[clean-list] RE: Clean and scientific programming

[Brian Wilfley]

Let me put in a word for a particular type of "scientific" programming
which Clean ought to be able to handle and which I would be interested
in.  This type of work is characterized as follows:

1) Small amounts of code to investigate particular algorithms.  The
algorithms may be either for analysis of experimental data or
theoretical calculations.  The point is that huge levels of numerical
performance are not required.

2) Easily and reliably  modified code.  This is important because the
algorithms are not settled or agreed upon.  One needs to try different
approaches and one needs to know that the trials are meaningful, that is
that the code not be the victim of bugs.  (I know bugs are inevitable,
but it helps if they can be tracked down and fixed with a degree of
assurance of a correct solution.  The main thing that helps this, in my
opinion, is small number of lines of source code per module.)

3) The ability to plot results.  Usually 2-D plots are good enough for
me, but the other big use I've had is for image display.  This point is
crucial.  There seem to be scores of languages that support 1) and 2)
above, but that fall flat on this point.  My theory is that a) good
plotting programs are hard to write, b) they are especially hard to
write in a form that is portable, c) those that exist make the job of
plotting as difficult as the job of designing the algorithm in the first
place: too many lines of code to make a graph.

Having set out these requirements, I have to confess that the system I
use most is Matlab.  And a big reason is that 3) above is satisfied.
The code one writes for matlab is usually short (until the problems gets
to a certain size IMO.)  But others are shorter and more succinct.  But
it works great for plotting simple plots.  And simple plots are usually
what is required.

To me the advantage of a system like Clean is that 1) and 2) are well
served.  But if 3) is not, I'm stuck.

But not defeated...

Brian

Brian P. Wilfley
Senior Scientist
Signature Bioscience, Inc.
21124 Cabot Blvd.
Hayward, CA 94545
ph: 510 576 2416
fx: 510 576 2434
bwilfley@signaturebio.com