SEDML_SWTCopasi

SED-ML WebTools & COPASI

SED-ML WebTools

In a first step, a default simulation with standard settings was created using SED-ML WebTools Version 2.4.

1. open SED-ML WebTools v2.4

2. upload SBML file (Bachmann2011.xml)

3. set Start Time 0, End Time 250 -> Simulate

4. download SED-ML file (DefaultSimulation.xml)

5. minor manual modifications (added label for all species, changed id for plot & report, changed file extension .xml -> .sedml) -> DefaultSimulation.sedml)

COPASI

The generated default simulation was then used to create a SED-ML file in COPASI v4.33 to reproduce Supplementary Figure 9.

1. open COPASI (COPASI 4.33 (Build 246))
2. import SBML file (Bachmann2011.xml)
3. import SED-ML file generated in SED-ML WebTools as described above (DefaultSimulation.sedml)
4. Plots: deleted default plot, added plots for all parameters included in Supplementary Figure 9
5. Tasks -> Time Course -> Run (results)

6. export SED-ML file (SuppFig9_COPASI.sedml)
7. validate SED-ML file in SED-ML WebTools as described here)
8. download amended SED-ML file from SED-ML WebTools (SuppFig9_COPASI.xml)
9. minor manual modifications (corrected model source, changed file extension .xml -> .sedml) -> SuppFig9_COPASI.sedml