 14:08 |
| kanzure | uh | 14:14 |
| kanzure | I just sent out an email yesterday | 14:14 |
| kanzure | http://heybryan.org/pipermail/hplusroadmap/2008-July/thread.html | 14:14 |
| kanzure | have you received any of those at the bottom? | 14:14 |
| jm | no | 14:16 |
| jm | last one was Vol 9 issue 10 | 14:16 |
| kanzure | crap | 14:17 |
| kanzure | I'm working on it | 14:17 |
| jm | but it's possibly my mail provider | 14:17 |
| kanzure | no, it's not | 14:17 |
| kanzure | I'm using smtp-server.austin.rr.com for my relay host | 14:17 |
| kanzure | I need to change this to something else | 14:17 |
| jm | ah ok but my provider sucks anyway | 14:18 |
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| kanzure | Hey all. | 16:23 |
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| kanzure | I'm looking for an SMTP relayhost that will accept outgoing email from heybryan.org. | 16:23 |
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| ybit | kanzure: perhaps ##networking will know | 16:53 |
| kanzure | http://www.aaai.org/AITopics/pmwiki/pmwiki.php/AITopics/Quotations | 16:54 |
| kanzure | I need some ai quotes from games | 16:54 |
| kanzure | I want to add it to the source :) | 16:54 |
| kanzure | this would be so hillarious :-( | 16:54 |
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| kanzure | "I learned-if that is the right word for knowledge which comes in a sudden flash of insight-I was given to understand that She manipulated whole sciences and thought systems as I might string words into a sentence. But her "sentences" were as huge and profound as the utterances of the universe itself She had reached truths and ways of knowing far beyond even the meta-philosophies of the alien Fravashi." | 17:15 |
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| ybit | hehe, Phreedom sent me a link that is related to ai quotes: http://adweek.blogs.com/adfreak/2008/07/then-well-grab.html | 18:22 |
| kanzure | Epic fail. Thanks. | 18:47 |
| kanzure | http://www.ch.ic.ac.uk/svg/ SVG + CML (chemical markup language) to render structural diagrams. | 18:52 |
| kanzure | though I'm not too hapy about the "XML parsing failed" errors on the page ;-) | 18:53 |
| kanzure | *happy | 18:53 |
| kanzure | ybit: One of those links that you've spoutted out recently was about setting up one of the local SPARQL databases of bioinformatics information, right? | 19:08 |
| kanzure | There was something that I saw a while back on an HPLC server that had something very similar to it and it was probably the same thing. But the amount of storage space required to run one of those things locally looked unreasonable the last time I checked. | 19:09 |
| kanzure | What were your thoughts on that? | 19:09 |
| kanzure | and it might be interesting to correlate some of those '325 million triples' with http://bloodgate.com/graph-demo and http://bloodgate.com/graph-easy/ and then the 'Google Moupse' page | 19:11 |
| ybit | "One of those links that you've spoutted out recently was about setting up one of the local SPARQL databases of bioinformatics information, right?" correct, and i've found out there's a more up-to-date program, along with updated information | 19:11 |
| * kanzure is still working on http://heybryan.org/graph.svg but figures he'll get back to work on the brainconqueror.pl script earlier | 19:11 | |
| ybit | i'll have to find the link for you | 19:11 |
| kanzure | *script later tonight | 19:11 |
| kanzure | Some of the openvirgle guys wanted to implement a simulator with the graph-easy or graph-demo pages (above) and the SKDB-YAML metadata validator, and honestly I don't know what they expect to simulate, *but* | 19:13 |
| ybit | From what I've seen, the amount of data they are using isn't insurmountable | 19:14 |
| kanzure | but I have been spending some of my recent freetime on http://boswars.org/ - an open source RTS that seems to implement lua scripts for most of its functionality ( http://lua.org/ ) -- so it might be interesting to implement that RTS framework with the same content and see what goes from there | 19:14 |
| kanzure | who's they? | 19:14 |
| ybit | neurocommons | 19:14 |
| kanzure | are we talking about Google Moupse or the informatics database? | 19:14 |
| kanzure | I see. | 19:14 |
| ybit | i was referring to " | 19:14 |
| ybit | TheFreeDictionary Google | 19:14 |
| ybit | ? | 19:14 |
| ybit | Word / Article Starts with Ends with Text | 19:14 |
| ybit | grr | 19:15 |
| kanzure | yeah .. | 19:15 |
| ybit | " But the amount of storage space required to run one of those things locally looked unreasonable the last time I checked." | 19:15 |
| kanzure | yes, I know | 19:15 |
| ybit | okay | 19:15 |
| ybit | (klipper never works right) | 19:15 |
| kanzure | neurocommons isn't exactly HLPC | 19:15 |
| ybit | what is hlpc? | 19:16 |
| kanzure | hold on | 19:16 |
| kanzure | http://hcls.deri.ie/hcls_demo.html | 19:16 |
| kanzure | HCLS | 19:16 |
| ybit | ah | 19:16 |
| kanzure | 'The following queries access a SPARQL endpoint hosted at DERI. The underlying triplestore contains over 325 million RDF triples of biomedical information. The information covers a large array of biomedical knowledge: from basic molecular biology over literature annotation up to anatomy and physiology.' | 19:16 |
| ybit | yeah, i have that open | 19:17 |
| ybit | google has seems to be losing its edge in finding info lately | 19:17 |
| ybit | seemed* | 19:17 |
| kanzure | I want something more tractable to come out of this stuff though. Whether it's the Google Moupse interface + the graphviz-in-the-browser or the real-time strategy simulator/'game', I want something that can either generate testable hypotheses, or otherwise make something _functional_ and useful out of this. | 19:18 |
| kanzure | erm | 19:18 |
| kanzure | the end of that should be "and useful out of this" | 19:18 |
| kanzure | the SNP data set on top of Google Moupse is iffy -- that might work -- and then we need the Google Maps API to come to the rescue with some cross-user tagging and sharing of tags or some such | 19:18 |
| kanzure | that would be somewhat interesting .. could probably correlate that with SNPedia (especially since Dan comes in here every once in a while) | 19:19 |
| kanzure | but it's not optimal | 19:19 |
| kanzure | maybe the fMRIds website - the one that gives out free MRI data sets -- could be used for real-time 3D reconstruction of the brain -- but then what value do you get out of genetic mutation information or regions of the brain? | 19:20 |
| kanzure | Supposedly you could see what the behavior study was doing, like "making people count to five" and so we could associate that with the genes with the heaviest expression in those areas, *maybe*. | 19:20 |
| kanzure | That's technically not a good way to make those sorts of assumptions. | 19:20 |
| kanzure | The high genetic expression could be due to other factors of course, like maybe that's just the structural basis and not anything to do with real time metabolism-related gene expression and so on, | 19:21 |
| kanzure | but it's certainly a start, and definitely a better start when we know the MRI data sets are from patients with well-established psycho-abnormalities | 19:21 |
| kanzure | so if it's a structural MRI study of somebody with a well-established psycho-abnormality, investigating a structure of the brain known to be related to the disease or whatever, then that might be useful for 3D reconstruction, tagging, and the brainconqueror.pl script | 19:22 |
| kanzure | other than that, I'm drawing blanks. | 19:22 |
| kanzure | coding up the underlying framework to BlueBuilder or whatever ti is that Markram's team has, would be a good start, since it would let others drop in simulation elements from YAML metadata and SKDB packages ;-) | 19:24 |
| kanzure | it won't be as fancy or interesting as seeing visuals | 19:24 |
| kanzure | especially since the algorithms are supposedly computationally intensive | 19:24 |
| kanzure | and also since I'm not too interested in brain simulation at this point. | 19:24 |
| ybit | sounds good to me | 19:28 |
| * ybit goes to look for the link mentioned earlier | 19:28 | |
| kanzure | from a user-perspective the functionality can be (1) neurotagging their own issues on the site, (2) MRI data sets studies and 3D reconstruction, whatever, (3) real time streaming server software for neurofeedback of the sort that OpenEEG got into (and that open-rtms needs to get into) | 19:29 |
| kanzure | from the long-term perspective, I think I'll assume (1) DNA synthesizer/synthesis, and (2) neural tissue cultures, then exploring the genetic basis of grammatically/taxonomically interesting 'psychological diseases' from the neurotagging database, automatically, in a lab somewhere | 19:30 |
| kanzure | so the DNA synthesizer will make a mutated gene, splice it in, grow a tissue culture, play around with stimulation schedules with the neural tissue and that batch, and see what the differences are | 19:30 |
| kanzure | and that's basically leading up to the brain farm | 19:31 |
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| ybit | Finding the link could take a week, hopefully less | 19:37 |
| ybit | i talked to a couple guys from neurocommons earlier and one said a new installer will be unveiled in a few weeks, and the other told me its already to be installed | 19:43 |
| ybit | so it might take awhile to get a clear answer | 19:43 |
| ybit | i went ahead and checked out the repository found here: http://svn.neurocommons.org/svn/trunk/ | 19:43 |
| kanzure | what is it that it is being installed ? | 19:47 |
| kanzure | http://sw.neurocommons.org/2007/kb-sources/ ? | 19:50 |
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| ybit | i think it's the same program from last night, updated | 20:01 |
| ybit | err, the Banff demo updated (to be clearer) | 20:01 |
| ybit | kanzure ^ | 20:04 |
| kanzure | I see. | 20:05 |
| ybit | not sure if writing your name helps, but it does for me since it flashes my sys tray | 20:05 |
| ybit | i remembered that a second screen was helpful on a few occasions, but i'm having difficulties getting this outdated graphics card to work properly in xinerama mode | 20:06 |
| kanzure | it does help | 20:08 |
| kanzure | I saw it, but I kind of phased out and I don't know what I'm doing right now | 20:09 |
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| ybit | found out the new program is in beta, waiting to get receive access to it now | 20:36 |
| ybit | i'll forward you a copy of the conversation | 20:37 |
| ybit | There you go | 20:37 |
| * kanzure will get to it 'eventually' | 20:43 | |
| kanzure | Maker Faire or Austin Space Exploration? | 20:43 |
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| ybit | which one has streaming video? :) | 21:18 |
| ybit | kanzure, if you like rts games, you may like spring | 21:29 |
| kanzure | ybit: linkage? | 21:39 |
| ybit | not yet | 21:41 |
| ybit | still waiting for a response back | 21:42 |
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| ybit | kanzure: | 21:56 |
| ybit | kanzure: | 21:56 |
| ybit | do you | 21:56 |
| ybit | have skype? | 21:56 |
| ybit | will you get on now? | 21:56 |
| ybit | please? | 21:57 |
| ybit | kanzure_ | 21:57 |
| kanzure | I am on. | 22:02 |
| kanzure | in fact, I've been on | 22:02 |
| ybit | aisrev is my screenname | 22:02 |
| ybit | what's yours? | 22:02 |
| kanzure | kanzure | 22:03 |
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