SBML Translators
The SBW translators take an SBML file containing a model of a biochemical network and generate files containing the translated models that are compatible for use in another programming language or application. MATLAB, Oscill8 (via the XPP translator), FORTRAN, C, C#, and Java are currently supported. The Translators for C, C# and Java generate model code that can be executed much faster than MATLAB. This is useful in running simulations of large models.
MATLAB Translator
XPP Translator
The XPP translator converts the description of a biochemical network in SBML to ODE format as required by Oscill8. This is done by identifying the conservation relations in the network (using the Conservation module) and extracting the differential equations for the independent species.
FORTRAN Translator
C Translator
The SBML to C Translator encapsulates the model described by SBML into C functions. The model is represented as set of ordinary differential equations. The translator can also generate a hosting application that can be linked to the model file to generate a complete simulation package. The generated hosting application uses the 4th order Runge-Kutta Method or a system of ODEs with initial conditions the simulate the model.
C# Translator
The SBML to C# Translator encapsulates the model described by SBML into a C# class. The model is represented as set of ordinary differential equations. The translator can also generate a hosting application that can be linked to the model file to generate a complete simulation package. The generated hosting application uses the 4th order Runge-Kutta Method or a system of ODEs with initial conditions the simulate the model.
The current version of the SBML to C# Translator (3.00) has functionality to reduce the order of the system by eliminating dependent species from the network.
Java Translator
The SBML to Java Translator encapsulates the model described by SBML into a Java class. The model is represented as set of ordinary differential equations. The translator can also generate a hosting application that can be linked to the model file to generate a complete simulation package. The generated hosting application uses the 4th order Runge-Kutta Method or a system of ODEs with initial conditions the simulate the model.
Installation
The SBML Translators are fully supported on Windows, Mac, and Linux.
The Matlab, XPP, and FORTRAN Translators are installed with SBW, which can be downloaded from http://sys-bio.org/research/sbwIntro.htm
The C, C#, and Java Translators must be downloaded and installed separately. SBW must be installed before installing these translators. Running the executable will install the translators and register them with SBW. The translators can be downloaded from http://public.kgi.edu/~rrao/SBMLTranslators/