00:02:32 hello 00:03:27 payday, beer, and ben and jerry's ice cream - does life get any better? 00:10:39 hehehehe... I guess not :-) 00:12:00 I am completely new to the field of bioinformatics... I mostly come from a computer sciences background. But my wife is a microbiology and immunology researcher and I am trying to learn as much as I can in the field in the hopes that I might be of some use to her one day. 00:12:57 I was wondering if someone could help me understand the process of data acquisition in mass spectrometry. In particular, I am trying to know what type of raw data a mass spectrometer outputs. 00:13:46 I understand there are many ways to use those wonderfull beasts... so my question might not make much sense :-) 00:14:56 isn't mass spec used mostly for chemistry? 00:15:03 i haven't touched a machine since i took organic lab 00:15:53 Not entirely... as an example, you can digest peptides and use mass spectrometry to sequence them. 00:16:08 *** synthase has quit (Read error: 110 (Connection timed out)) 00:16:25 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 00:16:39 as with sanger sequencing? 00:17:18 in the lab i work in, we just send purified PCR samples to an on-site sequencing lab and they perform it for us 00:17:32 my boss deals with the raw data, so i can't be of much help to you :( 00:19:30 hehehe... that's quite alright... I was just looking at sanger sequencing on the web. I'm not biology expert :-) I merely try to fit the pieces together from what my wife tells me LOL 00:20:12 well major props to you for doing that, if i had majored in something besides genetic then this stuff would scare the hell out of me 00:20:51 luckily i'm genetics and my girlfriend's biochem, so we're on the same page 99% of the time, even if half the time she's just listening to me to get me to shut up 00:21:48 LOL... well, I guess its just the way science couples are :-) I just find her field more interesting than mine so I'm the one doing the listenning. 00:34:19 To clarify my earlier question, I am trying to understand how gas chromatography coupled with mass spectrometry works as far as data output goes. 00:37:30 *** craigoz (n=craigo@202.63.56.72) has joined #bioinformatics 00:40:47 *** synthase has quit (Read error: 60 (Operation timed out)) 00:44:41 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 00:52:15 Nevermind my previous statement... LOL... 00:52:39 Liquid Chromatography, not Gas... basically looking for sample data of an LC-MS run... 01:40:54 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 01:41:13 *** bbalajirao has parted #bioinformatics () 02:07:59 *** coolhp has quit () 02:17:05 *** levitation_ has quit (leguin.freenode.net irc.freenode.net) 02:17:05 *** Lunar_Lamp has quit (leguin.freenode.net irc.freenode.net) 02:18:15 *** levitation_ (n=levitati@noorus.aklubi.ee) has joined #bioinformatics 02:18:15 *** Lunar_Lamp (n=Lunar_La@unaffiliated/lunarlamp/x-038437) has joined #bioinformatics 02:18:32 *** Lunar_Lamp has quit (Connection reset by peer) 02:18:37 *** Lunar_Lamp (n=Lunar_La@pateam.planetarion.com) has joined #bioinformatics 02:18:42 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 02:19:17 *** bbalajirao has parted #bioinformatics () 02:22:40 *** levitation_ has quit (leguin.freenode.net irc.freenode.net) 02:29:48 *** levitation_ (n=levitati@noorus.aklubi.ee) has joined #bioinformatics 02:49:21 *** svensko`laptop (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 02:50:59 *** svensko has quit (Remote closed the connection) 03:41:36 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 04:26:38 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 04:26:47 *** bbalajirao has parted #bioinformatics () 04:43:36 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 05:18:27 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 05:18:42 *** bbalajirao has parted #bioinformatics () 05:21:48 *** vimes656 has quit () 05:56:42 *** synthase has quit (Success) 07:05:47 *** Splicer has quit () 07:21:24 *** clarezoe has quit (Remote closed the connection) 07:43:31 *** CrimsonScythe (n=CrimsonS@unaffiliated/crimsonscythe) has joined #bioinformatics 07:48:52 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 08:05:13 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 08:05:50 *** bbalajirao has parted #bioinformatics () 08:11:22 *** clarezoe has quit ("暂离") 08:16:42 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 08:38:13 *** craigoz has quit ("Leaving.") 09:16:06 *** bbalajirao1 (n=balaji@203.77.201.162) has joined #bioinformatics 09:16:46 *** bbalajirao1 has parted #bioinformatics () 09:56:58 *** highvoltz has quit () 10:17:02 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 10:51:49 *** vimes656 has quit () 11:03:27 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 12:24:28 *** gotgenes (n=chris@hc6521d71.dhcp.vt.edu) has joined #bioinformatics 12:53:59 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 14:20:41 *** faceface (n=dmb@p57A0F995.dip.t-dialin.net) has joined #bioinformatics 14:20:49 I am increasingly outraged 14:20:58 who should I complain to? 14:21:50 Just take a look at this... http://www.google.com/search?hl=en&q=%22The+world+of+globular+proteins+appears%2C+to+a+naive+observer%22&btnG=Search 14:22:09 A nice Google search with a nice hit right? 14:22:30 wrong - its commercial content dressed up like a normal hit 14:22:53 notice there is no cached version? Because the text that is hit is *access restricted* 14:23:30 I wonder how much money wiley had to stuff down the pants of the Google lap dancers before they got into bed together... 14:23:49 I bet they persuaded themselves they were doing 'Good(^TM) 14:23:53 ' 14:23:57 grrr!!! 14:23:59 etc 14:24:20 so... which channel is google in? 14:25:10 I'll slap some sense into them... in the mean time - I would like you all to 'help them improve' and complain about 'the distinction between commercial and free content' 14:25:27 here is the recommended text of my one man advocacy (anti willy) campaign... 14:26:41 How long will it be until my searches pull up 1000's of hits, all of them requiring subscription of some kind, or some other non-free *FALSE POSITIVE* hits? \n\n Please do not get in bed with bastards like Wiley. Sure - we all know the pleasure of sleeping with a bastard, but the next day you will hate yourself. \n\n Where is the 'clear distinction between commercial and non commercial content' that we have come to know, *trust* and lov 14:26:41 e? \n\n Please do not archive subscription only content. 14:27:25 if that dosn't make them hand back the millions I don't know what will! 14:29:34 this has been happening for ages, faceface 14:29:45 grrr...errrr? 14:29:48 really? 14:29:53 yes 14:29:57 really? 14:30:00 only joking 14:30:07 who, how, and in what ways? 14:30:36 google always returns hits to journal articles 14:30:42 that are access restricted 14:30:47 at least in the past couple of years 14:30:48 at least 14:31:18 well, I think its dispicable, and that anyone finding such a hit should kick up a fuss 14:31:23 despicable 14:31:28 why? 14:31:49 0. google is a BUSINESS 14:32:07 CowbertDH, here is the 'clear distinction between commercial and non commercial content' that we have come to know, *trust* and love? 14:32:08 and I don't think it's really too misleading 14:32:16 CowbertDH, your joking! 14:32:26 unless you're complaining about the time wasted 14:32:34 its a false positive hit 14:32:37 clicking on links that take you to restricted access sites 14:32:42 faceface: it's only false FOR YOU 14:32:53 its a bullshit hit pretending that I got an answer to content that I don't habe 14:32:54 have 14:33:00 since your institution obviously doesn't have a subscription to that journal 14:33:08 CowbertDH, let the website give subscribers a 'google search' 14:33:20 let google advertize their asses off on behalf of wiley 14:33:34 eh? 14:33:36 let google index all the 'sample content' that wiley is willing to offer 14:33:44 my institution? 14:33:55 yeah 14:34:01 I am a man at home searching the internet for information... I am getting a bunch of adverts back 14:34:23 OK, OK... I know... I choose to use google, and fool me for having expectations of quality 14:34:29 why are these adverts? I thought they just sent you to the page with the article and then wiley or whoever makes you login 14:34:38 but for the love of evil - why ??? 14:34:39 if you aren't autoproxied via the institutional login 14:34:53 seriously, I don't see the problem with that 14:34:57 CowbertDH, they are adverts because they are links to commercial content 14:35:05 I don't see how you can miss it 14:35:16 since at least it gives me an abstract, and if I need the article I can get it some other way 14:35:34 faceface: what you're gonna complain about pubmed next? 14:35:36 OK, nothing is stopping google in principle from returning a huge list of adverts - of course they aren't really 'Good' 14:35:50 "OMG IT ONLY RETURNS NON-FREEJOURNAL ARTICLES TO ME" 14:35:55 CowbertDH, but its a hit within the body of the article! cant you see how wrong that is! 14:36:12 CowbertDH, pubmed searches abstracts only - and keywordds 14:36:18 and the point is - I know the rules. 14:36:24 the rules? 14:36:25 if I go to google books, I know the rules 14:36:45 I know that pubmed isn't a content provider - just a particular type of search 14:36:58 and google is? 14:37:21 google, however, I *believed* to be an index of the content 'on the internet', i.e. the all unifying, all field leveling, all encompasing, user create INTERNET. 14:37:44 google provides adverts to services which is fine 14:38:05 but the adverts are clearly distinct from the the 'hits in the archive of internet content' 14:38:22 it *is* internet content 14:38:34 just that *you* my friend, has no access to it ;) 14:38:35 that is a part of why google has grown so sucessful - the content is here - here are the adverts, here are the sponsored links 14:38:41 CowbertDH, elitest 14:38:46 richie 14:38:50 *** highvoltz has quit () 14:38:50 westerner 14:38:51 google up "darkweb" 14:38:55 or hidden web 14:38:57 what is that? 14:39:19 * faceface seriously considers 'yahoo searching' it up... 14:39:27 http://en.wikipedia.org/wiki/Deep_Web http://www.lib.berkeley.edu/TeachingLib/Guides/Internet/InvisibleWeb.html 14:39:31 CowbertDH, I just think its evil 14:39:44 the links you are seeing to journal articles is basically at the boundary of the surface web and the deep web 14:40:03 I don't understand why you'd want google to stop indexing them 14:40:09 because who else would? 14:40:16 CowbertDH, I think they are talking about non-visible elements no? 14:40:21 huh? 14:40:35 the deep web is web content that's not indexed 14:40:42 (publically, anyway) 14:41:23 CowbertDH, I don't mind if Google indexes them, and sets up 'site searches' for ppl like wiley, or marks them as 'advertizing'. However, I have come to expect hits in google to be part of THE INTERNET - not some subscriber only stuff... 14:41:29 seriously 14:41:39 why should i be penalized if you can't accesss the indexed content 14:41:47 who's elitest now? 14:41:52 penalised how? 14:42:08 you need to go to wiley and hit their 'site search', or you hit pubmed 14:42:09 you're proposing that google no longer index artciles 14:42:16 YES 14:42:24 right, and that's removing a service for me 14:42:55 and its falsely creating a service for 99% of the world 14:43:00 I might be able to buy it (pun intentional) if google interoperated with pubmed or something and sent me to the appropriate abstract 14:43:05 but I see how your needs are greater.... 14:43:22 not good enough for me 14:43:24 the only negative I see for *you* is the time wasted 14:43:43 by clicking on links that go to content you can't access 14:43:54 I don't like clicking adverts that are 'by complicit expectation' (or something) not supposed to be adverts 14:43:57 what you're telling me *I* should do, should apply to you, reciprically 14:44:00 the first tast is free 14:44:04 taste 14:44:30 if you end up at the "You can nonly see this content via subscription" then is to ILL the article from some institution that has access to it 14:44:56 CowbertDH, how would you feel if you went to google and typed "how to do linear regression" or something like that, and you got back 1000s of results, and OMG... they are all commercial 14:45:09 there's commercial and there's commercial 14:45:20 it's not like google doesn't reutnr that 14:45:21 believe me, wiley are commercial 14:45:41 CowbertDH, but straight adverts are clearly marked 14:45:46 google might return companies that provide me services that do linear regression 14:45:50 are they now? 14:46:17 CowbertDH, its very important! 14:46:29 there is a line between the adverts and the 'hits to content' 14:46:38 literally... a line 14:46:49 uh 14:46:57 I'm not sure which google you're using because I get both 14:47:06 other search engines, notably Yahoo, didn't make that distinction, which is why google became popular 14:47:09 the only distinction is pagerank stuff that people pay for 14:47:12 it was part of their philosophy 14:47:27 something which they are shitting all over with this strategy. 14:47:31 seriously 14:47:43 I'm totally against stuff migrating *back* to the deep web 14:47:55 CowbertDH, the deep web article that you returned seems to be about pages that are not indexed - i.e. the opposite of what I am complaing about 14:48:02 ah... oK 14:48:24 I see ... I thought the deep web was what we are seeing. 14:48:56 the deep web is content that's not indexed 14:49:05 by something like google 14:49:52 CowbertDH, my suggestion is this - Clearly, google knows what they are doing each and every time they archive subscriber only content - how else would they get access. In that case, the results of hits to subscriber only content could be clearly separated from content that is 'free to all' FREE!!! that way, people without privileged access could ignore those FALSE POSITIVES. 14:49:59 CowbertDH, OK 14:50:20 I don't see why they are false positives still 14:50:27 they are just returning hits from the deep web 14:50:31 Free as free drinks, text, speach 14:50:38 which OTHERWISE WOULDN'T BE RETURNED 14:50:55 CowbertDH, then surly it isn't the deep web in that case 14:51:07 CowbertDH, return in a separate section is what I am suggesting 14:51:18 they are false, because when I click on the link, the content isn't here 14:51:20 ok 14:51:20 there 14:51:32 again it's all about 'me me me' :) 14:51:41 http://www.google.com/search?hl=en&q=%22The+world+of+globular+proteins+appears%2C+to+a+naive+observer%22&btnG=Search 14:51:52 CowbertDH, I know that isn't an unreasonable position 14:52:10 hmm 14:52:11 advances are made by people like you you you :) 14:52:36 I wonder why it doesn't return me to the abstract-only from FEBS if I'm not logged in 14:52:42 maybe that's what needs to change 14:55:34 man, I go off to code and miss several pages worth of discussion :-) 14:56:28 I need to get some coding done, but I WAS TOO BUSY TRAWLING THE DARKWEB 14:56:47 hehe 14:56:58 (Trolling? :) 14:59:57 oops ;-) 15:00:11 thanks for the feedback CowbertDH 15:00:15 ;) 15:00:20 * CowbertDH plays devil's advocate 15:00:26 I should get back to work! 15:00:28 *** faceface has quit ("So long, and thanks... probably.") 15:23:01 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 15:31:24 *** nsh_ (n=nsh@87-94-146-186.tampere.customers.dnainternet.fi) has joined #bioinformatics 15:31:42 *** nsh_ is now known as nsh 15:35:28 *** CrimsonSickle (n=CrimsonS@unaffiliated/crimsonscythe) has joined #bioinformatics 15:41:55 *** CrimsonScythe has quit ("Leaving...") 16:24:55 *** highvoltz has quit (Remote closed the connection) 16:25:06 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 16:48:39 *** nsh_ (n=nsh@87-94-146-186.tampere.customers.dnainternet.fi) has joined #bioinformatics 16:58:12 *** nsh has quit (Read error: 110 (Connection timed out)) 17:41:37 *** highvoltz has quit () 18:02:55 *** ybit has quit ("Konversation terminated!") 18:11:34 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 18:16:38 *** nsh_ has quit (Read error: 110 (Connection timed out)) 18:41:54 *** Splicer (n=p@h134n2c1o261.bredband.skanova.com) has joined #bioinformatics 19:20:57 *** vimes656_ (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 19:21:24 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 19:31:07 *** gotgenes has quit ("I am a meat popsicle.") 19:38:42 *** vimes656 has quit (Read error: 110 (Connection timed out)) 19:45:17 *** vimes656_ has quit (Remote closed the connection) 19:45:57 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 20:50:03 *** CrimsonSickle has quit ("Leaving...") 21:21:15 *** craigoz (n=craigo@202.63.56.72) has joined #bioinformatics 22:04:05 *** kanzure has quit (Remote closed the connection) 22:05:39 *** vimes656 has quit () 23:42:26 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics