Theoretical Biology & Bioinformatics

tree of life
Rob J. de Boer

Rob J. de Boer

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grind.R

Phase plane analysis is a powerful approach for analyzing mathematical models comprised of a few ordinary differential equations (ODEs). Grind.R is an R-script allowing one to easily study such models by numerical integration, phase plane analysis, finding and following steady states, and fitting to data. Look on the grind.R webpage for more info. (grind.R replaces a previous C-program called GRIND)

Estimating relative fitness from competition experiments

We maintain a webserver for estimating the relative fitness (1+s) from virological competition experiments.

CASH

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 be 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

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