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Table 2 Comparison of SBML-capable simulators

From: The systems biology simulation core algorithm

Program Version   Difficult SBML   Fully SBML test SED-ML Programming GUI API Platform Comments
    elements   Suite compliant   language   access   
   Fast Algebraic Events        
   reactions rules         
BioUML 0.9.4 In α Java JavaScript Independent  
COPASI 4.9.45 () C++ (with Windows, Mac OS X,  
        multiple bindings)    Linux, Solaris  
iBioSim 2.4.5 In α Java, C () Windows, Mac OS X,  
       version     Linux (Fedora 17)  
JSim 2.10 Java Windows, Mac OS X,  
LibSBMLSim 1.1.0 () C (with multiple) Windows, Mac OS X,  
        bindings)    Linux, Free BSD  
Simulation 1.3 Java Independent  
core library            
VCell 5.0 Java frontend, Independent Internet
        C/C++ server     connection
        backend     required
  1. The table gives an overview about the most characteristic features of SBML-capable simulation programs (April 19th 2013). It shows which programs support the SBML elements fast reactions, algebraic rules, and events. Another key point is whether all models of the most recent SBML Test Suite[24] can be correctly solved. Note that in the SBML Test Suite column, a dash means that not all of its models can be correctly solved, because not all SBML elements are supported. LibSBMLSim, which is a simulation API written in C, can only read models given in SBML Level 2 Version 4 and SBML Level 3 (indicated by the checkmark in brackets). Similarly, a dash in the column for events means that not all possible cases for this language element can be correctly solved. COPASI, for instance, supports events in SBML, but not all of the current constructs. It should be mentioned that not all programs primarily focus on the use of ODE solvers. In iBioSim, for instance, the stochastic analysis of SBML is more important[52]. Furthermore, some programs such as VCell or COPASI do not use SBML as their native format. BioUML, iBioSim, and the Systems Biology Simulation Core Library, are the only simulation tools from this selection that pass all models of the SBML Test Suite across all levels and versions of SBML. Most programs provide direct access to their API. COPASI, LibSBMLSim, and the Systems Biology Simulation Core Library have particularly been designed for the use as a solver backend. The program iBioSim can be executed in a script, e.g., for batch processing of multiple models.