SEDML_Test

Testing of SED-ML files

Testing SED-ML files in a different environment or using different tools is of great importance to ensure reproducibility and interchangeability. This page describes the performed validation and testing tasks.

Simulating the COMBINE archive using Tellurium

After integrating the generated SED-ML files into the COMBINE archive as described here, the first version of the COMBINE archive was downloaded from COMBINE Archive Web (bachmann.omex). The omex file was then loaded and executed using Tellurium.

import os
import tellurium as te

workingDir = _(directory containing the omex file)_
omex_path = os.path.join(workingDir, 'bachmann.omex')
output_directory=os.path.join(workingDir, 'output/')
te.sedml.tesedml.executeCombineArchive(omex_path, workingDir, printPython=True, createOutputs=True, saveOutputs=True, outputDir=output_directory)

The results, including plots (.png / .pdf) and model data (.csv), were added to the final version of the COMBINE archive (./result), with separate subfolders for each SED-ML file (i.e. each figure).

Interchangeability of validated SED-ML files

1. The SED-ML files Fig3.sedml and SuppFig9.sedml to generate the plots for Figure 3 and Supplementary Figure 9, respectively, were loaded into COPASI v4.33 together with the model. The results of the time course simulation can be found here, including plots (.png), model data (.txt) and COPASI files (.cps).
2. All SED-ML files created in Tellurium (Fig3.sedml, Fig4.sedml, Fig5.sedml, SuppFig9.sedml) were loaded into SED-ML WebTools v2.4 together with the model and simulated. The results, including plots (.png) and model data (.xml), were downloaded as a COMBINE archive, extracted and can be found here, with separate subfolders for each figure. Unfortunately, the .xml files could not be uploaded into the final COMBINE archive at this stage(see issue #72).