Rob J. de Boer
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GRIND is a powerful system for easily analyzing systems of ordinary differential equations and maps. We use it for phase plane analysis in our courses, and in our own research for quickly analyzing mathematical models with just a few equations. GRIND allows you to do numerical integration, draw trajectories, do time plots, draw nullclines, compute a Jacobian and its eigenvalues and vectors, and do simple bifurcation analysis. This is all driven by a simple command language. GRIND works on Windows, Mac OS, and Unix platforms. It uses X11 or OpenGL for its interactive graphics, and creates PDF and PostScript graphical output of publication quality. Look on the Grind webpage for more info.
We recently developed a simplified version of GRIND for R (grind.R) using the deSolve and rootSolve R-packages. With grind.R one can perform similar phase plane analysis in R. Grind.R is easy to install, and people liking R will also like grind.R. Check the following tutorial.
CASH is a fast and easy Cellular Automata simulator written and programmable in C. Its main advantage is its speed and its fast and colorful X11 graphics. The CASH library has a large number of routines defining operations over the CA. These are all optimized for parallel and/or vector machines. CASH can downloaded and a PDF version of the manual is online available.
For Redhat linux you also can obtain a binary RPM and build the RPM from the source rpm in the SRPMS directory using the command: rpm --rebuild PROGRAM.src.rpm For Ubunto/Debian you can visit the website of Levien van Zon.
Ref2bib is a package translating Medline (medlars) or ISI citations into bibtex entries. Ref2Bib can be downloaded and a PDF version of the manual is online available. For linux you also can obtain a binary RPM. You can build the RPM for your system from the source rpm in the SRPMS directory using the command: rpm --rebuild PROGRAM.src.rpm
FUI is a program for fitting models to data. It was developed in Los Alamos. A version than runs under Linux and Mac OS can be downloaded.
Estimating relative fitness from competition experiments
We maintain a webserver for estimating the relative fitness (1+s) from virological competition experiments.