[BiO BB] How to write Algorithms

Jan Torleif Pedersen JATP at Lundbeck.com
Wed Sep 26 10:21:49 EDT 2001


I have have as a byline been following this thread and I am deeply puzzled
about the whole concept.

An algorithm is the embodyment of a piece of mathematics, which in turn is
the embodyment of a theoretical experiment. In my mind you need to be able
to understand scientific problems and how to explain and describe these in
terms of mathematics. Once this is done one can consider numerical solutions
to a given problem. Just being able to implement an amoeba minimizer,
reverse heap sort, binary trees etc etc does in my mind have limited to no

The analogy I would like to draw is having all the tools for building a car,
without ever having seen a car - what is the point ?

Finally, I think all the books suggested are great and I have myself used
them extensively, so please do not misunderstand my point, which is - Find a
problem first and then start thinking about how you want to solve it.

			--- Jan

Dr. Jan T. Pedersen
Dep of Computational Chemistry
H. Lundbeck A/S
Ottiliavej 9, 2500 Valby

email: jatp at lundbeck.com
phone: +45 36 30 13 11
FAX : +45 36 30 13 85

-----Original Message-----
From: Indraneel Majumdar [mailto:indraneel at indialine.org]
Sent: Wednesday, September 26, 2001 4:04 PM
To: bio_bulletin_board at bioinformatics.org
Subject: Re: [BiO BB] How to write Algorithm

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

> 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 ;-)
"Mastering Algorithms with C" does have some of the heaps, trees, queues
etc. I'll get the perl book too to see how it's easier.

Thanks a lot,

> -- 
> Unix is like a toll road on which you have to stop every 50 feet to
> pay another nickel.  But hey!  You only feel 5 cents poorer each time.
>              -- Larry Wall in <1992Aug13.192357.15731 at netlabs.com>
Didn't Linux appear a year before that?


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