[Bioclusters] education II

Joe Landman bioclusters@bioinformatics.org
15 Sep 2002 13:37:58 -0400

I think it is obligatory to note the following:

	BioPerl:	http://www.bioperl.org
	BioPython:	http://www.biopython.org
	BioCORBA	...

and a few others.  

The Lingua Franca for bioinformatics appears to be Perl.  Python is a
nice language as well for building glue logic.  Some people prefer it to
Perl, some not.  Ruby is gaining followers, but I am not sure how
quickly.  I am not sure what is happening with BioJava or the rest of
the bio-efforts.

The point should be to program in whatever language you are comfortable
in for your own work, and make sure you can use various common tools as
needed.  There are many tools for Perl, some for Python, some for
others, specific to bioinformatics.  You want to avoid arcane languages
for code sharing if at all possible.  You also want to avoid odd library
functions that others may not have.  This is where Perl and Python
really shine relevant to other languages, with CPAN and the relevant
Python repository.

Both Perl and Python can glue other systems/languages together.  Have a
look at the Inline module for Perl.  Python makes life easy for
extension writing, and there is a good coupling with Java (via JPython
and other libraries).

Others may have thoughts/comments. 

On Sun, 2002-09-15 at 13:00, Daniel Comesana wrote:
> To extend the AdamM's answer, I want to put on the table the Python
> language.
> To start from zero, maybe a better and more structured "script option" than
> Perl (however Perl is widely used, since it was used for a lot of years),
> but, since my formation was in computing (assembler / Pascal) , Python seems
> to me more structured and easy to learn.
> I used Python, even under Windows plataform with zero changes to run under
> Linux.
> You have a nice on line support on http://www.python.org/
> It also have runtimes for Solaris and Irix.
> Best wishes
> Daniel
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Joseph Landman, Ph.D
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615