Software dependencies

Prerequisites

The SBMLevolver has been developed and tested only under Linux, and it will probably also run under any current MacOS operating system. No Windows version is planned, since the effort needed for porting is too big at the current stage. For installation of the program, the following freely-available libraries are needed and should be installed in the order in which they are given here.

1. GSL

   : The GNU Scientific Library. If this one is not included on your Linux distribution, it is obtainable from http://www.gnu.org/software/gsl/.

2. Xerces

   : The XML-Parser is needed to read SBML and should be available with your Linux distribution:
   make sure you have libXerces-c and libXerces-c-devel installed.
   If it's not available within your distro, you might get it from http://xerces.apache.org/. One current particularity is that you need to install libsbml (see below) using the Xerces XML parser, otherwise the SBML_odeSolver installation will cause trouble.

3. Sundials Cvode

   : A suite of numerical solvers. It is available from http://www.llnl.gov/casc/sundials/. Use version 2.3.0

4. libSBML

   : This library deals with SBML structures, it is available at http://www.sbml.org/.
   If you have a GNU C compiler prior to gcc-4.3.x, be happy, use version 3.1.1.
   Since gcc-4.3.x is more strict, you'll have to apply the patch described here or use the patched version of libsbml-3.1.1 from here.

5. SBML_odeSolver

   : Simulation of SBML models, available at http://www.tbi.univie.ac.at/~raim/odeSolver/.
   Since the latest Version does not work any longer for sbmlevolver, use the old version which may be downloaded here (this is a snaphot of an older CVS version).
   You also might want to install the Graphviz (http://www.graphviz.org/) and/or Grace (http://plasma-gate.weizmann.ac.il/Grace/) libraries before installing the SBML_odeSolver, since they add capabilities to visualise reaction networks and graphically show the time-course of model simulations. However, these are not necessary.
   Before installing, you should have a look in /usr/local/lib: if there are files libODES.* remove them before installation, otherwise you will run into trouble during installation of sbmlevolver!

6. Now you're ready to install sbmlevolver

7. lp_solve

   (optional): Solves linear programming problems, get it from http://groups.yahoo.com/group/lp_solve/. Currently, version 5.5 is in use.

Installation instructions

For instructions regarding installation of the software, see the

INSTALL

file included in the software package.

Step-by-step guide

A tutorial how to install the software packages can be found here.