| --- Log opened Mon Jun 27 00:00:07 2011 | ||
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| dbolser | kanzure: still awake? | 01:55 |
|---|---|---|
| dbolser | my dad has a theory that ultrasound causes autism | 01:57 |
| kanzure | oh crud ed didn't know about the transcranial ultrasound stuff | 02:31 |
| kanzure | (ed boyden) | 02:31 |
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| kanzure | dbolser: volpraic acid seems to be a pretty good model | 02:42 |
| 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 |
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| dbolser | kanzure: want me to write some stuff on dna pol classification? | 02:49 |
| kanzure | sure | 02:57 |
| kanzure | i know about ec 2.7.7.* so i might run some analysis over the pdb files or something | 02:57 |
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| dbolser | kanzure: I was going to suggest that you collect all known dna-pol sequences | 06:13 |
| 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 | 06:14 |
| 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 | 06:15 |
| 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. | 06:16 |
| 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. | 06:17 |
| 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 | 06:18 |
| dbolser | for bonus marks, what are the core residues of each subunit? | 06:19 |
| 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. | 06:20 |
| 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 | 06:21 |
| 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 | 06:22 |
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| 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 | 06:24 |
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| kanzure | dbolser: why do you suggest hierarchical marov machines instead of just clustering? | 10:21 |
| dbolser | hmms are a way of sequence searching that is more sensitive than single sequence alone | 10:23 |
| 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 | 10:24 |
| dbolser | http://www.ncbi.nlm.nih.gov/pubmed/9837738 | 10:25 |
| 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 | 10:26 |
| dbolser | kanzure: can you stick that into a chrome extension for me? | 10:27 |
| kanzure | maybe later let me wake up first | 10:27 |
| 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 | 10:28 |
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| 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 | 10:29 |
| 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 | 10:30 |
| dbolser | is y close to x or a or b? | 10:31 |
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| 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 |
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| dbolser | like I said, prolly overkill | 10:31 |
| dbolser | the main take home point is... HMMer3 is really great, really fast, and really easy to use with a good manual | 10:32 |
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| dbolser | so build some hmms, and get a sequence database to cluster | 10:32 |
| kanzure | okay. | 10:33 |
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| 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 | 10:33 |
| superkuh | There's not enough postural sway in the shoulders. | 10:35 |
| 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" | 10:36 |
| fenn | please state your opinion in the form of an answer, not observations about whether it looks right or wrong | 10:40 |
| kanzure | robot | 10:40 |
| superkuh | robot | 10:41 |
| kanzure | http://rpgjs.com/ hah "import rmxp" shit's crazy | 10:42 |
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| 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 | 13:51 |
| 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 | 13:53 |
| kanzure | fenn: really i'd also accept suggestions for how i can emulate your problems on my end | 14:01 |
| fenn | proceed as if there were no bug, then when someone complains, see what's in common | 14:06 |
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| kanzure | this all sucks so much | 14:09 |
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| AlonzoTG | Anyone listen to Alex Jones yesterday EveningL | 15:53 |
| AlonzoTG | ? | 15:53 |
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| @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 | 16:08 |
| @kanzure | eh, photocleaving seems kinda useless since you can't uncleave the nucleotides | 16:11 |
| @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 |
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| @kanzure | polymerases have been built to accept dNTPs attached to fluorophores, so that is potentially workable.. | 16:12 |
| @kanzure | (and then you need a way to switch on/off or step the polymerase molecule) | 16:13 |
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| @kanzure | fenn: http://www.reddit.com/r/raldi/comments/i8z20/frustrating_unix_pitfall_of_the_day_esoteric_cron/ | 17:41 |
| @kanzure | maybe that was our problem with davinci | 17:42 |
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| ybit | ksjj;lafdj;lkdsajf;lajsdf | 19:13 |
| thesnark | ###!@!!!##$$gfsd | 19:17 |
| @kanzure | what is this | 19:18 |
| jrayhawk | rage | 19:18 |
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| @kanzure | debian neuroscience survey results | 23:59 |
| @kanzure | http://neuro.debian.net/survey/2011/ | 23:59 |
| --- Log closed Tue Jun 28 00:00:07 2011 | ||
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