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11:15:03 <sparta> i have done my BTECH in electrical engineering but want to do higher studies in Bioinfo. Want is the best way to get started?I am learning Perl.How much knowledge in Biology/Chemistry is required?
11:15:36 <orbitz> Depends on what side, a fair amount to be any good
11:15:47 <orbitz> hopefully Perl won't bethe language of bioinf for too much longer
11:16:40 <sparta> oh really , what other languages would come handy?
11:16:54 <orbitz> I dunno, but anything sucks less ass than perl
11:17:24 <sparta> okay
11:17:52 <faceface> sparta: learn Perl
11:18:00 <faceface> its a great language
11:18:10 <orbitz> don't listen to him
11:18:13 <orbitz> it's a trap!
11:18:19 <faceface> lol
11:18:20 <sparta> yeah its seems good though I am just a novice :-)
11:18:31 <orbitz> it's horrible for large projects
11:18:33 <faceface> sparta: for a beginner, Java is a good place to start
11:18:39 * faceface agrees
11:18:57 <pingou_work> faceface, just go for any C :D
11:19:13 <faceface> C? what is this C?
11:19:17 <pingou_work> no idea :D
11:19:24 <faceface> P rules!
11:19:28 <pingou_work> faceface, it was there before R :D
11:19:32 <faceface> (Perl that is)
11:19:37 <pingou_work> R rules P :D
11:19:42 <sparta> thats a beautiful language i feel--- C!
11:19:47 <faceface> but S was before R
11:20:02 <pingou_work> faceface, the exception :)
11:20:05 <faceface> sparta: no... typical non-perlish mistake ;-)
11:20:10 <pingou_work> S was closed source
11:20:19 <faceface> C is not beautifull - its a concrete block compared to a poem
11:20:25 <orbitz> use Ocaml, we get super fast code and it scales to large projects, and it gives you some solid compile tiemgurantees:)
11:20:29 <faceface> perl is a beautiful butterfly
11:20:34 <pingou_work> I prefer python to perl even if I know more perl than python
11:20:49 * orbitz has been hackign perl again at my new job, it's painful
11:20:51 <faceface> ppppp pytihon?
11:20:51 <pingou_work> Perl can be crapped but any code can be crapped ! :)
11:20:58 <sparta> there are lot of options when it comes to languages :-)
11:21:03 <orbitz> i finally rewrote everything in python in a day because perl was just too difficult to get workign properly
11:21:14 <faceface> orbitz: ah ha!
11:21:18 <pingou_work> ^^
11:21:30 <faceface> I'll prove perl is the best to you!
11:21:34 <faceface> the perl bible says so
11:21:36 <orbitz> the down side is, last i used biopython it was compelte garbage
11:21:40 <orbitz> and bioperl still ruled
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11:21:47 * orbitz needs to start biocaml
11:21:54 <orbitz> although, biohaskell already exists, mayb ei'll use that!
11:22:00 <pingou_work> biopython is not as strong as bioperl
11:22:07 <pingou_work> perl is still much more used in bioinfo
11:22:16 <orbitz> dam scientists pretending they are programmers
11:22:22 <pingou_work> bioruby exist also...
11:22:28 <pingou_work> orbitz, you get the point ;)
11:22:28 <orbitz> oh sweet baby jebus
11:22:32 <faceface> sparta: to answer your real question, and to ignore the flames that I set - your level of bio will depend on your area of interest.
11:22:38 <sparta> yeah nay book on bioinfo has perl..i have not seen python
11:22:54 <sparta> okay
11:23:00 <pingou_work> sparta, you have bioperl biopython biojava bioruby... pick your choice ;)
11:23:11 <orbitz> it's probably only like 5 to 10 years before the current batch of bioinformaticians realize that their first gen software cannot keep up with the requireemtns of the applications
11:23:15 <faceface> sparta: understanding protein sequence will be a good place to start
11:23:31 <sparta> hmm..okay
11:23:34 <orbitz> any of you see http://fold.it?
11:23:41 <faceface> orbitz: that is why I designed 'auto perl' 
11:23:48 <faceface> orbitz: :D
11:23:55 <orbitz> haah what is auto perl?
11:23:57 <orbitz> liek autolisp?
11:23:58 <faceface> sparta: protein sequence / DNA sequence
11:24:09 <faceface> its a way to autogenerate code... that I just inventedx
11:24:25 <faceface> you evolve your perl code... somehow
11:24:25 <orbitz> oh hot
11:24:29 <orbitz> haha
11:24:31 <faceface> ;-)
11:24:42 <orbitz> i actuallythink ocaml would not be half bad for bioinf
11:24:43 <faceface> still... you can autogenerate Java from UML in RAtional Rose
11:24:49 <orbitz> native binaries are blazingly fast
11:24:50 <toru> I agree!
11:24:59 <orbitz> and it still has teh expresiveness of higher languages
11:25:01 <toru> don't know to what, but I agree
11:25:02 <orbitz> you really get the best of both worlds
11:25:18 <faceface> I'll have a look
11:25:26 <faceface> at the moment I am fully R
11:25:45 <faceface> C is to C++ as R is to S?
11:25:54 <orbitz> no
11:25:56 <orbitz> S came before R
11:26:03 <orbitz> and only becuse S is closed source
11:26:04 <faceface> I'll have to invent C+=2
11:26:05 <pingou_work> yes it is the other way around
11:26:18 <faceface> but is the name R chose because it augments S?
11:26:25 <orbitz> actually, maybe J would be a good bioinf language
11:26:25 <pingou_work> and actually R is based on S and Scheme
11:26:28 <faceface> PQRS?
11:26:30 <orbitz> it is made for fast matrix work
11:26:49 <pingou_work> never heard about J ^^
11:26:50 <faceface> Java is more or less teh 'scalable standard'
11:26:55 <orbitz> J is pretty cool
11:27:00 <pingou_work> J==Java ?
11:27:02 <orbitz> no
11:27:06 <pingou_work> ok :)
11:27:13 <orbitz> http://jsoftware.com/
11:27:19 <orbitz> Java isn't so scalable though
11:27:24 <toru> faceface: c++ is object-oriented
11:27:27 <faceface> really?
11:27:42 <pingou_work> C also no ?
11:27:42 <faceface> really @orbits
11:27:43 <orbitz> even Sun is raelizing Java's days are numbered and trying to turn the JVM into mor eof a language target than a java platform
11:27:50 <toru> C is not
11:27:52 <faceface> toru: objectes are good
11:27:54 <orbitz> C++ is multiparadigm
11:28:03 <orbitz> it allows you to express some OOP concepts
11:28:06 <orbitz> but is nto limited to them
11:28:06 <toru> I agree, biologist are bad programmers (i am a biologist)
11:28:06 <faceface> R is object based (old school)
11:28:19 <orbitz> faceface: functionsa re better
11:28:29 <toru> any pythonist here?
11:28:30 <pingou_work> faceface, yes but the object is more than transparent :)
11:28:39 <orbitz> toru: i prefer it over many other chocies
11:28:48 <faceface> but the object is ... cool
11:28:59 <orbitz> objects aren't all they are made out to be
11:29:05 <faceface> objects are excaping software
11:29:17 <orbitz> the primary reason people like objects, inheritence, is actually generally poro design
11:29:21 <faceface> orbitz: you and yur function based design paradigms
11:29:42 * faceface is reading a book on OO project design methodologies
11:30:00 <toru> orbitz: yes, but the problem is not in which programmimg paradigm is used. Is how people program: many biologist don't even know concepts like unit testing, etc
11:30:16 <orbitz> toru: yeah, that is evident from their perl loveaffair:)
11:30:30 <faceface> toru: have you seen 'where is the real bottleneck in scientific computing"?
11:30:35 <orbitz> toru: is it getting beter though? are there enough programmer bioinf people to pick up the slack?
11:30:37 <toru> what is it?
11:31:01 <toru> what is it 'where is the real bottleneck in scientific computing"? 
11:31:02 <faceface> toru: a computing coursed based on the complaint that  you voice
11:31:28 <toru> ahah
11:31:28 <faceface> the bottleneck is bad code
11:31:50 <faceface> http://www.americanscientist.org/template/AssetDetail/assetid/48548
11:31:54 <faceface> its all open.
11:32:12 <toru> thank you, I didn't know of it
11:32:47 <faceface> "Six years and one dot-com boom later, I received funding from the Python Software Foundation to bring that course up to date and to make it available on the Web under an open license so that anyone who wants to use it is free to do so."
11:33:24 <toru> eheh I use vim
11:33:31 <faceface> SWINE!
11:33:36 <pingou_work> kate && vim
11:33:44 <pingou_work> new flame ? :D
11:33:46 <faceface> oh.. wait... its in the article...
11:33:48 <faceface> ;-)
11:34:06 * pingou_work sent it to the printer...
11:34:14 <toru> ahah wasn't it vim vs emacs?
11:34:24 <toru> :
11:34:26 <toru> :)
11:34:26 * faceface pretents to ignore toru
11:34:32 <pingou_work> torbjorn, it is too limited then :D
11:34:43 <faceface> well.. take care... 
11:34:46 <pingou_work> you have to make it broader !
11:35:01 <pingou_work> and anyway every one knows that emacs sucks...
11:35:02 <pingou_work> :D
11:35:16 * pingou_work runs away...
11:35:16 <sparta> what about organic chemistry..we have to no that a lot too?
11:35:26 <sparta> know'
11:35:33 <pingou_work> sparta, it depends what you are working on
11:36:10 <toru> I worked in an institute where people used to use emacs without activating anti-aliased fonts
11:36:24 <toru> faceface: :)
11:36:33 <_dan> anything that has support for differnet fonts is clearly an abberation ;)
11:36:45 <pingou_work> lol
11:36:59 *** pingou_work changed the topic to: " Welcome to #bioinformatics! | http://BioDatabase.Org (biological databases) | http://Bioinformatist.Org (bioinformatics software) | http://Bioinformatics.Org (open-access institute) | Don't ask to ask, just ask! Don't have a question? Tell us something new! | We are slow moving pathogens... so hang around if you want to be infected...|<_dan> anything that has support for differnet fonts is clearly an abberation ;)"
11:37:05 <orbitz> emacs all the way!
11:37:08 <pingou_work> quote of the day ^^
11:37:25 <_dan> :)
11:37:42 <orbitz> http://i.thefairest.info/funniest_thumbs/a05Is7.jpeg
11:38:06 <pingou_work> lol
11:38:27 <torbjorn> pingou_work: I have no limits thank you very much
11:38:48 <pingou_work> torbjorn, you finally arrived here !! :)
11:39:08 <orbitz> is it going to jinx it if i point out this is the most convo here in years?
11:39:30 <orbitz> yep...
11:39:47 <pingou_work> torbjorn, I configured kate to give me three space identation ;)
11:40:07 <toru> but can I ask you a thing? I am looking for a phd position. Do you know any place where I can learn bioinformatics and programming well? It is very difficult to find good place to learn bioinformatics
11:40:25 <pingou_work> toru, if you find the answer let me know :)
11:40:38 <pingou_work> I am more or less looking at the lab in UK
11:40:41 <faceface> there it is at last! http://www.swc.scipy.org/
11:40:45 <toru> :)
11:40:50 <pingou_work> couple of them seems to have nice phD subject over there
11:40:51 <orbitz> http://i.thefairest.info/funniest_thumbs/iluE1R.jpeg
11:41:16 <orbitz> toru: can you program?
11:41:30 <toru> orbitz: yes, mostly python and perl
11:42:39 <toru> well, http://xkcd.com/353/
11:42:42 <faceface> torbjorn: pingou_work apply to the LMB in Cambridge
11:43:09 <faceface> toru, most biochemists would be hard pushed to know much organic chemistry
11:43:21 <pingou_work> faceface, you know someone to who you could recommend me ?
11:43:34 <faceface> if you want to do hard core protein structure work its usefull.. but most people just fein knowledge
11:43:39 <orbitz> toru: if you have time i would sugges laerning a functional language, even if you don' have any real application for it, it is very beneficial to being a beter programmer.  that's not reallyw hat you asked of course, just throwing it otu there
11:44:17 <toru> orbitz: no thank you for the discussion
11:44:23 <toru> do you mean C or R?
11:44:29 <faceface> pingou_work: er... I suppose so ... Cyrus Chothia / Sara Teichmann / Madan Mohan ... but who are you? ;-)
11:44:41 <orbitz> Ocaml/Erlang/Haskell
11:44:51 <pingou_work> faceface, it is written in your kiwi ;)
11:44:51 <orbitz> Haskell is probably the major extreme
11:44:53 <faceface> (I don't really know those lot, but they would recognise an email from me I suspect).
11:45:01 <toru> oi
11:45:10 <toru> are they difficult to learn? :)
11:45:24 <orbitz> haskell i would say yes.  Erlang no, and Ocaml no
11:45:31 <orbitz> Erlang is probably the easiest of the bunch
11:45:37 <faceface> pingou_work: ooohhhhh your THAT pingou ;-)
11:45:48 <_dan> who  is after phds??
11:45:49 <_dan> http://www.plankton.dircon.co.uk/Cardiff_Bioinf_PhD_advert.pdf
11:45:50 <pingou_work> faceface, you did not know ?? ^^
11:45:55 <orbitz> but the requireemnts of beign functional put some restrictiosn on how you can solve problems
11:46:05 <pingou_work> _dan, I am :)
11:46:06 <toru> _dan: I am thanks :)
11:46:16 <faceface> sure thing p... send me your 'reference' and I'll squiggle it around and send it on (i.e. write your own reference as you see fit)
11:46:29 <toru> if any of you would like to come in Italy, you can just ask :)
11:46:48 <orbitz> do biotech companie ever hire good programmers who are working on their bioinf degrees?
11:47:03 <toru> orbitz: I think dr. Scheme is also functional?
11:47:26 <toru> ehm Scheme, not dr. Scheme :)
11:47:44 <orbitz> toru: Dr Scheme is an impleemtnation (meant for learning).  it supports functional programming to some degree but most people tend to write scheme in a very imperative style
11:47:56 <orbitz> one which is not possible in something liek haskell or ocaml
11:48:12 <toru> ok thanks
11:48:31 <orbitz> for instance, in Ocaml, Haskell, Erlang, obejcts are immutable
11:48:49 <torbjorn> cool
11:48:55 <orbitz> recursion is the only way to usefully loop
11:49:14 <orbitz> Ocaml has some weak language constructs for a for loop and while loop, but they are gnerally not used
11:49:52 <faceface> this is the page of the course in the article posted ... http://www.swc.scipy.org/
11:49:59 <orbitz> faceface: cool ahnks
11:52:12 <orbitz> i'm not any good at it, but i <3 my haskell even though it kilsl braincells
11:52:14 <faceface> _dan access codes?
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11:52:48 <_dan> ?
11:53:02 * _dan worries he was typing passwords into irc
11:53:07 <faceface> the PDF you posted ;-)
11:54:14 <_dan> http://www.plankton.dircon.co.uk/Cardiff_Bioinf_PhD_advert.pdf
11:54:20 <_dan> no access codes required :p
11:54:32 <toru> it is so difficult to come to do research in the UK... most of the time you have to be already resident :(
11:54:50 <_dan> toru: yeah its a problem
11:55:20 <_dan> we have a russian national we'd like to take on who is married to a UK national and resident here for 3 years but its still hard
11:55:38 <_dan> very annoying
11:55:47 <toru> yeah :(
11:55:55 <toru> I'm not even resident :(
11:57:17 <toru> ok, I have to go. Ensembl APIs are calling me :)
12:00:00 <faceface> "Discovering the Access Codes to Enable Repair"
12:00:16 * nsh blinks
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12:20:24 <sparta> what are the different career paths available in bioinformatics?
12:22:13 <pingou_work> _dan, is it also so complicated within the EU ?
12:22:27 <pingou_work> I mean when you come from a country within the EU
12:23:18 <_dan> pingou_work: i think its dependent on the source of funding more..
12:23:26 <_dan> i mean we have american and thai phd students
12:23:50 <_dan> i think that the costs escalate for the PI 
12:23:56 <_dan> as the students are 'external'
12:24:00 <_dan> this puts people off
12:24:14 <pingou_work> hm
12:24:31 <pingou_work> is it like in France that you have to find the funding by yourself ? 
12:24:46 <_dan> well the funding will normally be part of a larger grant
12:24:54 <pingou_work> or is it like in the NL that when they offers a phD position the funding is already arranged
12:37:53 <faceface> sparta: developer vs. researcher
12:42:34 <toru> sparta: http://www.bioinformaticszen.com/2008/01/world-of-bioinformatics-quest/
12:43:35 <toru> pingou_work: yes, it is about funding. Most of the grants are only for people already residents, but I think it is the same for many countries
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