[BiO BB] How to write Algorithm

hzi at uol.com.br hzi at uol.com.br
Wed Sep 26 23:15:50 EDT 2001

On Wed, Sep 26, 2001 at 09:03:37AM -0500, Indraneel Majumdar wrote:
> On Wed, Sep 26, 2001 at 08:35:30AM -0400, John S. J. Anderson wrote:
> > Indraneel Majumdar <indraneel at indialine.org> writes:
> > 
> > > There is a very nice O'reilly book: Developing Bioinformatics
> > > Computer Skills
> > 
> > I wouldn't really recommend this for reading about algorithms -- there
> > wasn't really any in-depth stuff in this book IIRC. (The book is still
> > good for what it is -- it's just not a book about bioinfo algorithms.)
> yes, you're right. It's a good book, but not specially about algorithms

Isn't this book a little too basic? I mean, I'm only reading it now,
and it's my first book on Bioinformatics (I'm a medical
student-Brazil), but I feel it's too basic:
- if you already know your way around a GNU/Linux box (we debianers
  say "GNU/Linux"...so sue me... :-) )
  In fact, if you use GNU/Linux or Unix, you can skip half of the
- if you're familiar with genetics

Would anyone reccomend another one? 

> > If you're a Perl programmer, especially a Perl programmer of the "I
> > used to be a biologist but now I do Perl even though I never had a
> > programming class in my life" variety, you should read chapters two
> > and three of the ORA _Mastering Algorithms with Perl_ book, which
> > discuss the implementation of some of the classic data structures
> > (heaps, B trees, stack/queues/deques, etc.) in Perl. You will learn a
> > staggering amount.
> Thanks for this great piece of information. I am a bioprogrammer of the
> variety you described (which couldn't have been put better ;-)

Sounds like good advice...
And how about "functional programming languages"? A friend of mine (a
mathematician) told me to check out a language called Haskell
It was __very__ different from __anything__ I'd seen before. Has
anyone here ever used it?
They have this a qicksort algorithm written in haskell, and I was
amazed to see how beautiful (conceptually) it looked in haskell.
For sure, it isn't for text processing, but hey, who cares?

And what about Tannenbaum's "Data structures in C". He's supposed to
be a pundit...



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