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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

 
      

version

     

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,

 
          

Linux

 

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.