Help biologist choose a new programming language

Simon Andrews simon.andrews at bbsrc.ac.uk
Fri Feb 7 05:19:41 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.
> >
> > 2) A language that doesn't force me to obsess about the details of
> > OOP.
> >
> > 3) I would like to return to graphical applications eventually.
> > Therefore the language should have a GUI library, either
> > Windows-specific or cross-platform.
> >
> > 4) Speed is nice, but secondary.

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.

>From a productivity point of view I would say that Perl is a much better
choice.  When combined with the BioPerl modules it allows you to get
tasks completed with the minimum amount of development time.  If you're
after all out speed, then a well written Java or C program will be
quicker, but frankly compute time is cheap compared to programmers
time.  I know that most of the Perl scripts I write will be run less
than 10 times, so the important thing is getting the job done, and Perl
is very good at that.

For the cross-platform and GUI aspects Java probably comes out on top. 
Tk (or Qt or GTK) works and is OK, but has some limitations, also Perl +
associated modules are probably less widely installed than Java so you
may need to invest in a Perl compiler if you want to distribute to
others easily.

In the end the best answer is to try both.  They both have their
strengths and weaknesses, and you'll probably soon get a feeling for
which one suits you better.  The other good way to choose is to find
someone else working close to you who knows one or other of these
languages.  It's always useful to have an expert handy :-)

Hope this helps


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