00:04:02 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 00:04:02 *** svensko has quit (Read error: 104 (Connection reset by peer)) 00:21:41 *** synthase has quit (Read error: 110 (Connection timed out)) 00:21:46 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 00:26:11 *** vimes656 has quit () 00:44:23 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 00:44:23 *** svensko_ has quit (Read error: 104 (Connection reset by peer)) 02:00:08 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 02:40:38 *** vimes656 (n=vimes656@203.200.58.142) has joined #bioinformatics 03:25:30 *** Biopunk (n=p@h13n2c1o261.bredband.skanova.com) has joined #bioinformatics 03:27:15 *** pingou_ (n=pierrey@AMontsouris-152-1-13-47.w82-123.abo.wanadoo.fr) has joined #bioinformatics 03:35:31 *** kanzure has quit ("Leaving.") 03:38:18 *** Splicer has quit (Read error: 110 (Connection timed out)) 03:38:53 *** pingou has quit (Read error: 110 (Connection timed out)) 03:58:49 *** synthase has quit (Read error: 110 (Connection timed out)) 04:14:38 *** Biopunk has quit () 04:18:29 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 04:36:17 *** pingou_ is now known as pingou 04:53:21 anyone here? i'm looking on some input on what coding language to learn 04:54:12 basically i'm wondering if python or perl would serve me better in bioinformatics 05:03:59 perl is *the* language for bioinfo 05:04:09 thought so, thanks 05:04:10 but python give more structure 05:04:30 and java is more powerfull because of its OO 05:04:33 someone just sent me http://steve.yegge.googlepages.com/ancient-languages-perl 05:05:45 perl is easy to learn 05:05:49 close to php too 05:06:14 yeah, i'm reading "beginning perl" right now but i'm still on the second chapter which is "Working with Simple Values" 05:06:21 ;-) 05:06:25 I read it too 05:06:31 nice book to start with 05:06:57 *** Mathias (n=designin@cpe-76-170-66-183.socal.res.rr.com) has joined #bioinformatics 05:07:08 *** Mathias has parted #bioinformatics () 05:07:17 the guy has a point though, larry wall does seem a bit odd 05:07:21 :P 05:07:44 this book claims that i'll be able to write basic programs by the time i'm done with the 4th chapter, were you that lucky? 05:08:38 http://www.wall.org/~larry/ 05:09:05 I have been to the end of the chapter 4... as usual google learned me most of the rest 05:09:10 :p 05:09:27 yep i just finished exploring that site, melted my eyes 05:09:50 "No, I'm not going to change it just because it's not your favorite... " 05:15:07 wow i still can't believe this guy had sex AT LEAST four times 05:16:05 "I have four children" 05:16:33 scary thought 05:39:33 *** synthase has quit (Connection timed out) 05:39:55 *** toru (n=gioby@81-208-83-234.fastres.net) has joined #bioinformatics 05:45:00 _dan: ping 05:53:26 *** toru has quit ("Ex-Chat") 05:57:04 picking on the language question, I programmed in Perl for more than 7 years, but now I don't use it anymore. I find python much easier to code and to maintain 05:57:39 so, comparing biopython and bioperl, what does bioperl have that biopython doesn't? 05:58:17 much more... :D 05:58:20 I know there are some stuff, specially since bioperl older and more userd, but I can't see a list anywhere 05:58:31 perl moby exist :) 05:58:54 * pingou prefers python to 05:59:49 I don't know perl moby. Is that the webservices thing for perl? 06:00:40 forget it 06:00:44 google is my friend :) 06:01:15 yes it is 06:01:28 the biomoby implementation for perl 06:01:58 and the bioMoby-python is no good? 06:02:26 is not really present 06:02:32 perl and java are the main two 06:03:05 ok, I see 06:05:30 I work with web, at the moment 06:05:41 don't have experience in bioinformatics yet 06:06:02 But I'm learning a little bit of it 06:06:14 and of bioperl and biopython 06:07:32 I would love to work in the bioinformatics field, because biology is something I love 06:08:06 =) 06:08:09 same for all 06:09:47 are you working in the field? 06:11:16 yes a bit 06:11:21 still student in fact 06:13:22 ok 06:38:56 *** craigoz (n=craigo@202.63.56.72.dynamic.rev.aanet.com.au) has joined #bioinformatics 06:40:26 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 06:51:28 *** craigoz has quit ("Leaving.") 07:07:11 <_dan> morning 07:08:17 _dan: hi :) 07:08:30 <_dan> hola pingou 07:08:33 <_dan> hows things? 07:08:52 had a question on jmoby but found the answer ;) 07:08:56 else fine 07:08:58 and you _dan ? 07:09:09 * _dan wouldnt have been much help on that front anyway he suspects :) 07:09:11 <_dan> im good 07:09:19 <_dan> head buried in webservices books and matlab 07:09:25 <_dan> neither of which I know much about 07:09:26 <_dan> lol 07:09:30 webservices ? 07:09:44 don't use matlab go for R ;) 07:09:50 <_dan> i use R all the time 07:09:53 torbjorn: tell him ;) 07:09:55 <_dan> just that the people I work with dont ;) 07:10:02 octave then :D 07:10:33 <_dan> well that's what I have installed on my laptop instead of matlab 07:10:34 <_dan> ;) 07:10:38 _dan: which knid of webservices ? 07:10:39 ^^ 07:11:05 <_dan> not RESTful ones 07:11:13 ^^ 07:12:34 <_dan> although i did get a book on them 07:12:44 <_dan> and a lot of the code is in ruby 07:12:49 <_dan> which will be interesting 07:12:55 nice indeed 07:13:10 I should try to do a couple of hello world on ruby 07:17:34 whatnow? octave is great! 07:17:37 j/k 07:17:39 though it probably is 07:17:53 hvaent used it for 5 years 07:40:17 *** faceface has quit (Nick collision from services.) 07:40:45 *** facefaceface (n=chatzill@bioinformatics.org) has joined #bioinformatics 07:55:30 *** toru has quit ("Ex-Chat") 08:11:13 *** faceface (n=dmb@p57A0C315.dip.t-dialin.net) has joined #bioinformatics 08:37:38 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 09:57:21 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 10:16:01 *** toru has quit ("Ex-Chat") 10:54:17 anyone using wikiprofessional? 10:57:18 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:05:07 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 11:10:28 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 11:56:18 *** breinbaa1 (i=er@xs7.xs4all.nl) has joined #bioinformatics 11:57:08 *** highvoltz has quit () 11:58:34 *** breinbaas has quit (Read error: 104 (Connection reset by peer)) 12:02:04 *** vimes656 has quit () 12:03:02 *** vimes656 (n=vimes656@203.200.58.142) has joined #bioinformatics 12:18:44 *** breinbaa1 has quit (Client Quit) 12:26:49 *** vimes656 has quit () 12:26:51 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 12:31:08 *** conle1 (n=ibcliffo@spode.cs.vt.edu) has joined #bioinformatics 12:32:58 http://www.jobs.ac.uk/jobs/YZ613/Data_Analysts_2_posts/ 12:32:59 *** vimes656 (n=vimes656@203.200.58.142) has joined #bioinformatics 12:33:59 minimum of three-years experience of computational methods 12:34:26 pingou, how many do you have? 12:34:32 1.5? 12:34:32 faceface: none :D 12:34:36 oh... 12:34:40 I am not master yet ^^ 12:34:49 I will be graduate in december ^^ 12:34:51 well... its all experience ;D 12:34:57 ;) 12:35:29 with the master that would be almsot 2 year in bioinfo 12:35:35 *** Lynx_ has quit (Read error: 104 (Connection reset by peer)) 12:35:37 ... matter of point of view ^^ 12:35:51 and you seem to work hard, so call it 3... 12:36:04 lol 12:36:18 it is not reflect of the cv... 12:38:35 http://www.compbio.dundee.ac.uk/ftp/jobs/June2008/WT_Analyst_FINAL.pdf 12:39:06 pingou, I guess they are looking for a PhD, but it doesn't say so 12:39:44 some employers will be impressed if you don't have the requirements but apply anyway (with a covering letter to explain that you are simply the best candidate no matter what). 12:40:01 but I guess in this case it would be tough to convince them to give you an interview. 12:42:30 key role of the new appointments is to be a source of expertise and advice on 12:42:33 computational analysis for data-intensive “wet” biological research 12:42:35 sounds nice :) 12:43:35 Strong demonstrated programming skills in a high-level programming 12:43:38 language such as C/C++ or Java 12:43:42 :/ I need to work on that... 12:44:48 yeah... 'experience' with Java seems important these days. 12:44:58 faceface: do you see a dead line ? 12:45:14 i might try to apply just to see :) 12:45:14 4 th of next month? 12:45:26 yes that's for the application 12:45:42 I don't see when the job is supposed to start 12:45:54 no... I found that to be a problem in general 12:46:18 well will see then :) 12:47:46 thanks for the hit faceface , are you applying ? 12:50:49 ;-) not me 12:50:55 good luck with your application! 12:51:05 (I am moving to Dundee next month) 12:59:01 faceface: what will you do over there ? 13:02:03 next gen sequence assembly... which I will have to learn! 13:02:36 nice :) 13:03:43 I am looking forward to it a lot - I never worked intensively with genomic sequence data before, so its going to be really interesting. 13:04:38 I actually worked a bit with microarrays but never on assembly of contig or so 13:05:29 yeah, and I don't know how next gen stuff differs from last gen... its shorter reads I know that... perhaps its also highly automated... 13:05:48 no clue as of yet ;-) 13:06:02 buisy trying to 'wrap things up' here. 13:06:29 'd luck ;) 13:21:03 *** breinbaas (i=er@xs7.xs4all.nl) has joined #bioinformatics 13:26:32 http://www.ceh.ac.uk/personnel/CEH220_RadioChemist.html 13:28:05 *** kanzure has quit (Remote closed the connection) 13:28:20 26 users! 13:28:31 it is a record for this chan 13:28:38 \ó/ ! 13:30:08 * flu pops open some champagne 13:30:19 *** vimes656 has quit () 13:30:30 damn, we lost one :-) 13:37:13 *** synthase has quit (Read error: 110 (Connection timed out)) 13:37:33 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 14:04:19 well, I have to go 14:04:25 24 14:05:15 *** toru has quit (Remote closed the connection) 14:12:54 spamming BBB seemed to create a temporary blip in numbers... 14:13:03 (hint hint) 14:13:16 What's BBB? 14:13:40 Bioinformatics Bulletin Board (mailing list) 14:13:47 For computer languages, I mostly use C/C++, Ruby, and Tcl these days. 14:13:49 ah 14:14:29 I sent a mail saying "blah blah blah -- join irc://irc.freenode.net/#bioinformatics" 14:14:40 C++ eh? 14:15:01 thanks for joining BioWiki BTW... I still need to think of something to do with it... 14:15:41 Some people in my lab are working on a tRNA database so I'll put that up once it's open. 14:16:02 Yeah, I bet most of the programs I use are written in C or C++. 14:16:22 Sometimes I'm unfortunate enough to need a fortran program. 14:18:18 I just use Ruby for small, in-house scripting, though. 14:18:47 It's like like I have some massive Ruby project that's doing significant number crunching. 14:18:57 s/like like/not like/ 14:19:46 <_dan> phds : 14:19:48 <_dan> myExperiment people out there- -- anyone want to do a PhD in all aspects 14:19:49 <_dan> of social computing for e-Scientists, workflow analytics, collaborative 14:19:49 <_dan> design for workflows etc etc? 14:19:49 <_dan> Manchester has a whole bunch of studentship but time is running out - 14:19:49 <_dan> the deadline is June 20th! 14:19:51 <_dan> Carole 14:21:25 <_dan> that's at Manchester Uni CS dept by the way 14:24:16 *** vimes656 (n=vimes656@122.167.81.201) has joined #bioinformatics 14:35:58 Hey, I use software from that Dundee lab. 14:36:15 It's STAMP, a protein structure alignment tool. 14:36:37 It's written in C. 14:37:29 We incorporated it into MultiSeq, too, adding a few more features and tweaking the structure alignment metric. 14:41:28 Man, I've used 350,000 cpu-hours since last September. 14:41:56 I think I'm addicted. 15:00:21 *** highvoltz has quit () 15:27:27 wonklab, cool :D 15:28:14 _dan, PhD in social networking? Surly such stuff is just the irate dream of the daily mail editorial board? 15:28:45 <_dan> not of the post-myGrid crowd at Manchester 15:28:58 <_dan> http://www.myexperiment.org/ 15:29:14 Dr FaceBook I presume? (Only kidding ;-) 15:29:39 that looks really nice 15:31:04 <_dan> its come on quite a bit recently 15:33:59 seems similar to ideas that codeshepard was expounding 15:34:51 speaking of myGrid...is that project still going strong? I don't keep up with grid happenings these days. 15:35:45 0 Friends :-( 15:35:50 <_dan> well all the people are 'still around' there's been a bit of a post-myGrid diaspora but I think the real tangible thing that came out of it was Taverna really 15:36:22 <_dan> which is definitely 'still going' 15:36:40 can I 'invite' ppl to join? 15:37:37 <_dan> my username on there is 'dswan' 15:37:46 <_dan> i suspect I too have no friends 15:37:47 <_dan> ;) 15:37:57 hey! lets be friedns :D 15:38:32 'Request Friendship' - how often have I read those words! 15:38:36 <_dan> let me guess you are the new user 'Dan' 15:38:37 <_dan> :) 15:38:53 I can't help going for the neive name ;-) 15:39:04 naive 15:39:23 I actually thought I may have lost it to you 15:40:38 <_dan> no, i almost never atttempt to use 'dan' as a signup on teh assumption that it is gone lol 15:40:53 my favourite is this one... http://network.nature.com/profile/dan 15:41:26 <_dan> im not actually signed up to NN 15:41:37 <_dan> although people appear to moan about it on friendfeed 15:41:40 <_dan> at least they were yesterday 15:41:56 * _dan has been too busy trying to learn java today to be web 2.0 15:43:20 * faceface phone 15:48:40 1 friend! 15:49:47 <_dan> :) 15:49:56 *** vimes656_ (n=vimes656@122.167.81.201) has joined #bioinformatics 16:08:01 *** vimes656 has quit (Read error: 110 (Connection timed out)) 16:12:39 *** conley has quit (Nick collision from services.) 16:12:45 *** conle1 is now known as conley 16:13:02 *** conley has quit ("Leaving.") 16:13:34 *** conley (n=ibcliffo@spode.cs.vt.edu) has joined #bioinformatics 16:14:06 *** toru (n=gioby@81-208-83-234.fastres.net) has joined #bioinformatics 16:15:39 *** synthase has quit (Connection timed out) 16:39:55 *** vimes656_ has quit () 16:53:00 long phone call! 16:53:04 friendfeed? 16:53:09 thanks _dan 16:53:14 *** faceface has quit ("So long, and thanks... probably.") 16:55:39 _dan, do you know about Bruce Eckel's free java book? 16:55:48 that is how I learned java 17:52:13 *** toru has quit ("Ex-Chat") 18:11:45 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 18:48:42 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 19:24:41 *** kanzure (i=bryan@wireless-128-62-145-212.public.utexas.edu) has joined #bioinformatics 19:32:45 *** toru (n=gioby@81-208-83-234.fastres.net) has joined #bioinformatics 20:10:14 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 20:10:15 *** svensko has quit (Read error: 104 (Connection reset by peer)) 21:04:15 *** Splicer (n=p@h225n1c1o261.bredband.skanova.com) has joined #bioinformatics 21:06:53 *** toru has quit ("Ex-Chat") 21:21:56 *** clarezoe has quit (Read error: 113 (No route to host)) 22:06:41 *** kanzure has quit (Remote closed the connection) 23:29:41 *** synthase has quit (Read error: 110 (Connection timed out)) 23:29:45 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 23:33:14 *** vimes656 (n=vimes656@122.167.81.201) has joined #bioinformatics 23:33:55 *** vimes656 has quit (Client Quit) 23:44:04 *** vimes656 (n=vimes656@122.167.81.201) has joined #bioinformatics 23:50:06 *** vimes656 has quit ()