My turn to jump into this fray. A few responses to some
specific quotes first:
from David Mathog at Division of Biolgy, CALTECH:
>>Doesn't really matter, but Fortran is being unbundled and I don't know
>>if Linux has a fortran compiler.
>> If Linux has no fortran 77 compiler then it
>would be the only major platform that does not. ANSI C is certainly
>available everywhere. However, the only free ANSI C compiler that I know of
>these days is Gnu C. ANSI C on all other platforms is already an extra cost
>item. If you think not, check your maintenance/ licensing agreements. So
>what if compilers cost money? So does the operating system, so does the
>hardware, so does support. This is the real world.
GRRRRRRRR !!!! As an impoverished graduate student, I dumped all my
pennies into a 486 PC on which I ran 386BSD and later NetBSD, both FREE
posix-compliant (Unix (tm)) operating systems. I was unable to locate
a free F77 compiler for this system, so I couldn't use the fortran code
available to me. I _was_ able to make good use of gcc and develop software
at home which I could then quickly port to `real machines' belonging
to supportive faculty in my computer science department (where was the
computational support from my biochem department ? Don't ask...).
This _is_ the real world, and real money is hard to come by -- especially
for the students who will likely be the first to experiment with the
software you want used.
from John Barton at IBM T.J. Watson Research Center:
>Instead, let's work to see software
>publication compete with journal publication in terms of quality and value.
My current assignment is to develop a GUI for D. Jones' protein threading
software (given an amino acid sequence, an `energy' function, and a fold
library, rank the library entries according to `fitness' for the input
sequence). I am convinced that David can write some of the fastest and
tightest C code for any platform around; unfortunately, he's admitted to me
that he never intended for anyone else to even _see_ the code I'm working
with now. We want to release source code for this project, but it must be
nicely engineered and well commented -- like a peer reviewed journal
from James Tisdall at University of Pennsylvania:
> I'm adding graphics to DNA Workbench now, but it isn't finished yet.
>The graphics package chosen is Tk (of Tcl/Tk) available for Xwindows.
> Finally, my major design goal in writing DNA Workbench was to build
>for myself a computing environment that makes it easy to experiment with
>algorithms for computational biology.
I too have chosen to use Tk to develop the threader interface, though
I've stayed with Tcl for the control code. Given the easy extensibility
of Tcl in C, I am developing a set of Tcl extensions specifically for
working with (primarily structural) protein data. We hope to encapsulate
a number of algorithms, such as double-dynamic programming and our
various structure analysis routines, into Tcl commands. Although these
will not be the fastest implementations available, it is intended that
they be comprehendable by other researchers and form the basis for a
Tcl/Tk computing environment for working with protein structures.
If you have an interest in `PX, the Protein eXtensions to Tcl/Tk' or
wish to comment, please contact me at the Internet address below; I
would be very pleased to hear fom you.
Rob Miller, Ph.D. `On an Errand out of the wilderness'
Biomolecular Structure and Modelling Unit (BSM),
Department of Biochemistry and Molecular Biology,
University College / Gower Street / London WC1E 6BT.
Tel: 44 71387 7050 x2303
Fax: 44 71380 7193
home: 44 442 65092
Internet: rmiller at bsm.bioc.ucl.ac.uk