SBML_odeSolver

                          SOSlib
               The SBML ODE SOLVER LIBRARY

   For more information about the SBML ODE Solver Library,

                           see:
       http://www.tbi.univie.ac.at/~raim/odeSolver/
                     or send email to:
                  [email protected]

INTRODUCTION

The SBML ODE Solver Library (SOSlib) is a simple command-line tool and
programming library for (1) constructing a system of ordinary differential
equations (ODE) from chemical reaction networks and (2) numerically
integrating the time course of concentrations of chemical species and (3)
basic visualization of model structure and integration results. It is based
on SBML, the XML standard for description of biological reaction networks,
the SBML library libSBML for parsing SBML and constructing the ODE system,
and on CVODE for numerical integration of the derived system of
ODEs. Optional data visualization modules allow printing of integration
results directly to Grace and drawing graphs of the reaction network, and a
Jacobian interaction graph of the ODE system via graphviz’ graph drawing
library.

The SBML ODE Solver can be used as a programming library, similar in style
to the use of libSBML. Please, see the examples directory for usage within
other programs, and linking issues.

INSTALLATION

The file INSTALL in the main directory gives instructions how to
build SOSlib with GNU Tools autoconf/automake.

The file README.txt in folder Win32 gives instructions how to
build SOSlib as a Visual C++ project.

More detailed information can be accessed online at
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/

USAGE

After installing the program, type

odeSolver <sbmlfile.xml> [options]

Please start the program with option -h/–help (type `odeSolver -h’)
for more information on program and output control via command-line options.

Short tutorials on usage of this and other SOSlib applications can be
found online at
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/app.html

ARCHITECTURE

Currently, the SOSlib has been tested on Fedora Linux,
Mac OS X/Darwin and Windows. It is written in pure ISO C and
should thus also run on other systems.
We would highly appreciate any reports!

BUG REPORTS
Please see online at
http://www.tbi.univie.ac.at/~raim/odeSolver/support/

BASIC FUNCTIONALITY

The SOSlib takes a SBML file of level 1 or level 2 (see
http://sbml.org/documents/) as an input. A SBML file describes networks of
chemical reactions and initial amounts/concentrations of the participating
chemicals; additionally it can include predefined events and rules.
The chemical reactions can have a mathemitcal definition of its rate law,
which is represented by a kinetic law' in SBML. The kinetic law’ differs
from a usual rate law, in that it describes change of amount instead of
concentrations.

The SOSlib then constructs a set of ordinary differential equations (ODEs)
for the rate of change of all chemical species’ concentrations (d[x]/dt =
f(x)) from the reactions where the species appear as reactants or
products. ODEs will not be constructed for species concentrations that are
already defined by SBML assignment or rate rules. A Jacobian matrix of the
resulting ODE system, i.e. the derivatives of the rates towards all other
concentrations (that are defined by an ODE), is constructed, if all
equations are differentiable (i.e. continuous).

The ODE system is constructed as another SBML model, which can also be
printed out when option -o or --printsbml is given.
This SBML can however ignore SBML intentions: the resulting species' can also describe parameters or compartments, and not only chemcial species. Every ODE is represented as an SBML rate rule’.
Such a pure ODE model, encoded in SBML, could also be directly passed to
the program.

NOTE THAT: the SOSlib can thus also be used as a SOLVER for
ANY ODE SYSTEM, if the user is willing to ignore SBML definitions and
describe her ODE system in (potentially wrong!) SBML.

Then the ODE system is passed to a function that calls CVODE to numerically
integrate the ODEs, i.e. calculate the time development of concentrations.
CVODE uses the generated Jacobian matrix or an internal approximation, if one
or more ODEs contain discontinuous expressions, or the user has chosen so.

The results can be printed to the calling terminal (stdout), to a file or
to XMGRACE, if the optional grace module has been installed.

Additionally the reaction network can be drawn as a bipartite graph, using
the optional module based on GRAPHVIZ graph drawing algorithms and its
graphical output. The dependecies of rates on species concentrations
as given by the Jacobian matrix (if defined), can also be drawn as a graph.
This can sometime be useful to get a quick impression of relevant
interactions, e.g. feedback loops, in the system.

Please await the (upcoming) detailed documentation in the `doc’
directory of one of the next versions of this distribution,
for more details on the procedure and usage. Contact the authors (email
adresses above), if you have further questions.

Have Fun!