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Help biologist choose a new programming language

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Fri Feb 7 06:55:58 EST 2003

> John Ladasky wrote:
> 1) A low barrier to entry for performing simple tasks, such as
> processing text files.  This will allow me to accomplish the job I
> want to do right now.

In my mind, although Perl is a great language for this sort of thing, it does
have the tendency to look like line noise. It's a very powerful and expressive 
language, but you have be to strict with yourself to make it look nice.

As others have mentioned there's a long choice, perl, tcl, python, java, C,

What you need to consider is whether you want a language just for the job you
have at hand, or a language for future development. Does it need to be
portable too? Java is supposedly very portable, but I can confidently say I'll 
have less trouble getting a Perl or Tcl program running across a wide spectrum 
of systems than I will Java...

Anyway, rather than turn this into a language war I thought I'd supply some
pointers to objective comparisons between languages.

An empirical comparison of C, C++, Java, Perl, Python, Rexx, and Tcl for a
search/string-processing program.
    www.ipd.uka.de/~prechelt/Biblio/ jccpprt_computer2000.pdf

    An interesting paper containing real reports of about 80 implementations
    of the same problem by different people, in a variety of languages. The
    paper draws conclusions on performance, speed of development, reliability
    and the like. Worth reading in my opinion.

The Great Computer Language Shootout

    A comparison of the performance of 30 languages spread over 25 benchmark
    tests. The performance alone is interesting, but not in my opinion the
    most valuable aspect of this site. Being able to see the same piece of
    code implemented in different languages is a great way to get an idea for
    the syntax and style of a language. No matter how fast or expressive it
    is, you have to like programming in it for it to be a worthwhile choice.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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