Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-05-08

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All times shown according to UTC.

Time Nick Message
02:49 drin left #bioperl
04:13 zeropointo joined #bioperl
04:34 zeropointo Hello
15:06 * jhannah waves
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20:56 zeropointo what's a good bioinformatics book/guide for a programmer working towards a molecular degree?
20:59 kblin bioinformatics or molecular biology guide?
21:11 zeropointo I'd say I still have a lot to learn in both areas. I just don't need the programming part explained to me.
21:12 zeropointo I'm a quick study and i'd like a quick study guide. Does that make sense?
21:13 kblin for molecular biology, I guess the standard book everyone uses is Roberts, Molecular Biology of the Cell, but that's a 1.6k pages monster
21:13 kblin for bioinformatics, I don't think there's enoug agreement on what this actually is to have a book :)
21:13 zeropointo i've had a look at the bioperl docs. which are very helpful. the learning curve seems to be the terminology involved in bioinformatics.
21:14 zeropointo ill  find an example. brb
21:16 zeropointo alright so here's somthing from the TR10 synth cell venter came up with.
21:16 zeropointo "... PCRs and genomic walks for known repeats and problematic
21:16 zeropointo areas generated an additional 551 Sanger reads. The combined
21:16 zeropointo sequencing data was assembled using Celera Assembler (Meyers, 2000)
21:16 zeropointo resulting in 7 contigs in 3 scaffolds, with a contig N50 of 279215
21:16 zeropointo bp. Average coverage was 11.5x. An additional 133 Sanger clone
21:16 zeropointo primer walks and genomic walks were generated to close the
21:16 zeropointo remaining gaps and cover low coverage regions. A completely
21:16 zeropointo finished genome was produced in 19 days[T2]."
21:17 zeropointo genomic walks? Sanger reads? contigs? scaffolds?
21:17 zeropointo coverage?
21:17 zeropointo see my dilemma?
21:17 kblin ok, fair enough
21:18 zeropointo i understand the biology well enough as a student, but there's a lot of additional bioinformatics stuff in there.
21:20 zeropointo maybe there is an introductory text explaining these concepts?
21:22 kblin http://ab.inf.uni-tuebingen.de/​teaching/ws02/abi1/welcome.html has a link to the lecture's script, let me see if I can find the part on sequencing
21:22 kblin http://ab.inf.uni-tuebingen.de/​teaching/ss03/abi2/welcome.html
21:23 kblin this is a basic "algorithms im bioinformatics" lecture, I think it should give a decent overview
21:23 zeropointo Hey this looks interesting, thanks. :D
21:25 kblin it's not totally current, that's the 2003 script, but the basics didn't change much
21:25 kblin and the current scripts are one file per lecture, totally annoying :)
21:53 carandraug left #bioperl

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