Perl vs. C for bioinformatics -> Java

Don Gilbert gilbertd at
Thu Feb 26 14:13:42 EST 1998

my two cents for beginning programmers in bioinformatics:
  1st: learn java

java will give you as much flexibility as the other languages
and more.  It is a good foundation for both simple and
complex software.  It is relatively easy to learn, plenty
of free tools and libraries are available.  The java
group is busy sucking in just about all other extant computing
methods available in other languages, and adding new ones
not as readily available elsewhere.

Java benefits include:
*       object oriented programming benefits: better reusability,
        easier maintenance, better extensibility, better at handling
*       Java portability (multi-platform) is the best available
*       extensive Java standard libraries and third party libraries
*       extensive Graphic interface library for making full programs
	that biologists will use.
*       easy to write Internet server and client programs
*       good integration with emerging network and database
        standards and methods, including CORBA, Java Database Connectivity,
        Java Remote method invocation.
*       potential for standard, reusable interface to many
        bioinformatics programs and services

  2nd: learn perl, c, c++, etc.
as time permits.  the more languages you can work with the
the better you can solve any task at hand.

ps. Perl currently has better string matching & manipulation
functions than I've seen in Java.  I've heard Larry Wall may
be working on a Java equivalent for these.  There are things i
will perfer to use Perl for over Java, but those are rapidly
declining, and in general my perl code are small hacks to glue
programs together, not a very reusable source.  For what it can
do, Perl is more mature in some ways, but Java is a more robust,
fuller language.

- Don
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at

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