This is John Rupley's personal site. As such it largely deals with what interests me now or has in the past. Nevertheless, there are several relatively non-narcissistic components:
A side-bar button, Eric Rupley / Ila & John Rupley, links to a web page with dot-sig-like minimal information on Eric Rupley, Ila Rupley, and John Rupley. The web pages associated with their accounts are at this time void or irrelevant.
A webpage, Code, has links to a set of pages, each having links in turn to source directories or files dealing with a particular sort of code. See Configuration for dot files, executables and hints for setup of the Unix side of Mac OS X. The executables are described either in Scripts or under src. All are written or compiled to run under Mac OS X.
The directory 0Downloads has gzipped tar files of the contents of the directories under Code.
Much of the code is for utilities or programs that I use frequently but are not part of the Mac OS X distribution:
note,
a simple program
for maintaining a file of dated notes and a Unix-style calendar;
recipes
software based on the 1988 alt.gourmand distribution;
with two collections of recipes;
simplex,
an implementation of the Nelder-Mead
algorithm for minimzation of a function and extraction of parameters;
rename
a general-purpose script to rename files;
blout, a one-line filter
to remove blank lines.
Some hard-to-find golden oldies:
tac, a reverse cat;
whereis, the old-style BSD version;
nrchbar,
for inserting troff-style change bars in text;
zap, for killing running programs that match a pattern;
dugraph,
a one-page graph of disk usage.
Somewhat specialized are a set of scripts in the S language, written to run under the R system for computation and graphics and to address particular biophysical problems:
molecular dynamics -
atom-fluctuations
and
driven-protein-motions;
statistical physics -
Zimm-Bragg helix-coil tranisiton theory
and
percolation;
fitting of data -
hemoglobin oxygenation,
nonlinear enzyme kinetics,
and
batch calorimetry.