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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@example.com 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!