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05:42:56 <pingou_work> hi
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06:22:10 <_dan> morning
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13:44:37 <kanzure> http://en.wikipedia.org/wiki/Wikiprofessional
13:49:40 <pingou> small question
13:50:07 <pingou> do we have a software that can display the sequencing curves from .scf file ?
13:54:14 <_dan> abiview
13:54:17 <_dan> in emboss
13:54:22 <_dan> for *nix
13:54:31 <_dan> 4peaks for os x
13:56:03 <pingou> thanks :)
13:56:10 <_dan> actually i hope abi view reads scfs 
13:59:07 <_dan> http://feeds.feedburner.com/~r/mndoci/~3/299901398/
13:59:17 <_dan> sure that's been referenced here before - wikiproteins
14:09:40 <pingou> .scf not an ABI file
14:10:28 <pingou> http://www.fileinfo.net/extension/scf should work
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16:33:39 * pingou is packaging EMBOSS for fedora :)
16:46:29 <pingou> hm... they give .jar... not good :/
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17:32:07 <_dan> Ryan Golhar (Informatics Institute, University of Medicine and Dentistry of New Jersey) has built RPMs for EMBOSS 5.0.0 and related applications. They are available from http://informatics.umdnj.edu/BioRPMs or from the EMBOSS ftp site:
17:32:11 <_dan> * ftp://emboss.open-bio.org/pub/EMBOSS/contrib/ 
17:32:14 <_dan> don't reinvent the wheel ;)
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17:39:15 <CowbertDH> not invented here tho
17:39:47 <CowbertDH> is there an srpm? maybe pingou can use that
17:40:20 <_dan> yeah the srpm is on that site
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17:48:30 <pingou> _dan, I tried to register but something went wrong ^^
17:48:41 <pingou> and I anyway suspect him to have done the same than me
17:48:48 <CowbertDH> the system is down the system is down
17:48:50 <pingou> the source provides the jar
17:50:57 <pingou> and there are only the i386 files :)
17:51:11 <CowbertDH> so you need to write a wrapper for the jar file? 
17:51:31 <pingou> depends if there are the files from which the jar have been produced
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17:52:34 <pingou> I like this website..
17:52:40 <CowbertDH> well I thought you could load it using <applet> etc
17:52:46 * pingou dreams about the biorepo for RPMs
17:56:43 <pingou> there are a couple of thing I do not get...
17:57:37 <pingou> but I might get the jemboss from that :)
17:59:06 <pingou> (but anyway I got EMBOSS working here)
18:14:41 * _dan makes coffee, watches football and thinks about bioinformatics a bit
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18:24:12 * pingou tides his room, does some ironing, looking tv...
18:39:19 <pingou> sudo irone
18:39:19 <pingou> Sorry, try again.
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19:54:09 <svensk1> Does anyone here know how good the bioinformatics programs are at UGA and UNC?
19:54:28 <Relentless|Away> unno
19:54:31 <Relentless|Away> *dunno
19:55:52 <wonklab> UGA has started a big push to improve their computational biology.
19:56:20 <wonklab> UNC's was still really small when I applied back in 2003.
19:56:36 <wonklab> It was an interdepartmental program, and you had to apply separately to a home department.
19:56:54 <wonklab> But they had a few people who seemed pretty cool.
19:56:59 <svensk1> do you know what kind of GPA demands they have?
19:57:13 <wonklab> Beats me.
19:57:27 <svensk1> looks like i'll only be able to graduate with a 3.2 :(
19:57:48 <wonklab> I think most schools can be convinced to ignore GPAs if you have good letters of recommendation.
19:58:21 <svensk1> good news then :D
19:59:12 <svensk1> the lab i'm currently working in said they would provide me with good letters of recommendation when i need them
19:59:20 <svensk1> still need to take the GRE as well
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20:18:53 <svensko> it seems like a lot of the graduate programs are interdisplinary
20:19:08 <svensko> GTs is part of the Biology college apparently
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20:21:37 <svensko> gotgenes: what in the world are you doing? 
20:23:02 <gotgenes> svensko: A few things: losing my DSL connection, reconnecting and getting booted from #python and other +e channels because my client reconnects as gotgenes_ (not registered), and finally, trying to link gotegenes_ to my gotgenes account, which I just did.
20:23:24 <gotgenes> Sorry.
20:23:59 <svensko> no apology needed, just making sure you weren't having a seizure or something :P
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20:28:36 * gotgenes_ sighs
20:28:39 <gotgenes_> Case in point
20:28:46 <gotgenes_> Never go with Verizon DSL.
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20:29:51 <svensko> i've always thought Verizon was one of the better ISPs? 
20:29:57 <svensko> I've heard nothing but pure hatred for Comcast
20:30:08 <svensko> but of course, that was all from pirates who are having their BT speeds capped
20:30:11 <gotgenes_> Verizon's killing me here.
20:30:27 <gotgenes_> Capped BT is better than none at all.
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20:31:27 <svensko> meh, i'm against piracy personally, it amazes me how whiney people can be when they're getting thousands of dollars of free music/software
20:31:36 <svensko> although i completely understand the legit uses of BT
20:40:15 <wonklab> Bioinformatics and computational biology programs are set up so differently from school to school.
20:40:23 <CowbertDH> yes
20:40:23 <wonklab> It's pretty annoying.
20:40:33 <gotgenes> Agreed.
20:40:33 <CowbertDH> mostly because of the entrenchement
20:41:06 <wonklab> I think we have three separate communities for bioinformatics here at UIUC.
20:41:19 <CowbertDH> does that count the medschool people?
20:41:22 <gotgenes> wonklab: Three?
20:41:46 <wonklab> One is in CS, one is with the plant and animal sciences crowd, and I'm in the biophysics one, which is interdisciplinary but heavily skewed towards physics and chemistry.
20:42:09 <CowbertDH> well there are offshoots of biomedical engineering as well
20:42:54 <wonklab> yeah
20:42:59 <CowbertDH> (I'm saying this because CS is often associated with engineering dept)
20:43:18 <CowbertDH> the plant/animal people are usually associated with the agriculture program
20:43:20 <wonklab> Yep, our CS is in engineering.
20:43:48 <CowbertDH> then the general one is usually coming out of the general science departments
20:43:55 <CowbertDH> plus usually there is a med school one as well
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21:19:24 <svensko> goodness O_O
21:20:38 <CowbertDH> sometimes the medschool can be pretty unwieldy too
21:20:58 <CowbertDH> since for exmaple, the drug trial people don't necessarily care about microarrays etc.
21:21:15 <CowbertDH> money
21:21:22 <CowbertDH> 's got a lot to do with it as well
21:21:46 <CowbertDH> it's easier to write a grant to say "I want to start a new bioinformatics thing" than try to add more funding to an existing org
21:22:37 <svensko> CowbertDH: what would you suggest i learn before going to grad school as far as programming languages?
21:22:47 <CowbertDH> what are you going to grad school for?
21:23:34 <svensko> i'm not entirely sure yet, i just finished a Bioinformatics course but i had a terrible teacher
21:23:38 <svensko> i'm leaning towards genome analysis though
21:24:43 <CowbertDH> so yo uare into the science ?
21:24:59 <svensko> i'm currently earning a BS in genetics at clemson university
21:25:06 <CowbertDH> cool
21:25:23 <svensko> i'm going to be a senior next year, population genetics sparked my interest in bioinformatics, the whole statisical side to it really intrigued me
21:25:25 <CowbertDH> are you actually interested in programming or do you think it might help you in some way?
21:25:36 <svensko> i've been teaching myself SQL and i'm going to teach myself perl next
21:25:40 <svensko> i'm interested in actually programming
21:27:16 <svensko> i'm hoping to get a job programming then eventually starting a business with the specific purpose of designing/coding FOSS bioinformatics programs
21:28:08 <CowbertDH> good luck with that :)
21:28:58 <svensko> thanks, i'll probably need it X(
21:29:20 <svensko> i've been reading the articles in Bio-IT World and it's pretty obvious that a alot of the software developing businesses out there are not screwing around
21:29:25 <CowbertDH> I would start with something more rigorous
21:29:34 <CowbertDH> bioITworld lol
21:29:50 <svensko> what would you suggest?
21:30:02 <CowbertDH> python, ruby maybe
21:30:08 <CowbertDH> java
21:30:42 <svensko> i've gotten 1000 different opinions on what to learn and it's nearly split between perl/python
21:30:58 <CowbertDH> perl leads to the dark side
21:31:13 <svensko> from what i've gathered perl is harder to learn and python instilled good habits in programming early
21:31:43 <CowbertDH> perl isn't hard to learn
21:31:51 <CowbertDH> it can teach bad habits early, which is bad
21:31:57 <CowbertDH> it can breed laziness
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21:32:09 <svensko> SQL hasn't been too bad, i've trying to come up with small ideas on how to apply it
21:32:23 <svensko> in the sense that i want something to show to grad schools to say "hey, look at what i can do!"
21:32:46 <CowbertDH> SQL is an exercise in discrete math
21:32:51 <CowbertDH> it's not turing complete
21:33:11 <CowbertDH> unless you're really using PL/SQL or something
21:33:20 <svensko> turing?
21:33:31 <svensko> yes, i was planning on using perl to script SQL
21:34:27 <CowbertDH> there is no way to loop in SQL
21:34:36 <CowbertDH> basically speaking
21:34:50 <CowbertDH> (there is neither looping nor recursion)
21:35:12 <CowbertDH> "Turing-completeness in SQL is implemented through proprietary extensions"
21:35:28 <svensko> ah
21:35:36 <CowbertDH> PL/SQL is such an extension I believe
21:36:35 <svensko> is it possible to have python intereact with SQL?
21:36:48 <CowbertDH> depends on what you mean
21:37:14 <CowbertDH> and what SQL platform etc
21:37:47 <svensko> yeah, so far all my experience is with pgsql
21:38:34 <CowbertDH> so you have been writing PL/pgSQL stored procedures?
21:38:55 <svensko> an eBay DBA said he may be able to get me an internship with eBay if I learn SQL :)
21:39:01 <svensko> writing? no, teaching myself pgSQL, yes
21:39:11 <CowbertDH> how do you teach yourself without writing?
21:39:40 <CowbertDH> programming is inherently a creative process
21:39:42 <svensko> i have used it for my bioinformatics course
21:40:28 <svensko> created a table with genes and their corresponding TFs then created views to select for particular TFs
21:40:39 <CowbertDH> there is SQL, used for queries and there is the language extension component PL/pgSQL which allows you do things like capture variables and do branching
21:40:40 <svensko> the thing is that i don't have any experience with perl or python
21:41:18 <svensko> right now i can create queries all day, but i have no way to script them 
21:41:31 <CowbertDH> right, so you might want to look at PL/pgSQL
21:41:36 <CowbertDH> (it's discussed in the manual)
21:42:03 <svensko> will do
21:42:08 <CowbertDH> that will allow you to create stored procedures that can be executed
21:42:56 <svensko> how is that different from creating functions?
21:53:42 <CowbertDH> not much different
21:53:59 <CowbertDH> except that parameter passing is much simplified
21:54:51 <svensko> functions are actually the next chapter i'm covering, so after that i went look into the pl/sql portion
21:55:21 <CowbertDH> yeah you could think of stored procedures as functions on steroids
21:55:35 <svensko> ah
21:55:53 <CowbertDH> like I said, it allows additional logic
21:56:04 <CowbertDH> (i.e. flow control)
22:02:04 <svensko> i see
22:02:07 <svensko> so much to learn
22:02:18 <svensko> i'm sorta afraid that i'll get into a graduate program and not know enough to stay afloat
22:02:33 <CowbertDH> bioinformatics graudate program?
22:02:43 <svensko> yes
22:03:31 <CowbertDH> is programming considered a prerequisite?
22:03:38 <svensko> no idea
22:03:49 <CowbertDH> well I think it's important to find out, don't you think :)
22:04:37 <svensko> probably :P
22:05:08 <CowbertDH> all programming comes down to is understanding how write something that handles some input and generates some output
22:07:16 <svensko> The Prerequisites needed include Principles of Biology(an introductory course), Computer Programming(at least one semester equivalent to Georgia Tech's CS 1301), Organic Chemistry(an introductory course), Calculus(one year, equivelent to MATH 1501, 1502), and Physics(one year.) GPAs have ranged betwe en 3.4 - 4.0 for this program but no minimium has been established. The general GRE should be taken with scores at least 1800(Fall
22:08:48 <CowbertDH> ok
22:09:36 <svensko> if it means i have to take a year off to take computer courses then i'm more than happy to do that
22:10:09 <CowbertDH> well so typically the first semester is teaching C++ or Java
22:10:43 <CowbertDH> doing some numerical stuff (write a program to generate prime numbers, write a blackjack program, etc)
22:11:16 <svensko> the first year of bioinformatics?
22:11:33 <svensko> err of a grad program?
22:12:16 <CowbertDH> first semster computer programming
22:12:27 <svensko> ah
22:13:05 <svensko> i also considered getting another undergrad degree in CS but people were telling me that i could teach myself the stuff i needed to know instead of spending another 2-3 years earning another undergrad
22:13:31 <CowbertDH> that's good advice, unless you really really wanted to learn everything :)
22:14:22 <svensko> i would rather have to learn programming on my own than learn what i've learned in genetics by myself
22:14:45 <CowbertDH> a rigorous CS program typically results in an expectation that the grad will be able to given a cpu, instruction set and write everything from scratch, literally
22:14:56 <svensko> yikes!
22:15:33 <svensko> but at the same time i'd rather learn that stuff and feel more comfortable in a grad program than struggle trying to catch up to the level that everyone else is already at
22:15:46 <CowbertDH> so you cover computing theory, digital logic, assembly, compilers, OS, networking, discrete math, databases
22:16:14 <CowbertDH> You should talk to a graduate advisor then
22:16:53 <svensko> i've been told that i can learn the basics of perl/python/sql during my senior year before i graduate
22:17:44 <CowbertDH> yes 
22:18:06 <CowbertDH> I still feel that the language itself isn't the important part
22:18:19 <svensko> what would you say is then?
22:18:37 <CowbertDH> most language differences are in their syntax
22:20:16 <svensko> makes sense
22:21:12 <CowbertDH> hold on
22:21:28 <svensko> alright
22:23:50 <CowbertDH> I think it is important, if you are heading towards programming, to really learn about programming
22:24:00 <CowbertDH> not necessarily a specific language
22:24:27 <CowbertDH> the language is there to help you practice the craft
22:25:33 <CowbertDH> the important thing is to think of the logic. the program flow.
22:26:32 <svensko> do you know of any good books on the topic?
22:26:54 <CowbertDH> well the bible is Knuth's "The Art of Computer Programming"
22:27:29 <CowbertDH> but good luck getting through that series :)
22:27:53 <CowbertDH> when I made the comparison to the bible, I was being sort of literal about it. It is some really really heady stuff
22:28:34 <svensko> so you're saying that learning the languages will be the easy part?
22:29:09 <CowbertDH> more or less, once you get the terminology and the though processes down
22:30:05 <CowbertDH> every manual on a given language has the basic "how do I use variables" "how do I do flow control" "how do I write functions or subroutines" "what builtin functions does this language give me and how do I use them"
22:30:31 <svensko> http://ecx.images-amazon.com/images/I/41on7GLAU1L._SL500_BO2,204,203,200_PIlitb-dp-500-arrow,TopRight,45,-64_OU01_AA240_SH20_.jpg
22:30:33 <svensko> you weren't kidding!
22:31:04 <CowbertDH> I mean that's really advanced stuff
22:31:08 <CowbertDH> what I was getting at though
22:31:43 <CowbertDH> was to get familiar with the way variables work. What control structures do in what contexts, how functions work, etc.
22:32:09 <CowbertDH> it doesn't really matter what language you pick to learn these concepts, except that some languages are better than others in making you consistent
22:35:00 <svensko> yeah i see what you're saying
22:52:11 <CowbertDH> still a big fan of pascal
22:52:20 <CowbertDH> basic even
22:52:46 <CowbertDH> although I think pascal is a bit more featureful so you don't run out room-to-grow as quickly with it
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23:47:07 <CowbertDH> lol just made up this term: shotgun coding
23:47:31 <CowbertDH> it's where you write bits of random code and put it into production without documenting it or putting into source control or anything
23:49:03 <svensko> Everyone knows that's how Windows Vista was made
23:49:32 <CowbertDH> lol