Format convertor from CSML 3.0 to SBML Level 2 Version 4.


Quick Start

  • Ensure that you have JDK1.6 (not JRE1.6) and above installed in advance.
  • Usage:
    1. From a command prompt (Windows) or terminal (Linux), go to the folder where you saved csml3-sbml24_converter.jar and sample.csml
    2. Enter and run the following command "java -jar csml3-sbml24_converter.jar sample.csml sample.sbml" (Note that users have to specify the CSML file name as the first argument and SBML file name as the second one)
    3. Open the resulting file(sample.sbml) on CellDesigner.
      • Select "Simulation" - "ControlPanel" of CellDesigner to investigate the dynamics in the case that the kinetic parameters are included in the CSML model.

Adjust simulation condition on CellDesigner

Since SBML only describes basic information of the model, when simulating an SBML model on CellDesigner, additional simulation information regarding simulation details such as simulation time (call End time in CellDesigner), sampling interval (call Num. of points in CellDesigner), chart setting are seperately saved in so-called SED-ML (Simulation Experiment Description Markup Language).
When one wants to perform the simulation, normally a ready-made SED-ML file is prepared to be loaded or one need to do a manual configuration.

Here we set the simulation condition by hand. Following figure demonstrates brief procedures to set simulation details and charts according to Cell Illustrator Online.