Getting Started

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Getting Started with Facile and Easystoch

Linux, Unix, and Mac OS X

Facile and EasyStoch are straightforward to install in a typical UNIX-like setup. The following instructions assume that the standard tools make and tar (and gcc for the EasyStoch stochastic simulator) are present in the user's path. A standard installation of the Perl scripting language (version 5.8 or higher) is also assumed, and system administrator privileges may be required to install CPAN Perl modules.

Ask your systems administrator for help if you experience difficulties with the installation.

Facile and EasyStoch are available in compressed tar format. To decompress, use either the shell command

tar -xvzf facile_RELEASE_V25.tar.gz

or

tar -xvf facile_RELEASE_V25.tar

if your browser automatically unzips files. This command will create a directory containing Facile. To check the installation, change to this directory and type:

./facile.pl -h

This command should display Facile's help page.

You may have to install a small number of CPAN modules if they are not already on your system. For example, the module Class::Std is required. Your systems administrator can install it (and any other missing module) using:

cpan -i Class::Std

The accompanying EasyStoch stochastic simulator is installed similarly:

tar -xvzf easystoch_RELEASE_V4.tar.gz

Change into the directory, and then type

make easystoch

to compile the C code into an executable.

More details are available from the Facile and EasyStoch manuals. There is also our paper on Facile, and some examples of input files below.

Windows

Facile was developed in a Linux environment, but should function correctly on any UNIX-like platform that provides a suitable shell (e.g. bash) along with standard UNIX tools and commands, such as tar and the Perl interpreter. If the accompanying EasyStoch stochastic simulator is used, the platform should also include GNU's make and the GNU C compiler, gcc.

On Windows, the simplest solution is to install CYGWIN. CYGWIN provides a bash shell and many standard UNIX commands and applications. When installing, include the make, gcc, tar and perl packages.

Once CYGWIN is running, Facile and EasyStoch can be installed by following the instructions above for UNIX environments.


Examples

We have three examples of the text files used by Facile as input: the Michaelis-Menten equations, a model of glycolysis by Cornish-Bowden and Hofmeyr, and a model of the phosphorylation-dephosphorylation cycle of a signalling enzyme by Markevich et al.