Utrecht University > Faculty of Science > department of Biology > Theoretical Biology & Bioinformatics >
Rob J. de Boer

Rob J. de Boer

Home | Research | Publications | Books | Software | Viral fitness | CV |

GRIND

GRIND is a powerful and simple system for analyzing systems of ordinary differential equations (ODEs) and maps. We use it for phase plane analysis in our courses and for our own research on mathematical models with just a few equations. GRIND allows you to draw trajectories, do time plots, draw nullclines (0-isoclines), 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 Mac OS, Windows and Unix platforms and creates X11, OpenGL, and PostScript graphical output of publication quality. Check a few examples given in the manual.

Windows

GRIND uses the minimal GNU for Windows (MinGW) system, and can be downloaded as "zip file".

Download the file and unzip that file in a preferred location (e.g., in My Documents).

This will create a folder Grind containing the required MinGW and GRIND programs, libraries, manuals, and a setup program. After unpacking the zip file run the setup.bat program in the Grind folder.

Next double-click the model.grd file in the Grind folder to let Windows know that .grd files should from now on be opened with the Grind\bin\grind.bat file that was just created by the setup program.

Unix

For Unix/Linux/Mac installations GRIND is available as a "tar file".

Download the tarfile, un-tar it, install it with make, and copy the grind script to a directory in the Unix path.

Your main concern is the choice of the graphics interface, which is OpenGL, X11, or both. On Linux systems both are typically available, and a "make all" will do the whole job. If you only have X11 do a "make x11". If you only have OpenGL do a "make gl". In the makefile you may have to set the CFLAGS variable, defining the location of include files. This is preset for a normal Linux environment. In the grind script you may have to set the -L option in the GLIB and XLIB variables. Here is an example for installation in /usr/local/src:
cd /usr/local/src
tar xvf grind-2.xx.tar
edit makefile (Check the setting of CFLAGS variable)
make all
edit bin/grind (Check the setting of -L in GLIBS and XLIBS)
cd models
../bin/grind monod (Test whether it all works..)
GRIND> bye
cd ..
make clean
cp bin/grind /usr/local/bin

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: Ubuntu

Mac OS

GRIND can be installed like on any Unix system (see above) provided you installed XCode from your Mac installation DVD. GRIND will run fine via the X11 driver. Follow the instructions given above, but do a "make x11" rather than a make all. Test whether it works using "grind -x model" (and later change the default in the grind script or make an alias). The much nicer OpenGL graphics can be made to work after installing "mesa" from MacPorts (mesa 7.6.1 worked fine).
Theoretical Biology & Bioinformatics / Last modified on 28 September 2012 / R.J.DeBoer@uu.nl