01:02:08 *** Splicer (n=p@h116n2c1o261.bredband.skanova.com) has joined #bioinformatics 01:11:45 *** CrimsonScythe has quit ("Leaving...") 02:10:50 *** Splicer has quit () 02:45:20 *** svensko has quit (Read error: 104 (Connection reset by peer)) 02:50:08 *** spal (i=ca36b033@gateway/web/ajax/mibbit.com/x-d4da08fe82da8d2f) has joined #bioinformatics 02:50:41 *** sparta (i=ca36b00b@gateway/web/ajax/mibbit.com/x-8f5c5d5ccf33e4dd) has joined #bioinformatics 02:56:13 *** spal has parted #bioinformatics () 03:01:02 *** kanzure has quit (Remote closed the connection) 03:07:39 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 03:08:57 Can anyone tell me which books to follow to get the basics of organic chemistry so that I can follow the DNA structure , the bases, bonding etc? 03:30:59 *** craigoz (n=craigo@202.63.56.72) has joined #bioinformatics 03:40:13 i guess organic chemistry basics are an important factor in Bioinfo.isnt it? 03:51:29 *** Hawk| has quit ("Ex-Chat") 04:01:20 probably in the biophysics portion 04:01:47 and protein structure maybe? 04:01:59 i'm more a fan of phylo and evodevo 04:02:02 okay 04:02:49 do you not have a bio background? 04:02:58 no i dont 04:03:12 i took two semester of organi 04:03:14 hell on earth 04:03:15 *** jm (n=jm@p57B9F4BD.dip.t-dialin.net) has joined #bioinformatics 04:03:36 okay before you could start the bioinfo course 04:04:01 you had a bio background? 04:04:31 bioinfo course online or at my university? 04:09:18 hmm I hav an electrical bachelors degree...what other prerequisites I would require 04:10:31 are you trying to take a bioinformatics course online or at a local university? 04:10:56 I was going through some introductory courses but I didnt follow much regarding the DNA structure , bases etc 04:11:00 i am currently earning a BS in genetics, and have had several genetics courses, biochem classes, organic chem classes, population genetics classes, and a bioinformatics class 04:11:33 yes i was searching for one onlien course 04:12:02 what was covered in the Bioinformatics class? 04:13:38 different online databases, regular expressions, some of the programs out there for gene prediction, promotor prediction, protein structure visualization 04:15:19 okay 04:17:55 if you're interested in organic you should try something at a local community college 04:18:05 your results may vary but organic is not something i'd want to teach myself 04:20:45 I am also not much interested but want some basics to understand the Gene and protein structure 04:21:21 i think the local community college will be good idea for that 04:38:46 *** Hawk| (n=mn@195.37.234.205) has joined #bioinformatics 05:50:35 *** Hawk| has quit (Read error: 113 (No route to host)) 05:50:59 *** Hawk| (n=mn@195.37.234.205) has joined #bioinformatics 06:53:18 *** synthasee has quit (Read error: 60 (Operation timed out)) 06:54:48 *** kanzure (i=bryan@66.112.232.35) has joined #bioinformatics 09:15:43 *** highvoltz has quit () 09:18:24 *** CrimsonScythe (n=CrimsonS@unaffiliated/crimsonscythe) has joined #bioinformatics 10:10:09 *** pingou (n=pingou@AMontsouris-152-1-42-194.w82-123.abo.wanadoo.fr) has joined #bioinformatics 10:10:38 Hi 11:27:23 *** toru (n=gioby@81-208-83-234.fastres.net) has joined #bioinformatics 12:06:51 *** toru_ (n=gioby@81-208-83-234.fastres.net) has joined #bioinformatics 12:12:37 *** toru has quit (Read error: 104 (Connection reset by peer)) 12:14:25 *** Hawk| has quit ("Ex-Chat") 12:59:13 *** craigoz has quit ("Leaving.") 14:08:53 *** kanzure has quit ("Leaving.") 14:25:08 sparta: If all you care about is chemical structure, just click around on wikipedia checking out chemicals. 14:25:32 Maybe get an organic chemistry book. 14:26:05 Actually, biochem textbooks are probably better. 14:26:17 At least they'll stick with biomolecules. 14:26:56 There's a few structures you need to get familiar with, and then everything gets a lot easier. 14:27:44 You might as well memorize the 1- and 3-letter codes for amino acids as you're going through the structures. 14:29:01 If you cover 20 amino acids, 5 nucleotides, fatty acids (alkanes/-kenes/-kynes), and a couple of sugars, you're good to go. 14:33:29 biochem reaction pathwways are stupid 14:33:52 they are printed on posters for a reason 14:33:57 (i.e. not for memorization) 14:38:21 Yeah, it's just good to be generally aware of the existence of certain pathways, like glycolysis, the TCA-cycle, electron transport, etc. 14:38:39 If you need any details, the charts are available. 14:43:30 yeah 14:43:32 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 14:43:54 but most courses force you to be like "so...what enzyme is used in step 5" 14:49:19 *** kanzure (i=bryan@dhcp-146-6-214-2.icmb.utexas.edu) has joined #bioinformatics 15:08:03 *** kanzure has quit (Connection timed out) 15:11:20 *** kanzure (i=bryan@dhcp-146-6-213-241.icmb.utexas.edu) has joined #bioinformatics 16:21:40 *** pingou has quit (Read error: 110 (Connection timed out)) 16:48:21 I'm not too fond of courses. 16:48:53 They tend to lean too much towards easily testable information. 16:49:04 Which also tends to be easily lookupable. 16:49:33 Learning on your own is where it's at! 16:49:54 Wait, maybe reading's where it's at. 16:50:04 If I remember my Cpt. OJ Readmore correctly. 16:52:04 wonklab: I HATE HATE HATE HATE courses 16:52:28 it's one of the reasons why I didn't try to push the grad school thing too hard 16:53:24 I don't learn as well from courses, either. 16:53:30 It kills my interest and motivation. 16:53:34 totally. 16:53:56 I'm always surprised at how efficiently a course can suck the coolness out of a topic. 16:54:06 hah 16:54:22 Course descriptions frequently sound pretty awesome, but they never live up to it. 16:54:41 Actually, I had some liberal arts courses that were pretty great. 16:54:48 Like going to a show every other day. 16:54:52 heh 17:09:54 *** alperyilmaz (n=alper@osbc-141.osbc.ohio-state.edu) has joined #bioinformatics 17:12:17 hi, i have 300,000 short sequences and I'm trying to BLAST them against a database, I noticed that only 50,000 of the short sequences are aligned then I noticed that around 250,000 of the sequences are identical to each other (eg. sequence1 has 2500 identical copies, sequence2 has 2000 copies). Is there an commandline argument for blast so that it does not ignore identical query sequences 17:12:39 if not, what is the alternative software which won't ignore such sequences 17:23:59 *** kanzure has quit (Connection timed out) 17:47:28 *** highvoltz has quit () 18:22:06 *** highvoltz (i=rogers@66.225.200.177) has joined #bioinformatics 18:45:21 *** kanzure (i=bryan@66.112.232.35) has joined #bioinformatics 19:02:58 *** alperyilmaz has parted #bioinformatics () 19:51:09 any stats people in here? 20:00:16 I like to stare at numbers. Does this count? 20:24:56 *** Splicer (n=p@h201n1c1o261.bredband.skanova.com) has joined #bioinformatics 20:39:31 *** toru_ has quit ("Ex-Chat") 21:05:20 stats is fun 21:27:52 Woah, why would someone want to run multiple BLASTs on identical sequences? 21:28:41 Especially when repeats are 5/6 of their dataset. 21:29:37 to test hardware? 21:30:14 ugh 21:30:35 oh, you're talking 4 hours back 21:31:36 each sequence is a special and unique snowflake in darwin's eyes 21:32:10 anyone here ever heard of PSM programs? 21:32:27 http://en.wikipedia.org/wiki/Professional_Science_Masters 22:38:02 I've met god across his long walnut desk with his diplomas on the wall behind him, and god asks me, 'Why?' 22:38:02 'Why did I cause so much pain?' 22:38:02 'Didn't I realize that each of us is a sacred, unique snowflake of spiritual unique specialness?' 22:38:27 (0.2points) 22:45:15 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 23:04:53 *** synthasee (n=synthase@68.63.20.12) has joined #bioinformatics 23:14:38 *** synthase has quit (Connection timed out)