00:22:41 *** mercutio22 has quit () 00:41:00 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 01:28:51 *** mercutio22 has quit (Remote closed the connection) 03:03:49 *** kanzure has quit (Connection timed out) 03:43:38 *** kanzure (i=bryan@66.112.232.172) has joined #bioinformatics 05:48:28 *** nordlicht (n=nordlich@141.53.70.85) has joined #bioinformatics 06:11:13 *** synthase has quit (Client Quit) 06:20:33 *** Iskr (n=i@host9-19-dynamic.56-82-r.retail.telecomitalia.it) has joined #bioinformatics 07:35:23 *** nsh (n=nsh@wikipedia/nsh) has joined #bioinformatics 08:02:13 *** CrimsonScythe (n=CrimsonS@unaffiliated/crimsonscythe) has joined #bioinformatics 08:05:49 anyone from an elsevier[cunts]-friendly institution? 08:06:12 * _dan shakes his head 08:06:14 <_dan> :( 08:06:16 <_dan> sux 08:07:16 * nsh collecting papers for a literature review; out of 10 so far, only sciencedirect has not recognised either the library of the universities credentials 08:08:21 *library's or university's 08:08:36 * nsh pretends to be another finnish university 08:17:34 * _dan has long envisaged a scientific p2p proxy network to allow people to pull papers with abandon 08:25:39 Academics shows unsuprising reticence towards anarchistic activities related to the people who implicitly control their careers 08:26:12 (piss-off the journal owners and publishing ability would likely go down while perishing probability up) 09:25:12 I don't know why ppl continue to publish wiht cunts 09:25:29 nsh: have you got what you want or do you still need help? 09:25:52 I still have 'literature wiki' on my stack... perhaps I'll have some time to spend on that soon 09:32:09 hey faceface. i was trying to access this article, being hoarded by elsevier: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T9H-491V0SX-BB&_user=10&_coverDate=08%2F31%2F1993&_rdoc=1&_fmt=high&_orig=browse&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=530b65ef49cf12c73055c54f01fef927 09:32:38 not to worry if you can't get it either though, we can order; i just like trees more than dutch arms-traders 10:01:21 *** yao_ziyuan (n=yaoziyua@222.188.130.206) has joined #bioinformatics 10:01:59 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 10:02:05 *** mercutio22 has quit (Read error: 104 (Connection reset by peer)) 10:08:37 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 10:19:26 *** highvoltz has quit () 10:21:02 *** mercutio22 has quit () 10:33:40 *** yao_ziyuan has parted #bioinformatics () 10:58:22 *** Splicer (n=p@h9n3c1o261.bredband.skanova.com) has joined #bioinformatics 11:03:05 *** biopunk has quit (Read error: 110 (Connection timed out)) 11:08:35 any know how to interpret an homology distance tree? 11:09:06 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:31:09 *** Splicer has quit () 11:37:42 *** CrimsonScythe has quit ("Leaving...") 12:01:12 nsh: interpret how? 12:05:35 * faceface cough *dcc* ;-) cough 12:05:46 cronmiller1993.pdf? 12:06:42 nsh arms traders? 12:07:27 _dan: I am trying to decipher the various ABI 'fields' - do you know of any good resources? 12:53:10 sorry 12:53:12 was in the lab 12:53:18 could you resend? 12:54:00 (elsevier['s parent company] run exhibitions for the weapons industry) 12:54:24 hehe 12:54:35 those silly swedes 12:54:40 well, i guess linear distance expresses homology degree. are the vertices simply taxonomic? 12:54:56 remember, alfred nobel got famous for inventing dynamite :) 12:55:16 * nsh smiles 12:55:26 you can mine with dynamite... 12:55:34 it's hard to beat an AK into a plowshare 12:55:38 (and thus modern high explosives industry was created) 12:56:18 though i did see a rendition of Verdi's Requiem recently where there were two figures brandishing automatic weapon replicas to quite dramatic effect) 12:56:22 yeah actually lots of HE is being used for antipersonnel minefield clearing operations these days 12:56:48 * nsh nods. prefer the little robot-based approaches meself: robots are cool 12:57:05 and pricey if one were to go boom 12:57:23 yeah, i'd just roll concrete cylinders over the field 12:57:34 minesweepers aren't particularly imaginative, i guess 12:57:44 anyway 12:57:51 BIOCRUFT:::: 12:58:08 * nsh wonders if there exists something like a co-regulation database 12:58:32 say, for any notable mutant, what is the up- and down-regulation statistics of other genes of interest 12:58:36 that would be useful to me right now 12:58:44 s/is/are/ 12:58:50 people usually chart that themselves 12:59:18 since it sort of only applies per study 12:59:24 yeah, but i chose to be incarnated at a time when there would be 6 billion other people about exactly for the purposes of letting them do the work for me 12:59:28 so fire up those microarray readers 12:59:35 meh :-/ 13:06:39 faceface, if i'm afk again and you feel the inclination to be so kind, could you mail the pdf to lauri.love@uta.fi 13:11:47 so, no expression/regulation/transcriptome databases with mutation-specific entries? 13:12:16 and there i was thinking bioinformatics had real ambition.. ;-) 13:18:30 nsh: grab it while its hot... 13:19:20 hit me up 13:19:34 erm... /dcc get 13:19:44 nsh there are lots of db's like that iirc 13:20:19 /DCC GET [ []] 13:21:02 There is a standard micro-arrary format, and some standard DB's full of data in that format... I am sure somewhere there is somethign to do with mutations... 13:21:21 * nsh tried /gcc first, heh 13:21:34 hey... why not search the resource I created for exactly this kindo of purpose... http://BioDatabase.Org 13:21:47 good idea! 13:21:52 (don't knwo why I didnt think of that) 13:22:16 specifically, i would like to know which genes are heavily upregulated in drosophila tko mutants 13:22:30 nsh: I'll email - its easier 13:22:35 (margh: this dcc isn't going to work. silly university network; thanks!) 13:23:50 nsh: I was hearing about that arms thing... I have bocotted JMB for that reason... 13:24:17 they must be sqirming now! 13:24:36 for real :-) 13:24:49 * nsh takes every opportunity to talk elsevier into the gutter 13:25:01 join my bocot! 13:25:06 they're way behind everyone else in terms of access rights, etc. 13:25:16 oh don't worry, i'm never publishing in any of their journals 13:25:23 ;-) 13:25:29 I'm just never publishing... 13:25:41 gahh... we missed the deadline for NAR DB :.( 13:26:36 NAR DB? 13:26:51 nsh: a search ('microarray') and a click yeilds this - http://biodatabase.org/index.php/Drosophila_microarray_centre 13:27:08 Nucleic Acids Research DataBase edition 13:27:17 I meant to get a paper for MB in there this year 13:28:09 I'll have to try BMC ... but they seem to be ignoring my attempts to spam all there database papers 'comments' with links to MB... and they are duplicating our work! 13:28:25 ok ok ... lets publish in ... erm... Nature! 13:28:47 * nsh smiles 13:29:03 i used to call Nature a tabloid, but i was reading mostly articles for public consumption at the time 13:29:04 http://biodatabase.org/index.php/Category:NARDatabase:Microarray_Data_and_other_Gene_Expression_Databases 13:29:07 GOD I HATE THE PUBLIC 13:29:14 (thanks and thanks) 13:29:32 oh, first is deadlink 13:29:34 * nsh searchs to fix 13:29:40 wha? 13:30:05 OH... I see... 13:30:14 how to edit external link pls?! 13:30:37 dang... its not dead in the NAR static version... I need to update... 13:30:53 nsh, just type the link in hte area that reads 'edit below here' and 'edit above here' 13:31:02 s/hte/the/ 13:31:29 its all a bit confusing, but the part in the purple box is required to be static 13:31:52 so i'd have to edit something in the transcluded template, or something it includes itself 13:31:53 mah 13:31:59 mediawiki: HAET 13:32:12 nsh: no - the idea of the template is that you shouldn't edit it 13:32:27 well, there are no urls in the actual page's code 13:32:28 nsh: do you hate it? or do you really LOVE it!? 13:32:31 ( http://biodatabase.org/index.php?title=Drosophila_microarray_centre&action=edit ) 13:33:00 nsh: yes... oh... yeah... you are *not allowed* to edit the part in the purple box 13:33:06 NAR's rules, not mine 13:33:20 sorry its so confusing... I need to think about how to make it clearer 13:33:42 13:34:01 http://the.updated.link 13:34:05 and a snyde comment 13:34:10 13:34:11 it let me change it in the template 13:34:18 nsh: go ahead ;-) 13:34:20 http://biodatabase.org/index.php?title=Template:NARDatabase:Drosophila_microarray_centre&action=edit 13:34:26 I fell short of actually protecting the templates 13:34:37 because in my heart I didn't want to ;-) 13:34:44 * nsh smiles 13:35:12 * nsh can't see anything partiularly database-y on their site though 13:35:25 I guess this page http://biodatabase.org/index.php/Template:NARDatabase:Drosophila_microarray_centre should carry some info... previously it did, but I dumbed it down 13:36:13 [[[ 13:36:13 The CDMC has set up two microarray experiment database servers with analysis software that can be used by CDMC customers for a nominal fee ($50 for User account set-up and first year use, and $100 annual renewal fee of account). The software is GeneTraffic® made by Iobion® Informatics an can be accessed thorough Internet Explorer 6.0 or greater on Windows XP. 13:36:16 ]]] --http://www.flyarrays.com/index.php?option=com_content&task=view&id=17&Itemid=33 13:36:18 meh 13:36:31 no data for me there 13:36:47 oh shit, have to kidnap virgins 13:36:50 bbiab 13:36:50 nsh: please tag on MB [[Category:Commercial bollox]] 13:36:55 ok 13:37:03 l8r 13:48:25 *** nordlicht has quit ("Verlassend") 15:52:09 *** kushalsejwal (n=kushal@59.178.221.53) has joined #bioinformatics 15:52:25 Hi guys 15:52:31 Anybody active there?? 15:53:23 *** kushalsejwal has parted #bioinformatics () 15:55:18 now, let's apply some elementary statistics 15:56:33 kushalsejwal was in the channel for 74 seconds. there are 86,400 seconds in a day. what is his confidence that there is no-one here today? 15:57:36 how many times would he need to repeat this drive-by-newbing randomly over 24h to achieve 50% confidence that no-one is speaking that day? 15:58:05 for extra credit: why are clueless people always in a hurry? 15:58:16 nsh: naughty, you just asked the bot in #physics how many seconds were in a day. "Elementary" indeed .. 15:58:46 * nsh is too cool for arithmetic 15:58:51 because they're worried they'll be hit by the cluestick 15:59:05 getting cluedin *hurts* 15:59:10 word 15:59:34 Also I suspect it's because they don't know how to idle in a channel. It's not like it's computationally intensive. :-) 16:00:23 i think some people were never taught nonsequential tasking 16:00:38 probably only think between breaths 16:00:57 * kanzure has to remember to breath sometimes 16:01:26 * nsh used to fear that if he thought about his breathing for long enough, he'd have to keep thinking about it or it'd stop 16:01:37 That's an awesome fear to have. 16:02:03 yeah, i traded it for the fear of spiders with whitney houston obsessions 16:02:08 didn't like that one so much 16:03:00 I still really like this one: 16:03:01 http://www.dichotomistic.com/mind_readings_spider%20minds.html 16:03:06 "do spiders have a mind?" 16:03:18 * kanzure is waiting (or working towards?) some more neuroscience of spiders to come up 16:04:21 i want them to give more spiders more psychoactive chemicals and take more pictures of their webs 16:04:34 it's like science, without all that reading, and with cool cobwebs 16:20:08 I was trying to figure out how spiders represent their own web in their brain 16:21:02 They don't see the whole thing. And yet they can do relatively fractal patterns. So they must be doing something interesting 16:21:08 and something algorithmic. 16:23:29 why would they need to represent it in their brain? 16:23:37 brocolli makes fractal patterns; has no brain 16:25:43 it's represented somehow within the organism 16:25:46 we know that much :) 16:25:54 I guess we could test it by removing their eyes or something 16:25:58 "Let's see if it spins a web now." 16:26:08 (molecular lesion of the optic nerves perhaps) 16:26:12 mmm, like how the russians proved that crickets hear with their knees 16:26:17 how'd they prove ti? 16:26:19 *it 16:26:21 : they cut off their legs and then shouted at them 16:26:25 none ran away :-) 16:26:29 and before? 16:26:44 (is a joke. loss of function is less precise an assay than gain of function) 16:27:07 if i had my eyes cut out, i might not want to spin a web even if i could 16:27:15 molecular lesions are less painful 16:28:26 Actually, it should be easy to simulat the spider brain or something 16:28:30 *simulate 16:28:46 * kanzure scuttles off to get some food 16:28:54 i don't think we can simulate a single neuron yet.. 16:29:23 * nsh hasn't checked though, but suspects that whole cell simulation is still in that misty future just over there 16:29:28 sure, sure 16:29:42 but there are some interesting approaches that people have been using 16:30:05 for example, Markram's approach of throwing as much as possible into the models 16:30:32 ion channel dynamics, membrane software, enzyme kinetics, plasticity models, .. 16:31:48 * nsh nods 16:45:04 *** CrimsonScythe (n=CrimsonS@unaffiliated/crimsonscythe) has joined #bioinformatics 18:24:38 *** highvoltz has quit () 18:47:22 *** biopunk (n=p@h9n3c1o261.bredband.skanova.com) has joined #bioinformatics 18:58:00 *** levitation_ has quit (Connection reset by peer) 19:13:39 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 20:56:19 *** platyhelminth_ (n=opera@88-122-18-86.rev.libertysurf.net) has joined #bioinformatics 21:08:20 *** platyhelminth_ has parted #bioinformatics () 21:26:27 *** nsh has quit (Read error: 110 (Connection timed out)) 21:27:42 *** nsh (n=nsh@eduroam-80.uta.fi) has joined #bioinformatics 21:42:52 *** nsh- (n=nsh@eduroam-80.uta.fi) has joined #bioinformatics 21:42:59 *** nsh has quit (Read error: 54 (Connection reset by peer)) 21:55:05 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 22:07:55 *** nsh- has quit ("NIET") 22:25:03 *** Iskr has quit ("Leaving") 22:37:38 *** CrimsonScythe has quit ("Leaving...") 23:37:23 *** kanzure has quit (Connection timed out) 23:39:22 *** kanzure (i=bryan@66.112.232.172) has joined #bioinformatics 23:48:32 *** levitation[A] (n=levitati@n7.campusnet.ee) has joined #bioinformatics 23:54:13 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 23:59:33 *** mercutio22 has quit (Read error: 110 (Connection timed out))