foxfirefey: Fox stealing an egg. (Default)
[personal profile] foxfirefey in [community profile] bioinformatics
I got really excited when I saw Bioinformatics Programming Using Python pop up on Safari O'Reilly, only to get kind of disappointed at first glance. At first I thought it would by a Pythonic version of the classics like Beginning Perl for Bioinformatics. But, it doesn't have any mention at all of BioPython, it seems, not even as a footnote.

Now I'm left wondering why not. I know that BioPerl is still more expansive, but is BioPython so lacking that it doesn't even merit a mention? That's a very sobering thing to think about, as somebody who's been really enjoying using Python over Perl lately.

In any case, this book mainly seems to center over basic language concepts, which is sad in some ways, because many of the examples are doing things that I imagine are "reinventing the wheel" if you're using a library like BioPython. Reinventing the wheel for learning has its merits, but it's not very useful to someone like me, who would find a primer that included an introduction into a powerful library that takes care of some of the drudge work more useful.

It's possible that this book is more useful (to people of my type) than my skimming indicates, but unfortunately I probably won't delve into it to find out.

on 2009-12-23 09:36 am (UTC)
yvi: Kaylee half-smiling, looking very pretty (Default)
Posted by [personal profile] yvi
But, it doesn't have any mention at all of BioPython, it seems, not even as a footnote.

??? What?

I use BioPython in my daily programming at university and while I do hear that BioPerl is larger, BioPython can do a lot of stuff from the basics (handling sequences, translating, converting formats) to very sophisticated stuff (handling protein structures and such). I haven't had to use BioPerl because BioPthon couldn't handle something yet.

A book that doesn't even mention that you can use BioPython doesn't sound very useful to me.


bioinformatics: A montage of biotech imagery, such as DNA helices and gel electrophoresis. (Default)

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