Best programming language for biology students?

Niels Larsen niels at darwin.life.uiuc.edu
Sun Apr 16 22:47:44 EST 1995


As Dean Pentcheff suggests, C can be the second language after Perl5. It
will follow naturally, because Perl is C-ish in some of its syntax. The
discussion started by someone asking what would be the best first language
to teach biology graduate students.

Tweaking existing packages however is more difficult and I doubt only a few
curious and persistent graduate students will do that.  Understanding and
debugging a big unreadable C or Fortran package written by not the greatest
programmers is serious hacking. I have found, that even for moderate size 
programs it is often faster to write it anew in "my-own-right-way". Biology
programs are often written by professionals, but in some other field than
computer programming. 

As for Tcl/Tk, it looks like the recent nTk package (see Perl FAQ in
comp.answers) provides native Perl calls to Tk without going via Tcl. It
also sounds like Tcl is a much weaker language than Perl and should be
avoided. [Tcl is not necessary in Scheme either, there is the sTk package,
see Scheme FAQ in comp.answers] In addition to being a decent general
purpose language (Perl 4 was less of that) Perl is used all over for Web
servers and clients, which will also be a thing students ought to learn to
be prepared.

I think I disagree a bit with Dean Pentcheff that students need learn much
about Unix or X. Just enough to swim. They are more likely to encounter a
Mac or a PC, than a Unix machine, at least currently. They need to learn
things that will work no matter where they go, and that can be fetched from
the network. This includes a portable editor (they exist too). Granted,
Linux soon runs on PowerMac, Mips, DEC Alpha and Sparc (in addition to
currently 386, 486 and 586 - which it brings significantly more speed out
of than DOS/Windows/NT does; should it be called MS-DOSNT).

                                                   Niels Larsen

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