Help biologist choose a new programming language

Jonathan G Campbell jg.campbell at
Thu Feb 6 08:40:40 EST 2003

John Ladasky wrote:
> Hi, folks,
> After devoting several years to programming the most troublesome
> computers of all, namely living cells, I am beginning to take an
> interest in programming silicon again.
> I need the ability to read flat-format text files, seek out some key
> words and sequence data, and analyze for patterns.  Not too difficult,
> right?
> Well, I followed one friend's advice and investigated Java, perhaps a
> little too quickly.  I purchased Ivor Horton's _Beginning_Java_2_
> book.  It is reasonably well-written.  But how many pages did I have
> to read before I got through everything I needed to know, in order to
> read and write files?  Four hundred!  I need to keep straight detailed
> information about objects, inheritance, exceptions, buffers, and
> streams, just to read data from a text file???
> I haven't actually sat down to program in Java yet.  

That's the problem.

> But at first
> glance, it would seem to be a step backwards even from the procedural
> C programming that I was doing a decade ago.  


> Here is what I think would make a good programming language for me
> (but feel free to try to convince me that I should have other
> priorities):
> 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.  

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.

Good luck,

Jon C.

Jonathan G Campbell BT48 7PG jg.campbell at 028 7126 6125

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