The Systems Biology Simulation Core Library

Roland Keller, Alexander Dörr, Andreas Dräger, et al.

The modelling language SBML (Systems Biology Markup Language) is the most important standard for the exchange of biochemical network models. A model stored in SBML can be interpreted as an ordinary differential equation system, which is the basis for numerical simulation. Besides rate laws, SBML contains additional elements such as rules and events. Because of many special cases, the interpretation of SBML is difficult. The Systems Biology Simulation Core Library (SBSCL) is implemented in Java and provides several numerical integration routines in connection with an algorithm for the interpretation of SBML. The implementation is based on the Java library JSBML , a specifically developed data structure to read and write models from and into SBML files and to deal with their structure in memory. The SBSCL can be used on every operating system for which a Java Virtual Machine is available. It can easily be integrated as an API (Application Programming Interface) into third-party programs. Current examples are SBMLsimulator and CellDesigner (since version 4.2). The library successfully simulates the 424 curated models from the BioModels Database (release 23, October 2012). Furthermore, SBML Test Suite version 2.3.2 is completely supported.

The following class diagram shows that the interpretation of SBML is separated from the numerical simulation, which simplifies implementation of support for other model formats:

Class diagram

Availability: The library can be downloaded at the project website. A documentation is also available there.


Please cite: Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A: The systems biology simulation core algorithm. BMC Systems Biology 7(55), 2013.


Contact: Roland Keller, Tel.: (07071) 29-76462, roland.keller (at) uni-tuebingen.de


This project is promoted by:

BMBF Virtual Liver