oi, computer geeks

[quesarah]

I'm checking out some of the Bioinformatics classes that are offered Winter 2006. The only class currently offered is Intermediate Perl Programming. OK that's over my head, so let's check out the prerequisite class Introduction to Perl Programming. Prerequisites for that class are: " Familiarity with UNIX, C and/or Bourne shells. The C programming language and sed/awk/grep is recommended."

OK, I have a passing familiarity with UNIX -- been a while since I've used it but I'm sure it'll come back. But C? Never used it. Here's my question: is this a topic that I'd be better off taking a class to learn? Or should I just grab a good reference and get reading?

Thanks.

Comments

[king-ghidorah.livejournal.com]

I find trying to teach myself programming languages a bit like hitting myself in the head with a hammer. I hurts the same, and is about as effective in teaching me to program. That said, I kind of understood a little PERL when I was trying to teach myself, and I have no C programming background. Of course, promptly forgot all I learned. I don't remember it being too horrible.

[among-the-waves.livejournal.com]

the perl class is probably taught in a unix environment so they probably want you to be able to get around on a command line. my guess is that you'll be ok but you'll probably want to check.

sed, awk, and grep are unix tools that allow you to use regular expressions, like if you want to search for a tab, the regular expression would be '\t'. perl uses regular expressions a lot which is why they mention it. again, you can ask the instructor, but they will probably go over this so my guess is you'll be ok.

do they use perl a lot in bioinformatics? i have no idea, just asking and wondering if it's the most useful thing. usually perl is used for stuff like parsing data out of files or sometimes for websites. i would have expected them to teach a more statistical based language like SAS.

[biogeekgrrl.livejournal.com]

It's my understanding that Perl is used a lot for handling ginormous sequence databases, pattern matching, etc. I don't know anything about how it compares to a language like SAS, so I can't say why perl is stressed instead of another.

[biogeekgrrl.livejournal.com]

Yeah, I taught myself some UNIX in much the same fashion with much the same results. It will probably be more effective for me to learn in an environment where I can immediately put my new knowledge to use; otherwise it'll go *pffft*.

[among-the-waves.livejournal.com]

i guess it depends on what type of work you'll be doing. if you like geeky math/stat stuff, you'll enjoy SAS more.

[biogeekgrrl.livejournal.com]

It's probably going to depend on what I can do with either language. I'm geeked out about pattern matching, structure modeling, and using these in silico tools to predict what biologicals are actually doing in vivo. That kinda turns my crank.