Help biologist choose a new programming language

Morten Lindow morten at binf.ku.dk
Fri Feb 7 05:19:57 EST 2003

Jonathan G Campbell wrote:
> Go with Java. You'll be at least twice as productive as with C++ or C.
> Of course, if _all_ you are doing (and aiming to do) is ripping text
> files apart and putting them together in another way, then the Perl
> suggestion is apt.

I'd say go for Perl! It excels at manipulating text (biological 
sequences) and there is a very useful collection of functions and 
objects at www.bioperl.org. With bioperl you can easily interface to 
databases and external analysis programs (like BLAST).Most of the hard 
(and boring) stuff of parsing files and handling in- and output have 
been done for you, so can start asking (and answering) the interesting 
biological questions.

Bioperl is being actively developed by some of the top scientists in 

And the learning curve is quite shallow, albeit rather long.

It runs easiest under unix (very easy installation for Redhat+Suse at 
www.biolinux.org ), but should also work on windows and macs.

good luck,

Morten Lindow
grad student in bioinformatics, Univ. Copenhagen.


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