2008-10-02.log

--- Day changed Thu Oct 02 2008
ybithttp://www.unicornscan.org/00:16
ybitpk, nooooo!02:28
ybit...02:28
ybitoi faceface02:28
ybitwhy are we not subjected to three faces currently?02:29
ybitprocto: what exactly is logarchy doing?02:53
ybitsounds like they have a good idea for a future civ02:53
UtopiahGHMLybit: want to apply to Blinkenshell?02:53
ybitUtopiahGHML: sure02:53
ybitif it takes awhile, i will have to do it tomorrow night or this weekend02:54
UtopiahGHMLnope the test=10min02:54
UtopiahGHMLthe rest is getting vouched by 2 persons and that just hanging around in the channel helping02:54
UtopiahGHMLif you are social it's like 2 days max02:54
UtopiahGHMLthen the following day the admin opens you account02:54
UtopiahGHMLso in the end if you are "dedicated" you could have it opened tomorrow :P02:55
UtopiahGHML(they "work" on .se time)02:55
ybiti might wait until this weekend when i am most active02:55
kanzureHi all.02:58
kanzureybit: skype please02:58
proctoybit: it's just a general framework that can be applied02:59
proctoybit: I'm involved with seasteading, and hoping to have a logarchy up on a seastead at some point during my life02:59
proctothing about logarchy is that it's compatible with different electoral, political, and economic systems02:59
kanzurefenn: nathan and michel on skype if you want to be bothered to have yet another chat protocol03:04
ybithttp://www.magcloud.com04:05
UtopiahGHMLI need a graph database library in PHP...04:07
ybitUtopiahGHML: http://datamob.org/resources maybe?04:09
ybithttp://www.infochimps.org -- i think this belongs on the hplusroadmap wiki somewhere...04:10
ybitor maybe it should just be bookmarked04:11
kanzure_what is it? 04:15
UtopiahGHMLybit: graph as in mathematical graph, networks, not visually displaying data04:16
ybitkanzure: infochimps -- "Free Redistributable Rich Data Sets"04:17
kanzure_cool :)04:17
kanzure_http://theinfo.org/04:17
ybitah, i visited theinfo.org recently. me likey04:18
ybitUtopiahGHML: http://www.hotscripts.com/Detailed/16749.html PHP+Graphviz tool04:19
ybita lot of php tools for graphiz: http://www.graphviz.org/Resources.php04:20
kanzureybit: soon you will have a fancy data set from me05:24
kanzureand throwing it into graphviz will be simple05:24
willPow3rkanzure, one login isn't enough?07:47
facefaceUtopiahGHML, graph database? What doing?07:50
facefaceybit, I have enough face07:50
UtopiahGHMLfaceface: relational database, no, object database, no, graph database specialized in network oriented datastructure, yes.08:18
facefaceyes08:24
facefacewhat doing?08:24
facefaceI wanted to write a MySQL 'graph plugin', but I didn'y get round to it08:24
UtopiahGHMLI guess the best thing to do is too look at a real life example :08:25
facefaceI had a big 'graph database' hand out at one point... 08:25
UtopiahGHMLhttp://neo4j.org/08:25
facefacekanzure___, are you still interested in this http://www.nature.com/nprot/journal/v2/n3/abs/nprot.2007.96.html?08:25
facefaceor was that last week?08:25
facefaceor should I say kanzure08:26
facefacethey do good stuff in Gronigen08:26
facefaceUtopiahGHML, OK, I know what a GraphDB is, my question is, what do you want one for? I am curious08:27
UtopiahGHMLoh08:28
facefaceI am interested in graph queries08:28
facefacespecifically traversing ontologies 08:28
UtopiahGHMLto evolve from a wiki with a classical filesystem or classical DB to a way to handle data it holds in a consistent fashion08:29
UtopiahGHMLand be able to have a fully "querable" wiki08:29
UtopiahGHML(mixing user modification and API modification basically)08:29
facefaceUtopiahGHML, its the future08:29
UtopiahGHMLthus facilitating automated agent suports08:29
facefaceUtopiahGHML, have you groked SMW yet?08:29
facefacecool08:29
UtopiahGHMLnop, doesn't ring a bell, what is it?08:30
facefaceI really want to get my head into SMW, semantic media wiki08:30
facefacebut I haven't had time08:30
facefaceits semantic web for mediawiki08:30
facefacethey have a query interface that seems to mirror XSLT08:30
facefaceor XPah08:30
facefaceit was so strange thinking about hierarchical queries after so many years of thinking about relations08:31
facefaceUtopiahGHML, about 'api modifications', the guy behind DPL is going in that direction with his DPL + graph vis wiki08:31
UtopiahGHMLhmmm yep I checked SMW a while ago (>1 year) but it wasn't what I was looking for at the time (too complex for the end-user and too little applications ready, basically very low ROI)08:32
facefaceROI?08:32
UtopiahGHMLreturn on investment08:32
facefaceUtopiahGHML, there is a SMW extension called Semantic Query or something08:32
UtopiahGHMLtechnical cost vs concrete features benefits08:32
facefaceOK08:32
facefacethis is friendly http://semeb.com/dpldemo/index.php?title=Dynamic_Page_List08:32
facefaceROI ROI08:32
UtopiahGHMLhaving just 23h57 per day you have to think ROI :)08:33
facefaceIt allows you to combine Wgraph with DPL to generate 'software' in the wiki08:34
facefacehttp://semeb.com/dpldemo/index.php?title=Main_Page08:34
UtopiahGHMLhmmm problem is my current wiki is using pmWiki, do those solutions prodive way to "import" existing data?08:34
facefacepmWiki?08:34
UtopiahGHMLvery flexible wiki08:34
facefaceUtopiahGHML, there are libraries for wiki to wiki conversion, then you need to run MW to enable the DPL / Wgraph stuff08:35
UtopiahGHMLbut that unfortunately doesn't provide a clear API and can't handle massive amount of data08:35
facefacehe is forging ahead08:35
facefaceUtopiahGHML, not in a 'live' system... I'm thinking of a one off migration08:35
facefacehttp://semeb.com/dpldemo/index.php?title=Scatter_Demo_208:35
facefaceits so cool08:35
UtopiahGHMLthe good think with MW is... that I guess it has the largest active community08:35
facefaceyup, and WP proves its scaleable08:36
Utopiahsorry, irssi crash...08:37
Utopiahfaceface: ideally Id use a structure like #OpenCog will use since Im into AI, the thing is (by luck?) my targeted architecture (hypergraph) is also what OpenCog decided to use08:38
facefacewhat is the open cog?08:38
Utopiahwhat I consider the more prosiming unifying AI project today08:38
Utopiah(what some like to call "AGI")08:39
facefaceUtopiah, ... you want ... your wiki to be intelligent?08:39
Utopiahnot really :)08:40
Utopiahwhat is the structure of a wiki?08:40
facefacewhat is the way of tao?08:41
Utopiahwhat is the structure of a brain?08:41
Utopiahthe hypergraph seem to be the most ready to use model for a convergence let's say08:41
Utopiahso let's imagine one who would to enjoy what the Net can offer since it's (probably) the fastest evolvy ecosystem today08:42
Utopiahone would want its data organized in a fashion that agent (including remote agents like API from other websites) to "play" with the data08:42
Utopiaheventually seing his system itself as a potential useful other agents08:43
facefaceyes, thats the idea of SMW08:43
facefacehave you read the 'cyber infrastructure for Biology' paper?08:43
facefacealso my friend Vincent has worked on some neat stuff like this08:44
facefaceyou can find his publications here: http://www.vincent-wolowski.net/08:44
facefaceBuilding a Semantic Search Engine. Presentation, Department of Chemical System Engineering, Komiyama Laboratory, Tokyo University, Tokyo, Japan, February 3, 2004. [.pdf]08:44
Utopiah 'cyber infrastructure for Biology' ? based on mimetic?08:45
facefacewhat what?08:45
facefaceno08:45
facefacenot mimetic08:45
facefacehttp://nrgwiki.nature.com/cyberinfrastructureforbiology/show/HomePage08:46
Utopiahhmmm the more I look at those WM extensions the more Im considering a switch... what do you think is the core of the MW community? (to check what is available now, what is the spirit, etc... and betting on how it will evolve)08:47
facefaceUtopiah, uncertain08:47
facefacesee #mediawiki08:47
facefacethey are active... there are a few good devs...08:48
facefaceByron is a controll freak...08:48
facefaceall revisions go through byron, and thats final08:48
faceface(ime)08:48
fenncontrol freak? wikipedia? you must be kidding!08:48
Utopiahdo you know if there is anything related to the use of GraphDB as the underlying strcture?08:48
facefaceheheh08:48
facefacethey are not too close to the wp community08:48
facefacethey are like... uh... users?08:48
wrldpcwiki is all controlhawks.08:49
Utopiahstrange way to see an open community but maybe it's efficient...08:49
facefaceUtopiah, no08:49
facefacejust a pairs list or something08:49
facefaceUtopiah, I wanted to get svn commit access to one extension in the MW svn server - it was a no go08:49
facefacejust one extension!08:49
facefacethat is why many extensions are developed off site, and also just directly on mediawiki.org08:50
UtopiahI see08:50
facefaceThere are so many extensions because of an unwillingness to integrate into the core08:50
facefacehowever... that said... there is a lot of exciting stuff going on in the extension community08:50
facefaceesp. bio.08:50
facefacewrldpc, turns out that way for some reson often08:51
Utopiahthe last thing that amazed you there?08:51
facefacewikipathways08:51
facefaceits a pahtway editor in the wiki08:51
wrldpcdoes anyone here actually sub to nature?08:51
facefacealso (a bit boring) I am excited by the 'data integraton' efforts in MW08:51
facefacewrldpc, http://network.nature.com/people/dan/profile08:52
wrldpcI sent off a rather pointed message encouraging them to go "free."08:52
wrldpcinteresting08:52
facefaceUtopiah, my MW / bio projects are pretty amazing too ;-)08:53
facefacehttp://pdbwiki.org/index.php/Main_Page08:53
facefacehttp://biodatabase.org/index.php/Main_Page08:53
facefacealso you should see http://bio.cc/index.html/index.php/Main_Page08:54
facefacewrldpc, write a 'letter to nature', get people to sign it08:54
wrldpcgood idea08:54
facefaceYou just got to cram it all in to 200 words :-)08:55
facefacewell... I need to go do my day job... any tips on how to get by on less sleep?08:55
Utopiahmore sport, better nutrition but overall the trick is...08:57
UtopiahPASSION! :D08:57
wrldpchey faceface have you heard of the project John Cumbers from Brown wants to do where people would swab their toilets and mouthes and so on and ...08:58
Utopiahbut ... A candle that burns twice as bright and twice as long08:58
wrldpcDoes anyone know about this?08:58
Utopiahnot sure it exsits, your choice though :)08:58
facefaceUtopiah, yeah... I get bored though ... I am a dysfunctional 08:58
facefacewrldpc, no08:58
facefacewrldpc, what is it?08:59
faceface'eco-genomics'?08:59
wrldpcbioinformatics project08:59
wrldpcsorta08:59
facefacelike environmental sampling?08:59
wrldpcthey want to track where stuff is ... open source, yes envirosamp08:59
facefaceits the future :-)08:59
wrldpcbingo08:59
wrldpchave a good day!08:59
facefaceyou too08:59
Utopiahfaceface: how can you be bored in such a time and place... :)08:59
wrldpcthanks08:59
facefaceUtopiah, I am 'purpose disoriented'08:59
facefaceI don't really know what I want or why... I am conflicted.09:00
Utopiahstrange since you seem to have your own projects09:00
facefaceanyway... I 'feel' like I should go do my boring day job... Its like a pressure... 09:00
facefaceI do them in my spare time... hence the need for less sleep09:00
facefacenice talking to you Utopiah 09:00
Utopiahmy pleasure09:01
Utopiahhave a nice day09:01
fennfaceface: try doing your personal projects while at normal job09:03
Utopiahfuck your normal job, move to what you really live for, find a way to monetize it.09:04
fennwell, yeah, but that takes passion09:04
Utopiahindeed09:06
Utopiahbut that's when your life really starts :)09:07
facefaceanyone married09:16
faceface?09:16
Utopiahgosh no09:21
facefaceheheh09:22
facefaceI thought I was taking a job that supported my interests09:22
facefacebut it was also a compremize for me and my wife09:22
facefaceI think I'll have to become a 'group leader' just to get to work on what I want to!09:23
Utopiahentrepreneur is the spirit09:23
Utopiahand it's a long time investment09:23
facefaceOK, lets start a business09:23
Utopiahthe risk is not not to bet but not to know that you are betting anyway09:23
facefaceI really need someone to talk to about that....09:24
Utopiahopportunity cost basically09:24
facefaceI have a killer idea if we can get to prototype within 6 months09:24
Utopiahwell, Im a idea management pro09:24
facefacecool... the problem with 'nextGen' sequencing is that its too good - too much data too quickly. We don't have enough disks.09:25
Utopiahyep09:25
facefaceturn the problem on its head - lets encode our DNA data as DNA, then we can store vast quantities of data in a cupboard09:25
facefacewe can get massive data transfer rates by shipping DNA using UPS09:25
Utopiahhmmm I met a woman on Berkeley working on a similar problematic but she wasn't going the same way09:26
facefacethe idea is to design a 'DNA encoding' that maximizes ease of reading09:26
Utopiahyep I see09:26
facefaceexactly, we have a slight edge09:26
facefacethe two novel things that we bring together are 09:26
Utopiahproblem is... cost of "DNA printing", isn't it very brittle and costly so far? (maybe not 2D structures thought, dunno)09:26
fennlol i have a direct DNA to DNA nano sequencer data storage machine - polII09:27
fennIII09:27
faceface1) the DNA encoding - lots of check sums and handeling of repeat regions, 2) the 'DNA protectant' molecule that we use to store data at rtp09:27
facefacefenn, its error prone ;-)09:27
facefaceUtopiah, exactly, we need to design a micro fluidic dna sequencing chamber09:27
facefacemicrofluidics is getting very cheap, so its easy to design and print a 'chip' that will controll the flow of ATCG into a reaction chamber.09:28
fenncost of DNA printing is what all the "retarded polymerase" stuff is about09:28
facefacereally?09:28
fennsorta09:29
facefacethat stuff where I was like 'what are you guys going on about'?09:29
fennit's also for realtime in-vivo expression of arbitrary genes09:29
fennbut whatever, it's vaporware09:29
facefacesure09:30
fenn<- bitter old man09:30
facefacetaq isn't expensive though09:30
fennis the patent up yet?09:30
facefaceI need a prototype no?09:30
fennoh i was just curious09:31
fennalways wanted a vat of e-coli spewing out metric tons of taq polymerase09:31
facefacebut my feeling is that there is only a short window on this one09:31
fenni dont really see what sort of situation would require dna data storage?09:32
fenni mean what do you do with it09:32
facefacefenn, when I sequence your genome for $10, then the genome of your gut, then the genome of your brain, then again at age 2 and again at age 6 and again and agin, 09:32
facefacethen stick it into DNA09:32
facefaceits a 'permanant record' for re-reading09:33
facefacelike a tape backup09:33
fennwhy not use tapes?09:33
facefacetoo expensive09:33
facefacetoo many data09:33
facefacetoo slow09:33
fennis there no compression algo?09:33
fenni mean you and me are 99% similar09:34
facefacewell...09:34
* faceface sulks09:34
facefacebut its good to talk about 'alternatives' 09:34
facefaceI mean a patent needs that right?09:34
facefacefenn, also tissue expression could vary a lot, next gen gives you expression levels, splice variants etc.09:35
fenndont get me wrong, DNA is a fantastic data storage device09:36
fennbut it's a pain in the ass to work with09:36
facefaceit seems to work09:36
facefaceah... you know about any microfluidic considerations when working with DNA?09:36
facefacethere is a formidible group in cambridge that develops microfluidics for biotech09:37
fennum, how do you get past the typo problem?09:37
facefacefenn, checksums09:37
fennprobability of a typo increases exponentially with sequence length09:37
facefaceand redundancy... like read correction on any modern disk09:37
facefaceI am sure we can think of some 'optimal encodings'09:38
fenni dont know much about how microfluidics actually works (beyond  a popular science level)09:38
facefacealso, we need read optimized ... i.e. taylored to certain hardware09:38
facefaceyou trap a bubble of your aquious reagent in an oil flow. then you can manipulate the bubbles 09:38
fennbut how does this actually build up a sequence?09:39
facefacei.e. read off bubble colour, sort, merge, store etc09:39
fennis it just the conventional modified NTP + cap molecule?09:39
facefaceyou have a chamber with some fixed primers and taq,  then you flow ATCG over the primer... actually I don't know!09:40
facefacethat is where my plan falls down... I'm an idiot!09:40
fennhrm09:40
fenn"where the bits hit the road"09:40
facefacesomehow we need to keep taq in the 'reaction chamber' then we need to flow ntp at a time, then we need to get out the DNA and put in new primers.09:40
fennflow one ntp at a time won't work09:41
facefacewhy?09:41
fenneither too much diffusion or it's too slow09:41
facefaceI don't mean one molecule, just one type09:41
facefacemicrofluidics is fast, you can process 100's of bubbles per second09:41
fennmy idea was that you sensitize the taq with some frequency of laser and this only allows it to pick up a certain nucleotide09:42
facefaceeach bubble needs to be one NTP.... and we need to only add one base per bubble...09:42
facefacefenn, any ref?09:42
fennno09:42
facefaceany chem to spontainously 'prime' the end of the DNA for reaction?09:42
fennnot needed, taq does that09:43
facefaceDNA-* + NTP -> DNA-NTP + * -> DNA-NTP-* +NTP -> DNA-NTP-NTP + * -> ...09:44
facefacefenn, but I only want to add one base at a time09:44
facefacetaq is there ready to add as many NTP's as it can get its hands on right?09:44
facefaceor do you controll that with ATP?09:44
facefaceI'll need to read up to get more details09:44
fennwell, the idea was to have another "clock" frequency09:44
fennso you have 3 lasers09:45
fenn2 spcify the nucleotide09:45
fennthe third cements it in place09:45
facefaceI'll do some reading.09:45
facefaceI think there is scope for a 'strategic aliance' ;-)09:46
fennthis was some idea i came up with years ago, i honestly have no idea if there's anything out there09:46
fenn" An undefined problem has an infinite number of solutions.09:49
fennwhat a bunch of crap09:49
fennmust have been a mathematician, not an engineer09:50
Utopiahthat's infinitely unuseful :)09:51
kanzure_Utopiah: for what it's worth, I too want graphdb or graph-fs, and *not* in semantic mediawiki form.11:00
Utopiahideally I would find a Lisp wiki using GraphDB...11:01
Utopiah(and super ideally be able to convert my existing wiki instance to it in 1 command ;)11:03
facefaceSimilarly to concepts in electrical engineering, the objective in the Synthetic Biology is the development of standardized DNA building blocks, which can be easily combined and which allow the reconstruction of cells, e.g. bacteria into bioreactors. Scientists in the Synthetic Biology thereby aim at the development of bioreactors capable of producing far more complex compounds than currently possible using the conventional methods of classica11:05
facefacel biotechnology11:05
facefacehttp://sb4.biobricks.org/11:06
kanzure_faceface: you might be interested in knowing of my synthetic biology circuit creator project11:07
facefacekanzure_, I just pasted for your benefit11:07
kanzure_http://heybryan.org/~bbishop/docs/biobricks/ contains my work in progress.11:07
facefacebut I'll have a look11:07
kanzure_faceface: surely you knew about biobricks beforehand?11:07
facefacenot that they had a conference11:07
kanzure_:)11:07
facefacehttp://www.marketwatch.com/news/story/geneart-ag-presents-its-work/story.aspx?guid={3E3BE543-8D0C-4BC1-973C-DD3B37908D76}&dist=hppr11:08
kanzure_yeah, I'm missing that this year11:08
faceface(when I pasted I didn't realize it was BioBricks)11:08
kanzurehttp://www.washingtonpost.com/wp-dyn/content/article/2008/10/01/AR2008100101149.html12:35
kanzurehttp://globalnation.inquirer.net/mindfeeds/mindfeeds/view/20081002-164190/In-Crisis-A-View-from-the-Trenches12:35
kanzurehttp://jama.ama-assn.org/cgi/content/full/300/13/158012:35
facefacejama?13:16
facefacegoogle won't let me look at the wahington post13:17
nshwgat?13:30
facefacegood idea13:30
faceface?13:30
fennwhat's with all the wall-street mumbo jumbo?13:37
Utopiahfenn: just bankers requiring explicit forced donations from non-bankers in order to boost their ROI despite the market fluctuations, nothing new really13:52
Utopiah(alias Robin Hood^-1 alias classical world resources redistribution)13:54
fenni meant why was kanzure posting links to these pointless newspaper articles13:55
nshthe contain encoded messages, clearly13:57
facefacecomplexity?14:08
* nsh was just being glib14:37
bkeroglubglubglub14:38
kanzure___fenn: received those links from somebody pointing out the commonality of 'complexity' between the recent articles17:06
kanzure___not sure it has much relevance of course :)17:07
* kanzure___ just saved and submitted http://heybryan.org/~bbishop/docs/me302/2008-10-02_terminal_support_final.jpg 17:08
kanzure___'part mating' is a joke.17:08
kanzure___a bad joke.17:08
fennhighly unenlightening, as any drafted diagram ought to be17:10
kanzure___you already know I'm being prodded into following a workbook :)17:15
kanzure___what's the longest you've gone writing code without testing it?20:36
kanzure___bwaahahah. four hours of coding and only one syntax error.21:09
kanzurehttp://heybryan.org/~bbishop/docs/repo/2008-10-02.pl22:39
kanzurewtf22:39
kanzureI don't remember writing the majority of that ..22:39
kanzure"This goes to the heart of the infamous "Grounding Problem" in machine intelligence and to a pragmatic view of semantics.  Simply put, the "meaning" of any referent corresponds with its observed effect within a particular context.  No end-to-end grounding is ever ultimately needed nor ultimately possible."23:13
kanzure"This strikes me as especially funny when it involves would-be AI creators imagining that a "relatively simple" computer program could encapsulate a process delivering "intelligence" while they remain blithely unaware and unconcerned about the essential contribution of the layers of software, microcode, electronic hardware, turtles all the way down... (within an environment of adaptation supporting such activity.)"23:13
kanzure"Interesting that the first successful private commercial launch to orbit was achieved right at the peak of the end of capitalism."23:28
kanzure7535923:57
kanzure:)23:57

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