Computational Systems Biology
Sauro Lab
University of Washington
Home  |   Downloads  |   News  |   Research  |   Papers  |   About Us  |   Contact Us  |   SBW Help   |   Jobs
     


What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
Courses 
Student Projects 
 
 
 
Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 
 

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.

:sbw:sbmltranslators:translators_main_600w.jpg

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/

Documentation & Help

 
sbw/sbmltranslators.txt · Last modified: 2007/02/03 13:08 (external edit)
 

    Home  |   About Us  |   Contact Us  |   Statistics
Recent changes RSS feed Creative Commons License Donate Powered by PHP Valid XHTML 1.0 Valid CSS Driven by DokuWiki