Dr. Jeff Denny's

Home Page

For a short CV, click here.

J. K. Denny, M. B. Daniel, and F. A. Kovacs, "Computing and Fitting SSNMR Powder Patterns with the Arithmetic-Geometric Mean and Edge Detection", Concepts in Magnetic Resonance, 30A(1); 1-20, 2007.

The python program to find chemical shift principal values using the AGM and and edge detection heuristic algorithm can be found here.
J. K. Denny and C. K. Trivett, "Cooling the Macon Volunteer Clinic", The UMAP Journal, 27(4): 431-447, 2006.

The model in Berkeley Madonna can be found here and in XPPAUT code can be found here.

Python code for computing a Latin hypercube sample for use in sensitivity and uncertainty analysis:

Berkeley Madonna (not free, but you can run the demo free)

This is easy to use and solves equations quickly.
(Example file: bilogistic.mmd)
pplane and dfield

These run in your browser via java and are really nice. For systems
of 2 equations, pplane does a fantastic job with nullclines and
classifying equilibria.
xppaut

This is free and is often used by researchers. It is VERY powerful
and has lots of options. Of course, this means it's not as friendly
as some of the others. It runs best in unix in my experience. So,
since the Mac runs under unix now, it runs great on the Mac. You will
need to have X11 installed to run it. (X11 comes free on the DVD of
system files with the Mac.)

(Example file: seir.ode)
Octave

This is free, open source software. It is very similar to Matlab, although the
ode solver commands are different. It's fantastic for matrix
computations (just like Matlab is). The ode stuff runs well, and I've
had success with it on the Mac. It took me a little while to get the
.m files working like I wanted, but now I'm happy with what I've got
running.

(Example file: ode.m and SolveOne.m)
SciLab

This is a powerful piece of free, open source software for modeling and computation.