

PREV NEXT  FRAMES NO FRAMES 
See:
Description
Packages  

org.simulator  This package simply contains a default main program to display very basic licensing terms and other information. 
org.simulator.gui  Contains classes that provide very basic functions that facilitate the creation of graphical user interfaces. 
org.simulator.gui.img  This package contains images and icons for the Simulation Core Library. 
org.simulator.io  Import and export of files. 
org.simulator.math  Classes that contain several mathematical operations. 
org.simulator.math.odes  The different solver classes that are all derived from AbstractDESSolver. 
org.simulator.sbml  Classes for storing and interpreting an SBML model. 
org.simulator.sbml.astnode  Classes for efficient numerical treatment of equations in form of abstract syntax trees. 
org.simulator.sedml  Classes for reading and executing SEDML files. 
The Java™ API Simulation Core Library comprises a collection of integrators for differential equation systems combined with an interpreter for the Systems Biology Markup Language (SBML). It is the first simulation library that is based on JSBML. The user can read an SBML model and simulate it with one of the provided numerical integration routines. All SBML levels and versions are supported. The library can easily be integrated into customized software, such as parameter estimation tools.
The Rosenbrock solver is best suitable for integrating stiff differential equation systems and also has a precise timing of SBML events. It is taken and adapted from Kotcon et al. Several solvers have been taken from the Apache Commons Math Library and wrapped into our library:
A model can be read in by using the SBMLReader class of JSBML. With the model in memory the SBMLinterpreter can create the differential equation system that provides the basis for simulation:
Model model = (new SBMLReader()).readSBML(sbmlfile).getModel();
SBMLinterpreter interpreter = new SBMLinterpreter(model);
The created differential equation system can then be simulated with a chosen solver and given time points. The result is stored in a data structure called MultiTable.
AbstractDESSolver solver = new RosenbrockSolver();
double[] timePoints = {0.0, 0.1, 0.2, 0.3, 0.4, 0.5};
MultiTable solution = solver.solve(interpreter, interpreter.getInitialValues(), timePoints);
The following example shows how to read in a File f (in SEDML format) and how to run a simulation described in this file afterwards. The simulation results are stored in a MultiTable.
SEDMLDocument doc = Libsedml.readDocument(f);
SedML sedml = doc.getSBMLModel();
Output wanted = sedml.getOutputs().get(0);
SedMLSBMLSimulatorExecutor exe = new SedMLSBMLSimulatorExecutor(sedml, wanted);
Map res = exe.runSimulations();
MultiTable solution = exe.processSimulationResults(wanted, res);
You just have to add the provided jarfile simulationcorelibrary.jar to the class path of your Java project. Then you have access to all classes of the library. This library depends on the following thirdparty libraries:
For SEDML support, the following additional libraries are required:You can run the simulation of the models in the SBML Test Suite by using the command below. TestSuiteDirectory denotes the directory containing your copy of the (entire) SBML test suite. Here we assume that the actual test cases are located in the subfolder cases/semantic/ within the TestSuiteDirectory on your computer. The simulation is conducted for the models with numbers from first to last (these numbers are the indices of the models in the test suite, without leading zeros).
java cp SimulationCoreLibrary_vX.Y_incllibs.jar org.simulator.SBMLTestSuiteRunner TestSuiteDirectory/cases/semantic/ first last
Please note that, you have to replace _vX.Y_ within the library's
name by the current release number, e.g., 1.2.
For example, if you like to simulate all test suite models ranging from 00259 to 00326, simply call the algorithm with first = 259 and last = 326.
Note that for the sake of a simple configuration, the simulation is started using default settings for the selection of the integration routine, step size etc.
In a similar way, you can also download and simulate all models from BioModels database:
java cp SimulationCoreLibrary_vX.Y_incllibs.jar org.simulator.TestBiomodels BioModelsDirectory/ first last
Again, you have to replace _vX.Y_ within the library's
name by the current release number, e.g., 1.2. Please use the variables
first and last without leading zeros as in the previous
case. The variable BioModelsDirectory gives the path to your local
copy of the BioModels database.
As in the previous case, the simulation is conducted using default settings.

Generated December 13 2012  
PREV NEXT  FRAMES NO FRAMES 