Downloading and installing The Bio-PEPA Workbench

A Linux-like environment with Bash is required to run the Bio-PEPA Workbench. We have tested the Workbench on 32-bit architectures Fedora Core 6 Linux and with Cygwin on Windows XP. We have tested the Workbench on 64-bit SUSE Linux.

The Bio-PEPA Workbench is implemented in Standard ML and currently uses the Moscow ML implementation as its runtime. To run the Bio-PEPA Workbench you will need to have Moscow ML installed on your machine. Under Cygwin we recommend that you install Moscow ML in C:\mosml.

The Bio-PEPA Workbench uses the StochKit stochastic simulation toolkit to perform exact stochastic simulations using Gillespie's SSA algorithm.

The StochKit framework uses the SPRNG random number generators if they are available, but can function without these. The SPRNG random number generators require you to have a Fortran compiler installed. We have used StochKit with SPRNG Version 2.0 but we have also used StochKit without SPRNG.

The Bio-PEPA Workbench uses VFgen to provide an intermediate representation of differential equations in XML format. The VFgen tool translates these into programs which are executable as C code linked against the SUNDIALS ODE library or Matlab.

The Bio-PEPA Workbench uses Dot to draw reaction networks, Gnuplot to plot graphs and ImageMagick to display these. The LaTeX document preparation system is used to produce reports. You need to have Dot, Gnuplot, ImageMagick and LaTeX available on your machine to run the Bio-PEPA Workbench.

Download

The Bio-PEPA Workbench

Download StochKit for Linux or StochKit for Windows/Cygwin and the current release of the Bio-PEPA Workbench.

Unpack the file which you got using one or other of the following two commands.

tar zxvf stochkit.tar.gz
unzip stochkit.zip


Unpack the Bio-PEPA workbench into the same directory.

unzip bpwb.zip


Your directory should look like this.

bpwb stochkit

Change to the Bio-PEPA Workbench directory and make the Bio-PEPA command executable.

cd bpwb
chmod +x bp


Run the Bio-PEPA Workbench. The following command runs the Bio-PEPA Workbench over all .biopepa files in the current working directory.

./bp

If the above command did not work then it may be necessary to re-compile the Bio-PEPA Workbench for your platform and then re-run the command.

(cd src ; make)
./bp