Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-10-17

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All times shown according to UTC.

Time Nick Message
03:52 mistermaps joined #bioperl
03:54 mistermaps Heya, I'm looking for help on a small project I'm working. I'm not looking for code exactly, more like a direction
03:55 mistermaps I want to find homologous sequences in a small database. Which means I have to compare all to all
03:56 mistermaps I'm not exactly sure the best way to execute this and then sift through the results.
04:01 mistermaps I realize it is late I'll try again later!
10:52 zapad joined #bioperl
10:52 zapad hello, i am here again
10:56 zapad i am a perl programmer. But also i want to become a genetic engineer. Where i must start ? I know it sounds pretty naive, but i really want to became f genetic engineer and ready to spend years for it. At least I want to obtain knowledges, which will allow me to work as programmer in company, which specializes on genetic engineering. Which sites and literature you advice or common plan what to do ?
12:54 kai uhm, tricky question :)
12:54 zapad yes
12:55 zapad but any ideas ?
12:57 kai genetic engineer as in lab work? or just the computational side of it?
12:59 zapad i am from third world country
12:59 zapad here is very bad with genetic equipment and labs
12:59 zapad so i choose computional side
13:03 kai then I'd start looking for a good text book on genetics :)
13:03 kai as a computer person the most important part of the job is to actually understand what the biologists are talking about :)
13:08 zapad what for example ?
13:09 kai sorry, need to head for a meeting
13:09 zapad can yoy give me a list of questions. answers on which i must know to work a last-sort programmer in biolaboratory ? :)
13:09 zapad ok
13:59 ank joined #bioperl
14:21 zapad guys, are you really have no ideas to help me ? :(
14:38 carandraug joined #bioperl
15:00 ashleydev zapad: get a text book
15:00 ashleydev try amazon.com
15:00 ashleydev read wikipedia.org
15:01 zapad no no no !
15:01 zapad i knew i'll hear it
15:01 zapad it of course right way, but it wil take too much time
15:02 zapad and i'll spend a lot of time on learning things which will not needed in my future activity
15:04 zapad in almost every science exists 2-5 books which cover 95% of basic aspects and references to other 5% of information
15:08 ashleydev yeah so find those.
15:08 ashleydev or find a problem you want to tackle
15:08 ashleydev and try to do it
15:08 ashleydev i.e. find a dataset of some DNA and try to sequence it
15:08 ashleydev or something
15:09 ashleydev then that will drive you to learn abou tit
15:15 zapad ashleydev, what means "to sequence a DNA dataset" ?
15:27 ashleydev zapad: http://www.nature.com/scitable/topicpage/dna-​sequencing-technologies-key-to-the-human-828
16:17 zapad ashleydev, according to this article, on what stage situated the dataset which i must get for sequencing ?
16:19 ashleydev i don't know find one.
16:20 ashleydev there's probably one that amazon hosts in S3
16:20 ashleydev it's just an idea.
16:20 ashleydev i.e find a problem you can try to solve (even if it's already solved) and use that to learn from
16:32 zapad ashleydev, for example i want to produce an new sort of oak, which will grow faster than original sample
16:33 zapad ashleydev, or something else, where task is to improve the characteristics of specified plant or animal
16:34 zapad but i think it is impossible without laboratory
16:34 ashleydev build your own lab
16:35 ashleydev (though that may mean you've already used one)
16:35 ashleydev and know what's needed
16:36 ashleydev http://makerfaire.com/pub/e/5297
16:36 ashleydev for example
16:36 ashleydev http://en.wikipedia.org/wiki/DIYbio
16:36 ashleydev another example...
16:37 ashleydev http://diybio.org/
16:49 zapad thanks
16:50 zapad next time i will formulate my questions more strict :)
16:53 zapad but can i do something useful without microscope  or gene cannon, with just some public dna dataset in, for example, fasta format and computer ?
17:36 ashleydev i suggest you try to find a public data set and play with it
17:36 ashleydev see what you can do, before you try to improve the state of the art
18:00 zapad I hope that there is one of them which is smaller than some hundreds of GB :)
18:07 leont joined #bioperl
18:10 leont There is no parser for sff yet, right?
18:11 leont (I'm writing one now)
18:39 leont Also, is Christopher Fields also in this channel?
19:09 rbuels leont: yes, he's pyrimidine.
19:10 rbuels leont: he hasn't had a lot of time to be on irc lately though
19:10 leont Ah, I was suspecting that
19:11 * leont should have known, the avatar on CPAN is a pyridimine molecule, why didn't he notice that before?
19:11 leont s/pyridimine/pyrimidine/
19:22 leont Anyway, I seems to be one of the last people left hacking on Module::Build, I was looking into the provides problem
21:07 ende joined #bioperl
21:08 ende Im getting indexing interruptions in Bio::DB::Fasta
21:08 ende https://gist.github.com/1293823
21:08 ende anyone got any idea what that is?
21:16 sl33v3_ joined #bioperl
21:32 jhannah joined #bioperl
22:29 buelsbot joined #bioperl
23:13 carandraug joined #bioperl

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