[BiO BB] Python or Perl

[Mike Marchywka]

Without knowing any important details ( see questions below), if you want
to learn more modern programming beyond a few bio packages, I would exapnd
on the other reply to your post and    would recommend downloading
cygwin ( cygwin.com and associated mail lists ) and java from sun.
The Sun tutorials should be good OO intros, the Java runtime gives you
getter diagnostics for learning- I wouldn't jump from interpretted runtime 
to
C+ right away and the scripting, while important and powerful, doesn't 
always
produce helpful error messages and is a bigger jump from BASIC.

http://cygwin.com/

http://java.sun.com/javase/technologies/core/index.jsp
( I'm not sure how the versions compare anymore, but you could download this
for example)
http://java.sun.com/j2se/1.4.2/download.html

Once you have a little familiarity with cygwin, I would suggest getting 
something
like rasmol and building it yourself ( I just did this myself,  much more 
lightweight than PyMol
and combined with scripts for downloading and manipulating pdb files can 
actually
create a useful system pretty quickly ).

What is on your school's program? I would imagine some programming or
computer stuff is part of your required course list. I'm asking mostly
out or curiousity but it may be helpful to understand how these
things are taught today. And, how is it you managed to learn
BASIC "these days" withouth learning anything else? I didn't know
it was that popular any more as OO seems to be taught early.

I had many years of programming - starting with BASIC and assembly code on
8080 and Z80 systems running CP/M and DOS- but was out of the field for a 
while
before learning object oriented things. I got started with Java - the Sun 
tutorials should be more than enough for anyone with a programming 
background.  I downloaded the
Chime plugin and was amazed at the wireframe rotating DNA- probably not 
impressive
to anyone here but really struck me at the time. Someone at work got me
going with cygwin- really great tool for learning or real stuff.


Comparing scripts to "real languages" for efficacy ( sorry, too much 
biotech...)
is very difficult.
I'm not sure if Sun will ever be able to beat C++. The last time I checked, 
the Intel
compiler and tools were pretty good at dealing with architecture or 
providing
optimization options. I had written a hand-coded assembler routine to do a 
wavelet
transform that used all kinds of special observations about the specific 
transform and
the machine architecture(registers, caches, pipelining, etc) . By the time I 
was
done, VTune and the wall clock results suggested the naively written C++ 
code,
compiled with Intel's version 6, wre pretty similar.  My point is that the 
compiler
seems to know a lot about the CPU and I'm not sure if Sun's hotspot or 
related
technologies can compete ( aside from the overhead time of doing runtime
optimizations). If you need to write code that reflects the CPU architecture 
or
is cache aware, this is easier in C++ as opposed to java. The Java runtime 
removes
all memory allocations issues from the programmer and has a somewhat 
unpredictable
garbage collector.


Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
404-788-1216 (C)<- leave message

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