--- Log opened Mon Jun 27 00:00:07 2011 01:44 -!- uniqanomaly [~ua@dynamic-78-8-85-147.ssp.dialog.net.pl] has joined ##hplusroadmap 01:55 < dbolser> kanzure: still awake? 01:57 < dbolser> my dad has a theory that ultrasound causes autism 02:31 < kanzure> oh crud ed didn't know about the transcranial ultrasound stuff 02:31 < kanzure> (ed boyden) 02:33 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has quit [Ping timeout: 264 seconds] 02:42 < kanzure> dbolser: volpraic acid seems to be a pretty good model 02:43 < kanzure> valproic 02:43 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Hyper-connectivity%20and%20hyper-plasticity%20in%20the%20medial%20prefrontal%20cortex%20in%20the%20valproic%20acid%20animal%20model%20of%20autism.pdf 02:43 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Enhanced%20long-term%20microcircuit%20plasticity%20in%20the%20valproic%20acid%20animal%20model%20of%20autism.pdf 02:43 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has joined ##hplusroadmap 02:49 < dbolser> kanzure: want me to write some stuff on dna pol classification? 02:57 < kanzure> sure 02:57 < kanzure> i know about ec 2.7.7.* so i might run some analysis over the pdb files or something 03:30 -!- alystair [alystair@24-246-14-18.cable.teksavvy.com] has quit [Ping timeout: 240 seconds] 03:35 -!- Pabreetzi0 [~Pabreetzi@cpe-174-096-012-143.carolina.res.rr.com] has quit [Ping timeout: 246 seconds] 05:52 -!- CryptoQuick [~CryptoQui@c-174-51-232-237.hsd1.co.comcast.net] has quit [Read error: Connection reset by peer] 05:53 -!- CryptoQuick [~CryptoQui@c-174-51-232-237.hsd1.co.comcast.net] has joined ##hplusroadmap 06:13 < dbolser> kanzure: I was going to suggest that you collect all known dna-pol sequences 06:14 < dbolser> of all subunits 06:14 < dbolser> then use them to build one or several HMMs using HMMer3 06:14 < dbolser> then use HMMs to collect more sequences 06:15 < dbolser> not sure what's best, but you could cluster into families, then make one HMM per family then search all sequences with your HMMs 06:15 < dbolser> the data will tell you alot about the structure of the families 06:15 < dbolser> finally, do some kind of phylogenetic analysis of subunits accross species 06:16 < dbolser> I'm not familiar with details ... 06:16 < dbolser> but lets say eukaryotes use subunit x, y and z, and bacteria use x, p, and q, and archaea use x, y. 06:17 < dbolser> you can then look accross species to see if these combinations are 'stable' or if some subunits drop out in pairs or if all possible combinations are seen etc. etc. 06:18 < dbolser> the last step brings it all together, family + complex evolution 06:18 < dbolser> i.e. does x' family of subunit x always appear with subunit d' family of subunit d, or do families mix 06:19 < dbolser> for bonus marks, what are the core residues of each subunit? 06:20 < dbolser> correlated evolution? 06:20 < dbolser> etc. 06:20 < dbolser> although it's a lot of work, you can break it down pretty easily 06:20 < dbolser> 1, build a sequence / subunit database of all known sequences and all known subunits. 06:21 < dbolser> 2, (I'd suggest) pre-cluster sequences based on full length sequence similarity into 50% similar families. 06:21 < dbolser> build an HMM from each family 06:21 < dbolser> search uniprot using all HMMs and itterate 06:22 < dbolser> now you have the most comprehensive dnapol sequence database possible 06:22 < dbolser> using uniprot gives you links to species, which you can structure using the NCBI taxonomy 06:23 -!- elmom [~elmom@hoasnet-fe2add00-191.dhcp.inet.fi] has quit [Ping timeout: 240 seconds] 06:24 < dbolser> finally, label your HMMs (for a given subunit) and cluster each sequence of that subunit by its distance to each HMM in the subunit... 06:24 < dbolser> perhaps that's overkill 06:24 < dbolser> your families should stand out afterall 06:40 -!- lumos [~lumos@afak134.neoplus.adsl.tpnet.pl] has joined ##hplusroadmap 07:00 -!- augur [~augur@208.58.6.161] has quit [Remote host closed the connection] 07:12 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has quit [Ping timeout: 240 seconds] 07:22 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has joined ##hplusroadmap 07:38 -!- augur [~augur@129.2.129.34] has joined ##hplusroadmap 07:44 -!- Pabreetzio [~Pabreetzi@adsl-74-235-171-103.clt.bellsouth.net] has joined ##hplusroadmap 08:10 -!- eridu [~eridu@gateway/tor-sasl/eridu] has joined ##hplusroadmap 08:14 -!- AlonzoTG [~atg@dsl092-168-049.wdc2.dsl.speakeasy.net] has quit [Ping timeout: 276 seconds] 08:29 -!- AlonzoTG [~atg@dsl092-168-049.wdc2.dsl.speakeasy.net] has joined ##hplusroadmap 08:45 -!- eridu [~eridu@gateway/tor-sasl/eridu] has quit [Quit: Leaving] 08:49 -!- AJolly [~quassel@unaffiliated/ajollylife] has quit [Read error: Connection reset by peer] 08:49 -!- AJollyLife [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has joined ##hplusroadmap 08:49 -!- AJollyLife [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has quit [Changing host] 08:49 -!- AJollyLife [~quassel@unaffiliated/ajollylife] has joined ##hplusroadmap 08:50 -!- lumos [~lumos@afak134.neoplus.adsl.tpnet.pl] has quit [Ping timeout: 240 seconds] 08:51 -!- eridu [~eridu@gateway/tor-sasl/eridu] has joined ##hplusroadmap 09:04 -!- eudoxia [~eudoxia@r190-135-74-141.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 09:18 -!- eudoxia [~eudoxia@r190-135-74-141.dialup.adsl.anteldata.net.uy] has quit [Read error: Connection reset by peer] 09:44 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has quit [Changing host] 09:44 -!- archels [~neuralnet@unaffiliated/archels] has joined ##hplusroadmap 09:54 -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has joined ##hplusroadmap 10:02 -!- eridu [~eridu@gateway/tor-sasl/eridu] has quit [Ping timeout: 250 seconds] 10:21 < kanzure> dbolser: why do you suggest hierarchical marov machines instead of just clustering? 10:23 < dbolser> hmms are a way of sequence searching that is more sensitive than single sequence alone 10:24 < dbolser> when google finds a pdf, how do I link you to it instead of to googles crappy url? 10:24 < dbolser> http://www.google.co.uk/url?sa=t&source=web&cd=1&ved=0CBoQFjAA&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%2Fdownload%3Fdoi%3D10.1.1.144.9721%26rep%3Drep1%26type%3Dpdf&rct=j&q=hmms%20discover%203%20times%20as%20many%20scop%20park&ei=krwITrK1CoGZhQf_2Lm2DQ&usg=AFQjCNFydzT3gsWZwJ7mPHziVpgVbhTUQg 10:25 < dbolser> http://www.ncbi.nlm.nih.gov/pubmed/9837738 10:26 < dbolser> so the HMM is for finding sequencs pre clustering 10:26 < kanzure> take out the url= part of it and run it through javascript:function decode(str) { return unescape(str.replace(/\+/g, ' ')); } decode(url) 10:26 < dbolser> then I like to define cluster membership as a vector of hmm distances 10:27 < dbolser> kanzure: can you stick that into a chrome extension for me? 10:27 < kanzure> maybe later let me wake up first 10:28 < dbolser> np 10:28 < kanzure> what is 'hmm distances' 10:28 < dbolser> basically, sequence x has a 'score' when aligned to hmm y 10:28 < dbolser> if you build several hmms, one per putative cluster 10:29 -!- AJolly [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has joined ##hplusroadmap 10:29 -!- AJolly [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has quit [Changing host] 10:29 -!- AJolly [~quassel@unaffiliated/ajollylife] has joined ##hplusroadmap 10:29 < dbolser> each sequence will have some slightly different score against each 10:29 < dbolser> but it's probably a waste of time here, I'm thinking about unknown families/clusters 10:30 < dbolser> lets say you have some cluster x, and it doesn't match very well to cluster a, that you have labeled as sub-family a' or cluster b, that you have labeled as sub family b', ok, so x is a new cluster. 10:30 < dbolser> now you have cluster y with similar properties 10:31 < dbolser> is y close to x or a or b? 10:31 -!- AJolly [~quassel@unaffiliated/ajollylife] has quit [Read error: Connection reset by peer] 10:31 -!- AJolly [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has joined ##hplusroadmap 10:31 -!- AJolly [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has quit [Changing host] 10:31 -!- AJolly [~quassel@unaffiliated/ajollylife] has joined ##hplusroadmap 10:31 < dbolser> by aligning all sequencs to all hmms (built using all clusters), you get some idea of it's 'position' in the familiy space 10:31 -!- AJollyLife [~quassel@unaffiliated/ajollylife] has quit [Ping timeout: 258 seconds] 10:31 < dbolser> like I said, prolly overkill 10:32 < dbolser> the main take home point is... HMMer3 is really great, really fast, and really easy to use with a good manual 10:32 -!- AJolly [~quassel@unaffiliated/ajollylife] has quit [Read error: Connection reset by peer] 10:32 < dbolser> so build some hmms, and get a sequence database to cluster 10:33 < kanzure> okay. 10:33 -!- AJollyLife [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has joined ##hplusroadmap 10:33 -!- AJollyLife [~quassel@c-68-57-192-88.hsd1.il.comcast.net] has quit [Changing host] 10:33 -!- AJollyLife [~quassel@unaffiliated/ajollylife] has joined ##hplusroadmap 10:33 < fenn> poll: is this a robot pretending to be a person or a person pretending to be a robot? http://www.youtube.com/watch?v=-hDwz72ataQ&feature=related 10:35 < superkuh> There's not enough postural sway in the shoulders. 10:36 < kanzure> jaw/lip movement is wrong 10:36 < kanzure> and i think the hair is glued down but that's true for many people anyway 10:36 < fenn> QuantumG: i too am interested in rossi's reactor, unfortunately he leaves out the "secret sauce" which renders it in the category of "another free energy claim i can't verify" 10:40 < fenn> please state your opinion in the form of an answer, not observations about whether it looks right or wrong 10:40 < kanzure> robot 10:41 < superkuh> robot 10:42 < kanzure> http://rpgjs.com/ hah "import rmxp" shit's crazy 10:46 -!- archels [~neuralnet@unaffiliated/archels] has quit [Ping timeout: 255 seconds] 10:55 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has joined ##hplusroadmap 10:56 -!- elmom [~elmom@hoasnet-fe2add00-191.dhcp.inet.fi] has joined ##hplusroadmap 11:07 -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has quit [Ping timeout: 250 seconds] 11:13 -!- eudoxia [~eudoxia@r190-135-4-133.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 11:19 -!- eridu [~eridu@gateway/tor-sasl/eridu] has joined ##hplusroadmap 11:23 -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has joined ##hplusroadmap 11:43 -!- augur_ [~augur@129.2.129.34] has joined ##hplusroadmap 11:43 -!- augur [~augur@129.2.129.34] has quit [Read error: Connection reset by peer] 12:01 -!- uniqanomaly [~ua@dynamic-78-8-85-147.ssp.dialog.net.pl] has quit [Quit: uniqanomaly] 12:08 -!- klafka [~textual@cpe-69-205-70-55.rochester.res.rr.com] has joined ##hplusroadmap 12:19 -!- augur_ [~augur@129.2.129.34] has quit [Remote host closed the connection] 12:21 -!- eudoxia [~eudoxia@r190-135-4-133.dialup.adsl.anteldata.net.uy] has quit [Read error: Connection reset by peer] 12:46 -!- lumos [~lumos@afak134.neoplus.adsl.tpnet.pl] has joined ##hplusroadmap 13:15 -!- lumos is now known as dr_lumos 13:19 -!- Guest89588 [~Jaakko@host86-131-177-233.range86-131.btcentralplus.com] has joined ##hplusroadmap 13:51 < fenn> interesting, apparently "the mismeasure of man" was based on a biased analysis of the data? (but not the bias described in the book) http://www.nytimes.com/2011/06/14/science/14skull.html?_r=2 13:51 < kanzure> cirrrcles 13:53 < fenn> wah 13:53 < kanzure> heyy wait wasn't i working on this with them http://rsif.royalsocietypublishing.org/content/6/Suppl_4/S523.short 14:01 < kanzure> fenn: really i'd also accept suggestions for how i can emulate your problems on my end 14:06 < fenn> proceed as if there were no bug, then when someone complains, see what's in common 14:09 -!- Pabreetzio [~Pabreetzi@adsl-74-235-171-103.clt.bellsouth.net] has quit [Ping timeout: 264 seconds] 14:09 -!- dr_lumos is now known as lumos 14:09 < kanzure> this all sucks so much 14:24 -!- klafka [~textual@cpe-69-205-70-55.rochester.res.rr.com] has quit [Quit: Computer has gone to sleep.] 14:39 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has quit [Ping timeout: 255 seconds] 14:47 -!- flamoot [42f18c6f@gateway/web/freenode/ip.66.241.140.111] has joined ##hplusroadmap 14:49 -!- archels [~neuralnet@541ED8B0.cm-5-7d.dynamic.ziggo.nl] has joined ##hplusroadmap 14:58 -!- epitron [~epitron@unaffiliated/epitron] has quit [Remote host closed the connection] 14:58 -!- epitron [~epitron@unaffiliated/epitron] has joined ##hplusroadmap 15:07 -!- eridu [~eridu@gateway/tor-sasl/eridu] has quit [Quit: Leaving] 15:11 -!- eudoxia [~eudoxia@r190-135-60-124.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 15:16 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 15:19 -!- flamoot [42f18c6f@gateway/web/freenode/ip.66.241.140.111] has quit [Quit: Page closed] 15:33 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 15:40 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 15:53 < AlonzoTG> Anyone listen to Alex Jones yesterday EveningL 15:53 < AlonzoTG> ? 15:58 -!- mode/##hplusroadmap [+o kanzure] by ChanServ 16:08 <@kanzure> "light-controlled nucleic acids typewriter" 16:08 <@kanzure> http://diyhpl.us/~bryan/papers2/polymerase/Light%20controlled%20synthesis%20of%20nucleic%20acids%20-%20Pinheiro%20-%202010.pdf 16:11 <@kanzure> eh, photocleaving seems kinda useless since you can't uncleave the nucleotides 16:12 <@kanzure> i think a better approach would be to evolve a dna polymerase that can incorporate dNTPs that have a chromophore attached in a 'neutral' state and that do not incorporate the nucleotide when the switch is 'open' or 'activated' 16:12 -!- strages [~makers@c-71-207-221-57.hsd1.al.comcast.net] has joined ##hplusroadmap 16:12 <@kanzure> polymerases have been built to accept dNTPs attached to fluorophores, so that is potentially workable.. 16:13 <@kanzure> (and then you need a way to switch on/off or step the polymerase molecule) 16:28 -!- lumos [~lumos@afak134.neoplus.adsl.tpnet.pl] has left ##hplusroadmap ["Leaving"] 16:31 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 16:44 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 16:44 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 17:10 -!- Netsplit *.net <-> *.split quits: ENKI-][, fenn 17:13 -!- Netsplit over, joins: ENKI-][, fenn 17:38 -!- thesnark [~michael@cblmdm24-53-167-49.buckeyecom.net] has joined ##hplusroadmap 17:41 <@kanzure> fenn: http://www.reddit.com/r/raldi/comments/i8z20/frustrating_unix_pitfall_of_the_day_esoteric_cron/ 17:42 <@kanzure> maybe that was our problem with davinci 17:59 -!- Guest89588 [~Jaakko@host86-131-177-233.range86-131.btcentralplus.com] has quit [Quit: Nettalk6 - www.ntalk.de] 18:22 -!- Pabreetzio [~Pabreetzi@cpe-174-096-012-143.carolina.res.rr.com] has joined ##hplusroadmap 18:32 -!- Pabreetzio [~Pabreetzi@cpe-174-096-012-143.carolina.res.rr.com] has quit [Ping timeout: 276 seconds] 18:59 -!- klafka [~textual@cpe-69-205-70-55.rochester.res.rr.com] has joined ##hplusroadmap 19:08 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 19:11 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 19:13 < ybit> ksjj;lafdj;lkdsajf;lajsdf 19:17 < thesnark> ###!@!!!##$$gfsd 19:18 <@kanzure> what is this 19:18 < jrayhawk> rage 19:24 -!- Pabreetzio [~Pabreetzi@cpe-174-096-012-143.carolina.res.rr.com] has joined ##hplusroadmap 19:56 -!- strages [~makers@c-71-207-221-57.hsd1.al.comcast.net] has quit [Ping timeout: 240 seconds] 19:58 -!- strages [~makers@c-71-207-221-57.hsd1.al.comcast.net] has joined ##hplusroadmap 20:06 -!- thesnark [~michael@cblmdm24-53-167-49.buckeyecom.net] has quit [Quit: Leaving] 20:20 -!- eudoxia [~eudoxia@r190-135-60-124.dialup.adsl.anteldata.net.uy] has quit [Quit: quit] 20:20 -!- augur [~augur@208.58.6.161] has joined ##hplusroadmap 20:43 -!- klafka [~textual@cpe-69-205-70-55.rochester.res.rr.com] has quit [Quit: Computer has gone to sleep.] 20:50 -!- klafka [~textual@cpe-69-205-70-55.rochester.res.rr.com] has joined ##hplusroadmap 21:49 -!- saurik_ [~saurik@carrier.saurik.com] has quit [Quit: leaving] 21:52 -!- saurik [~saurik@carrier.saurik.com] has joined ##hplusroadmap 22:32 -!- strages [~makers@c-71-207-221-57.hsd1.al.comcast.net] has quit [Quit: Lost terminal] 22:35 -!- klafka [~textual@cpe-69-205-70-55.rochester.res.rr.com] has quit [Quit: Computer has gone to sleep.] 23:59 <@kanzure> debian neuroscience survey results 23:59 <@kanzure> http://neuro.debian.net/survey/2011/ --- Log closed Tue Jun 28 00:00:07 2011