00:00:42 *** vimes656 has quit (Client Quit) 00:12:39 *** vimes656 (n=vimes656@122.167.81.201) has joined #bioinformatics 00:21:59 *** mercutio22 (n=htorres@c9516047.virtua.com.br) has joined #bioinformatics 00:38:53 *** mercutio22 has quit (leguin.freenode.net irc.freenode.net) 00:39:34 *** mercutio22 (n=htorres@c9516047.virtua.com.br) has joined #bioinformatics 00:41:05 *** vimes656 has quit () 01:27:59 *** mercutio22 has quit () 03:04:15 *** vimes656 (n=vimes656@203.200.58.133) has joined #bioinformatics 03:58:37 *** synthase has quit (Read error: 110 (Connection timed out)) 03:58:56 *** synthase (n=synthase@68.63.20.144) has joined #bioinformatics 04:17:52 *** Splicer has quit () 06:09:21 *** conley has quit (leguin.freenode.net irc.freenode.net) 06:09:53 *** conley (n=ibcliffo@spode.cs.vt.edu) has joined #bioinformatics 06:15:30 svensko I have a list of blogs here (or a sincere desire to spam): http://biodatabase.org/index.php/List_of_blogs_for_biologists 06:15:58 http://www.google.com/search?q=List+of+blogs+for+biologists shows up a lot more these days than when I first set up that list 07:09:57 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 07:58:35 *** toru_ (n=gioby@137.204.142.89) has joined #bioinformatics 07:59:38 *** toru_ has quit (Client Quit) 08:48:37 *** toru has quit (Read error: 104 (Connection reset by peer)) 08:49:46 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 08:49:53 *** toru_ (n=gioby@137.204.142.89) has joined #bioinformatics 09:06:07 *** toru_ has quit ("Ex-Chat") 09:38:25 *** toru has quit ("Ex-Chat") 09:39:50 *** berry_ has quit (Connection timed out) 09:52:11 *** kanzure has quit ("Leaving.") 09:55:15 *** berry_nl (n=berry@vpn-out.hsleiden.nl) has joined #bioinformatics 10:20:11 *** highvoltz has quit () 10:39:12 *** synthase has quit (Connection timed out) 10:55:29 *** svensko`laptop has quit (Remote closed the connection) 10:57:35 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:22:03 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 11:28:46 *** mercutio22 (n=htorres@200-144-94-39.epm.br) has joined #bioinformatics 12:06:24 http://morphbank.ebc.uu.se/mrbayes/ working for anyone? 12:10:05 nicht fur mich...t 12:13:12 highvoltz: nope, not working 12:13:25 The connection has timed out 12:13:28 doh. 12:13:53 does anyone know if mpiMrBayes is fom the same source code as MrBayes? ...or do I need a specific mpiMrBayes 12:14:15 no clue 12:14:24 I would guess its related but different 12:14:30 yeah 12:17:10 *** berry_nl has quit (Read error: 60 (Operation timed out)) 12:27:48 *** kanzure (i=bryan@dhcp-146-6-213-183.icmb.utexas.edu) has joined #bioinformatics 12:32:29 *** berry_nl (n=berry@vpn-out.hsleiden.nl) has joined #bioinformatics 12:56:01 *** vimes656 has quit () 13:07:33 Octave users? 13:07:38 Equivalency to matlab issues? 13:07:45 was it orbits? he is not around... 13:08:27 *** toru has quit (Read error: 104 (Connection reset by peer)) 13:09:11 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 13:09:37 kanzure: torbjorn says he uses one or the other 13:09:52 I have rarely seen him speak in here though... 13:13:20 bah 13:13:39 I don't know if I like all of these customized languages and commands in these weird interfaces. 13:13:49 Can't I just use a python interpreter prompt and go to town? 13:18:30 *speech* 13:18:44 i havent used octave for years 13:18:45 im afraid 13:20:20 *** svensko`laptop (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 13:26:35 gah! 13:27:40 *** xtmdster (n=xtmdster@ppp-70-251-19-45.dsl.hstntx.swbell.net) has joined #bioinformatics 13:27:45 *** vimes656 (n=vimes656@122.167.81.201) has joined #bioinformatics 13:28:09 whats the question btw? 13:28:20 Not quite sure. 13:28:30 I'm in a lab and want to start modeling some equations, but I'm not sure what for exactly. 13:28:45 Mostly to see what we should get out of the fluoroscopes 13:28:46 tried polyfit? 13:28:50 in what? 13:29:03 in octave 13:29:06 help(polyfit) 13:29:22 help("polyfit") # even 13:29:34 okay 13:30:01 or why not R ? 13:32:43 that is what I said :-) 13:33:09 hm R should have an octave plugin 13:35:14 I think it was orbits... (or was it wonklab?) arguing that octave was a great 'bioinformatics language' 13:43:50 * kanzure is looking into perl instead 13:43:52 good ol' perl 13:44:12 what kind of data is this? 13:53:22 *** nbarr (n=nbarr@213.162.13.162) has joined #bioinformatics 13:55:07 *** nbarr has quit (Client Quit) 13:58:34 *** vimes656 has quit () 14:35:41 *** toru has quit ("Ex-Chat") 14:41:31 *** svensko has quit ("Leaving") 14:44:48 * _dan always assumed octave was just matlab with added incompatibilities 14:52:30 torbjorn: No kind in particular. My model is here: http://heybryan.org/pipermail/synth2008/2008-June/000025.html 15:11:57 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 15:45:05 kanzure: Very interesting project yet again. Why don't you poor your model into an UML and set it up using OO driven technology. That way you have more freedom when you have to revise your model. 15:45:54 is it realistic to use perl in order to create some sort of pattern recognition program? 15:45:56 berry_nl: Would you say that the DNA would be an object, and then I just use an object for the solution, and model that ? I.e., populate it with 2.6 billion strands or something? 15:46:06 svensko: Depends on what you mean. 15:46:23 kanzure: Jep. 15:46:35 well i'm trying to think of a way to use SQL and perl, by setting up a database and then using perl to mess around with it 15:47:01 i was thinking it would be neat if i could get something like a sample of HIV genotypes and try to find patterns within the sequences 15:47:07 svensko: pattern recongition, as in sequence patterns ? 15:47:09 i realize it's 1000x more complicated than that 15:47:10 yeah 15:47:11 yeah, perl is suitable 15:47:12 absolutely 15:47:37 seems like it'd be a fun project to work on while i am trying to utilize perl 15:47:46 berry_nl: I need this to run on my laptop, not on a supercomputer. So I'd like to just do rate models of the DNA objects. 15:47:56 svensko: http://bioperl.org/ or something. 15:48:02 sadly i'm stuck doing calc II most of the summer, but i'm making slow but steady progress on perl :) 15:49:13 kanzure: ah oke hehe, then you might want to use a different way indeed. On the other way, why not build a small home computer cluster? I mean its not like you will need big blue for the calculations. 4 to 6 combined home computers will easily do the trick. 15:49:46 We've done the same at my uni and the results that came from it are satisfying. 15:49:58 berry_nl: I have no funding. 15:50:21 Yes, I know, the machines are like $20 each ;-) but 15:50:25 *** deeku (n=telppa@h199-182.wlan.ucalgary.ca) has joined #bioinformatics 15:50:50 still, I think I can get a script done in 30 minutes [if I can figure out how these pesky matlab scripts work ... I'm converting them to python/perl/something usable] 15:50:54 well if it is just not possible within your budget it is wise to say. Then we should just consider different options ;) 15:52:00 Never understood people who wanted to use matlab in the first place. But hey that is just me maybe. :-/ 15:55:01 This syntax makes no sense. 15:55:10 * kanzure bangs head against the wall. 15:55:31 Well, the file structure rather. I need some good header files. 16:07:11 *** deeku has quit (Read error: 110 (Connection timed out)) 16:17:32 <_dan> berry_nl: matlab is very entrenched in a number of scientific disciplines, our neuro people work almost exclusively in it 16:17:51 <_dan> whether it's the right tool for the job these days is irrelevant, it's what they know and feel comfortable in 16:19:20 *** wrldpc (n=wrldpc@pool-71-174-89-247.bstnma.fios.verizon.net) has joined #bioinformatics 16:20:21 <_dan> now if anyone has any experience in wrapping matlab stuff as web services, then please get in touch, so I can save myself some time over the next few weeks ;) 16:20:53 _dan: Yes I have seen this before. Its rather frightening. Especially if you have a somewhat older old school biologist saying things like: I don't see the point of bio-informatics, look at me I am a biologist and I can make my own little scripts. 16:21:10 * _dan nods in agreement at that :) 16:21:56 Those are the kind of things that make my jaw fall open and make me fall to my knees thanking my professors they are teaching me python, perl. OO Java and alike. 16:22:23 <_dan> we get 'we have lots of data help us analyse it! But by the way we don't wish to get involved in standards development, or sharing our data, or for that matter, our analysis technique' 16:24:07 I have tried helping pharmacists last summer doing a nation wide research. And it did not matter what I said. They did not want to use anything else then MS Access for the analysis. And they did not believe my "excuses" when I told them that I could not deliver because Access would not handle the huge queries. 16:24:28 Blegh! ignorant sheep. 16:25:29 * _dan grins 16:25:39 <_dan> yeah we have that issue with clinicians 16:26:59 <_dan> but we're winning the war there, at least with some of them :) 16:30:28 True, personally I can't wait to get my hands on some research. 16:31:12 <_dan> what are you studying at the moment (I assume you're studying, correct me if I'm wrong :))? 16:34:28 that's one thing i didn't like about my bioinformatics class, we covered databases in 30 minutes, learned nothing about the internals, and learned nothing about perl, python, etc 16:36:58 <_dan> tbh databases dont seem to be deeply covered on our course either 16:39:06 <_dan> or perl 16:39:09 <_dan> or python 16:39:15 <_dan> but java is covered in detail 16:39:24 ah 16:39:44 our course seemd to be composed of "you want to do this, what website would you do it at, and what would you do at that website to get what you want?" 16:39:55 our homework was literally step by step instructions to BLAST stuff 16:41:57 <_dan> ok, our course is a masters course (half taught, half research), but even that can be step by step (well some of the practicals definitely are) 16:42:28 ahh, this was undergrad meant for genetics and biochemistry majors 16:42:49 i would say 90% of the class didn't use their computer for anything other than writing lab reports and checking facebook 16:43:53 <_dan> :) 16:44:27 <_dan> we ran a cytoscape tutorial recently, i always find it interesting to see the proportion of tutorial/facebook activity from people stratified by age 16:46:24 _dan: After 7 years of working full-time in IT I decided to go study again, bio-informatics to be precise. 16:47:03 berry_nl, do you have a biological background? 16:47:11 Funny you two mention databases. I am preparing for an exam tomorrow. And they cover it in great detail. 16:48:01 yeah, i've been teaching myself SQL for a while now 16:48:13 go to chapter 9 I believe in the pgsql documentation, but gave up there (at functions) 16:48:33 the documentation is not meant to teach, it's meant to be a reference, and it's pretty obvious in that chapter 16:48:39 svensko: Nope. Only school I ever finished was elementary school and lower vocabulary school. After that I went to work. (programming software for pharmaceuticals so there is your link) Then at the age of 22 I gave a shot at a uni by doing a board exam (colleqium doctum) and got through hehe 16:49:49 ah 16:50:09 i've always wondered it would be easy to come from a programming background or come from a biological background 16:50:13 err easier 16:50:23 * _dan thinks the best thing about bioinformatics is the variety of routes that people take to get there 16:50:38 indeed 16:50:54 my population genetics class is what interested me... that and the stats class i was taking at the same time 16:51:07 * _dan is a biologist, undergrad & phd & postdoc who 'drifted into' bioinformatcs because of... general geerkery 16:51:55 Hmm for me the IT related classes are obviously easier. The biggest trouble for me was everything chemistry related because I never came in contact with that subject before in my life. 16:52:32 right... it seems like there are a lot of books to teach programming and such, but i can't imagine learning a lot of the genetics stuff i learned without someone guiding me 16:53:01 Well just going for my Bachelor (I believe that is undergrad) at the moment. But I am aiming for a Master and postdoc in the end. 16:53:10 <_dan> i think its harder to teach what is 'important to know' about biology 16:53:12 ah 16:53:38 <_dan> its easy enough to learn from books, but its mostly about getting up to speed if you've come via the IT route 16:53:45 general geekery got me into bioinformatics as well... during HS i was big-time into computers, then i went through my car phase, and now i'm more interseted in software 16:53:49 Oh if you ever need some literature on genetics we have quite a good list.... 16:54:20 <_dan> I would love to assemble a history of genetics, via classic papers for this reason 16:54:31 <_dan> that leads up to a computational finale 16:55:12 i can't wait til we have the computational power to make phylogenetic trees that are 100% accurate 16:55:36 Well I am at a point that I can't imagine pursuing anything else then bio-informatics. It was love at first sight hehe. 16:55:50 <_dan> think you need the statisticians to sort out that issue first 16:55:52 But then again I am a general geek :P 16:56:06 <_dan> in my experiences the phylogentics crowd cant agree on anthing with each other ;) 16:57:05 same berry_nl, i went into genetics expecting to be doing pure lab work, i never considered the use of databases, programming, etc in the field 16:58:24 There is one thing I do wonder. I don't know where you are from. But in my country (The Netherlands that is) Its a very rare field to work in. And thus there are only limited vacancies. How is this in your homelands? 16:59:23 i'm from south carolina, in the southeast of america... 16:59:35 <_dan> ok well I'm in the UK.. there is a large number of courses here, but I see posts advertised. I think there are more students than posts, but not many of the students in each year I would employ. The last 3 posts we advertised we had difficulty in filling 17:00:06 from what i've been told, there is a strong demand, but there is no one really interestedin the field. As my boss said "people are interested in either genetics OR computers, but rarely both" 17:00:25 Hmm _dan what area of the UK (my wife is British, so i wonder ;) 17:00:33 there are several schools here with bioinformatics PhD programs, but nothing near the amount of genetics grad programs 17:00:39 <_dan> I'm at Newcastle University 17:01:29 <_dan> but not from there originally :) 17:01:44 svensko, we have the same problem with attracting new students (I'm in the studendboard). They are either interested in programming or biology. But hardly ever in both 17:01:54 <_dan> whereabouts in the Netherlands are you? My father lived in the Netherlands for years 17:02:16 i'm jealous of you euros, i had a toxicology professor frmo the netherlands and from what he said it was a beautiful place 17:02:18 The Hague, studying in Leiden. 17:03:11 Oh I don't know svensko the grass always seems greener in your neighbours lawn. I have the same feeling about other countries ;) 17:03:15 <_dan> ah my dad used to live in Heerlen 17:03:32 Oh yeah I know that. I have a cousin from that area. 17:03:32 *** mercutio22 has quit () 17:04:07 So you speak a bit of Dutch too _dan? 17:04:32 <_dan> I'm afraid not, and neither does he, he somewhat failed to go native ;) 17:04:39 Oh sorry. It does not imply he is Dutch himself, my mistake 17:04:46 <_dan> no, he's not 17:04:53 well, in america, i would say half the population doesn't think evolution is occuring, and would rather remain ignorant than learn about what can be done with genetics 17:05:00 actually, i'd say 75% 17:05:40 <_dan> svensko: its a popular pastime amongst my friends to take on a 'pet YEC' and harrangue them with scientific support for evolution :) 17:06:21 I think that is because the us is very aimed at the theory of god and very religiously aimed in my view. (I think it is the other way round in the NL, 75% believes in evolution hehe) 17:06:38 <_dan> i was more distubed by the whole lack of federal funding for stem cell work in the USA 17:06:43 <_dan> that was a very disappointing decision 17:06:48 yep, another reason i'm jealous of euros 17:07:17 i remember seeing a church sign that said "Faith's number one enemy is reason" 17:07:22 i facepalmed 17:07:26 * _dan rofls 17:07:29 lol 17:07:42 That is just plain scary 17:08:02 And then they call muslims the fanatics hehe 17:08:03 it's something i deal with everyday 17:08:07 <_dan> right laptop is running out of magic juice - laters :) 17:08:14 later _dan ;) 17:08:18 later 17:08:40 whenever i tell someone that i'm interested in genetics their eyes widen big time 17:08:52 then ask if i'm going to create a monkey-octopus hybrid or something 17:10:27 speaking of which - there's a section in a local paper called "Rants and Raves" where you can anonymously send letters - someone sent a letter saying that evolution was false because she "didn't see monkeys turning into humans all around her" 17:10:36 Yeah well most of the Dutch are very open towards science. But it does not imply they don't give me the same cloudy look when i try to explain what i am studying heh 17:11:00 No you can't be serious :S 17:11:19 dead serious, i was thinking about writing a letter in response but it would have been a waste of time 17:12:07 bbl 17:12:16 I feel sorry for you. On the other hand, I was shocked when i heard Bush was re-elected. And then my second reaction was, well its their own fault their education sucks then :P 18:02:26 *** highvoltz has quit () 18:09:09 svensko: Due to the noise in sequence data, we'll never have perfectly accurate phylogenetic trees. 18:10:13 The big killers are mutations that wipe out information. 18:10:24 noise in sequence data? in other words our inability to detect without a doubt the sequences? 18:10:33 oh i see what you mean 18:10:34 Like deletions and reverse mutations (e.g. GUA -> GUG -> GUA). 18:10:53 right 18:11:18 We do our best, though. 18:47:43 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 19:40:23 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 20:08:48 *** berry_nl has quit (Read error: 110 (Connection timed out)) 20:13:26 *** kanzure has quit (Remote closed the connection) 20:23:22 * _dan wonders a) if anyone is up and b) if anyone is on twitter or friendfeed 20:23:56 <_dan> as I have just started using both services in the last week and always interested in similar minded users :) 21:37:58 *** Splicer (n=p@h242n2c1o261.bredband.skanova.com) has joined #bioinformatics 21:55:57 *** synthase has quit (Read error: 110 (Connection timed out)) 21:56:07 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 22:25:44 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 22:55:46 *** xtmdster has parted #bioinformatics ()