--- Day changed Mon Jun 16 2008
02:49 -!- fenn [n=pz@adsl-76-248-70-162.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap
02:49 -!- Topic for #hplusroadmap: Intro: http://www.youtube.com/watch?v=ZXKbzbeipmI http://diybio.org/ http://openwetware.org/ | diy bio toolkit: http://biohack.sf.net/ | Automated societal knowledge (put it to work): http://heybryan.org/exp.html | Channel wiki: http://heybryan.org/mediawiki/ | F/OSS perspectives on Kurzweil: http://heybryan.org/fernhout/
02:49 -!- Topic set by kanzure [] [Sun Jun  8 13:00:15 2008]
02:49 [Users #hplusroadmap]
02:49 [ faceface] [ freer  ] [ nsh     ] [ procto] 
02:49 [ fenn    ] [ kanzure] [ Phreedom] [ wrldpc] 
02:49 -!- Irssi: #hplusroadmap: Total of 8 nicks [0 ops, 0 halfops, 0 voices, 8 normal]
02:49 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
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07:38 < kanzure> fenn lives?
07:51 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has quit ["Leaving."]
08:31 < faceface> http://news.bbc.co.uk/2/hi/health/7179060.stm
10:26 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has joined #hplusroadmap
10:55 < kanzure> Any matlab users?
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11:02 < faceface> I use R
11:02 < faceface> is that matlab like?
11:03 < procto> not really
11:03 < procto> gnu octave is closer, as far as free stuff goes
11:05 < kanzure> I'm willing to use octave, but I would really like a GUI
11:06 < kanzure> I remember using octave a few months ago, it didn't look functional
11:06 < kanzure> I might as well just have opened up vim and begin writing out my own python
11:06 < kanzure> erm, perl
11:06 < kanzure> I'm still a perl > python guy.
11:06 < faceface> kanzure: there are ppl on #bioinformatics who use octave
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11:08 < faceface> perl is nice
11:09 < kanzure> I agree.
11:09 < kanzure> I'm going to be doing some differential equations for a model, so I want to see what sort of visualizations and solvers I can come up with.
11:09 < kanzure> Actually, I'm not even sure why I really need a solver, I just want to adjust some constants and some other variables and see how that changes the maxima/minima.
11:09 < faceface> browsign a linux distro package manager could be interesting
11:09 < kanzure> http://www.math.uic.edu/~hanson/Octave/OctaveODE-EG.html
11:10 < kanzure> faceface: Hm?
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11:41 < kanzure> http://www.johnlapeyre.com/pdl/pdldoc/newbook/ Scientific programming in perl
11:41 < kanzure> Aha.
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15:10 < ybit> kanzure, i agree, it takes way too long to mass upload bookmarks to del.icio.us
15:11 < ybit> it almost brought my computer to a halt way back when
15:11 < ybit> never tried it again 
15:11 < ybit> the comp. was certainly unusable for quite some time 
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16:10 < kanzure> Heh.
16:10 < kanzure> My point. :)
17:59 < kanzure> fenn: They are complaining about the base pairing probabilities with the address space. 
17:59 < kanzure> fenn: so they are coming up with these crazy models for doing all sorts of new biochemistry with things that aren't really proven yet
17:59 < kanzure> fenn: I was wondering if you might remember what the hell I was thinking when I was planning xxDNA
17:59 < kanzure> I thought we solved those problems?
18:00 < kanzure> another issue is that they are afraid that it all equilibriates to the same state, so there can't be separate components running on their own
18:00 < kanzure> I'm pretty sure this is wrong
18:00 < kanzure> fenn: I also came up with the selection experiments for the retarded polymerase for your writozyme
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20:58 < wrldpc> anyone played fold.it?
20:58 < wrldpc> http://fold.it/portal/adobe_main
20:59 < wrldpc> I need to learn perl.
21:05 < kanzure> http://perl.org/
21:05 < kanzure> http://search.cpan.org/
21:05 < kanzure> Familiarize yourself with 'perldoc perltut'.
21:15 < kanzure> To solve the problems with the amorphous computing, we're going to write a general software framework to test out some different ideas on the constraints of kinetics and so on, but I still think that we had something going. We just need some numbers on the likelihood of nucleic binding, and seeing if that's enough to do what we want.
21:29 < Splicer> i played it(fold.it)... I couldn't really get along with the GUI... I don't know how useful it actually is
21:31 < kanzure> You know, fold.it really makes sense in light of the compartmentalized evolution hypotheses of protein folding, and then the reverse of that evolutionary encoding (having everybody play around) is an interesting reverse attempt.
21:33 < Splicer> it is etheitcally pleasing
21:33 < Splicer> *esthetically
21:47 < fenn> wrldpc: perl is stupid. it's only good for regular expressions, which are now available in every language
21:49 < wrldpc> heh
22:06 < kanzure> perl makes your eyes bleed and rot in their sockets
22:06 < kanzure> fenn: So I was pacing, and I came ot the conclusion that the amorphous computing bullshit problems are only because I've forgotten that it's the same situation that necessitated SKDB in the first place.
22:19 < kanzure> http://scholar.google.com/scholar?q=machining+database
22:20 < kanzure> 'A study of a proprietary computerized technological machining performance database
22:20 < kanzure> EJA Armarego, D Ostafiev - 8th Int. Manufacturing Conference, 1998'
22:21 < kanzure> 'distributed network manufacturing prototype system (DNMPS)'
22:24 < fenn> the nist virtual manufacturing stuff looks a lot like what i was thinking http://www.cs.umd.edu/~nau/vm2/
22:24 < fenn> specifically the part "Automated Redesign for Improving Manufacturability"
22:31 < kanzure> http://www.design.caltech.edu/Research/Publications/02l.pdf "Efficient Automatic Engineering Design Synthesis via Evolutionary
22:31 < kanzure> Exploration"
22:31 < kanzure> yes, I've emailed Nau
22:31 < kanzure> he's hooking me up with some other guys (apparently)
22:32 < kanzure> based off of that last paper, wget -m -r http://www.design.caltech.edu/Research/Publications/ might not be a bad idea
22:36 < kanzure> fenn: here's an idea
22:37 < kanzure> what if you find one of the most basic articles, and then follow the chain of publications
22:37 < kanzure> i.e. the 'cited by' link
22:37 < kanzure> then try traveling via (1) longest intervals between publications that cite the last one, or (2) maximizing the number of publications in a time interval, or some sort.
22:59 < kanzure> "One of the major difficulties in extracting machining features is the lack of a systematic methodology to generate alternative ways of manufacturing a machined part."
23:04 < kanzure> fenn: try the abstract to 'Modeling and specifications of dynamic agents in fractal manufacturing systems'
23:18 < kanzure> [PDF] A Repository of Designs for Process and Assembly Planning - all 6 versions »
23:18 < kanzure> WC Regli, DM Gaines - Urbana - gicl.cs.drexel.edu
23:18 < kanzure> Abstract This paper provides an introduction to the Design, Planning and 
23:18 < kanzure> Assembly Repository available through the National Institute of Standards and 
23:18 < kanzure> Technology (NIST). The goal of the Repository is to provide a publicly ...
23:18 < kanzure> http://gicl.cs.drexel.edu/wiki-data/images/6/63/Repos_cad.pdf
23:19 < kanzure> Oh, it's Regli.
23:19 < kanzure> That's who Nau sent me to.
23:25 < kanzure>  
23:25 < kanzure> [PDF] Towards a Universal Knowledge Database for Design Automation
23:25 < kanzure> H Lipson, NP Suh - Proceeding of ICAD2000, First International Conference on …, 2000 - axiomaticdesign.com