[sbml-discuss] SBML ODE Solver Tokyo Release

Rainer Machne raim at tbi.univie.ac.at
Mon Dec 19 17:32:00 PST 2005


Dear SBML community,

The SBML ODE Solver has become a library.
We proudly present SOSlib 1.6.0 :: The Tokyo Release.

SOSlib is both a programming library (API) and a set of command-line 
applications for symbolic and numerical analysis of a system of ordinary 
differential equations (ODEs), derived from a (bio)chemical reaction network 
encoded in SBML. This release newly features basic sensitivity analysis 
routines!

Detailed documentation for installation on various platforms, for application 
usage as well as as for the API is available at our new website at 
http://www.tbi.univie.ac.at/~raim/odeSolver/.

It is written in ISO/ANSI C, can be build with GNU tools (autoconf/automake) 
but also comes with Visual C++ project files. Windows binary executables are 
available. The API allows full access to all internal structures and routines. 
Bindings for scripting languages are in development.

SOSlib extends libSBML functionality to providing API functions that:
- construct the equivalent set of ODEs from a biochemical reaction network 
encoded in SBML as libSBML Abstract Syntax Trees (AST)
- differentiate a given formula's AST with respect to an arbitrary variable, 
e.g. to provide useful derivatives of an ODE system, such as the jacobian 
matrix, it's determinant or a parameter dependency matrix
- efficiently evaluate an (indexed) AST given a vector of variable values

A fine-grained wrapper around the well established SUNDIALS library provides 
fast and reliable numerical integration of stiff and non-stiff ODE systems with 
`BDF' or `Adams-Moulton' methods. Sensitivity analysis is provided via SUNDIALS 
implementations of `staggered' or `simultaneous corrector' methods to calculate 
forward sensitivities of a given variable's integrated solution to parameter 
values. Adjoint sensitivity gradients and handling of DAE systems (SBML 
algebraic rules) are in development.

SOSlib is an open source project hosted by sourceforge and distributed under 
the LGPL license. It provides researchers and application developers with 
easy-to-use and highly efficient interfaces to well-established methods of 
theoretical chemistry/biology and systems theory to enable rapid scientific 
progress in the new field of Systems Biology. Developers and users are warmly 
welcome to contribute and/or criticize and/or suggest priorities for further 
development!

SOSlib is already used for high-throughput integration of evolutionary models. 
It is programmed for use in analytic applications (such as parameter 
optimization or feedback and bifurcation analysis) and within hybrid or 
multi-scale solvers or merely as an efficient back-end for systems biological 
GUI tools, such as already implemented for the CellDesigner. The actual usage 
of the library has been and will be strongly influenced by user feedback and 
suggestions!

Please don't hesitate to contact us via one of the possibilities given at 
http://www.tbi.univie.ac.at/~raim/odeSolver/.

Rainer Machne
for the SOSlib development team (see 
http://www.tbi.univie.ac.at/~raim/odeSolver/credits/)


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