SEDML Support

How to Translate back and forth from SED-ML/COMBINE Archive to Python script
 1.1 Introduction

Both SED-ML and Combine Archive have been proposed to ensure reproduction and distribution of simulation experiments. SED-ML (Simulation Experiment Description Markup Language) file is XML-based description of simulation setup. Combine Archive is ZIP based archive file that contains everything related to the simulation experiment, including, but not limited to, SBML model, SED-ML file, and associated data files. For the full specification, to go SED-ML and COMBINE Archive.

1.2 Translation from SED-ML/COMBINE to Python

The Import SED-ML and Import Combine Plugins are designed to provide simple, fast, and human/machine-readable translation from either .sedml/.xml or COMBINE archive files to readily executable python script. The plugins are fully integrated into Spyder for Tellurium since version 1.1.6. For more information on how to use the plugins, see Spyder Plugins.

1.3 Translation from Python to SED-ML/COMBINE

Currently, translation from Python to SED-ML/COMBINE is limited to the usage of PhraSED-ML. When a simulation setup is defined in PhraSED-ML language, it is simple to translate the simulation setup along with SBML file into a COMBINE archive. Following example shows how to export a model and a simulation setup into a COMBINE archive called ‘combineexmaple.omex’ using tellurium’s ‘experiment’ module.

import tellurium as te

antstr = '''
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''

phrastr = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''

exp = te.experiment(antstr, phrastr)

# Export as combine archive
exp.exportAsCombine('./combineexmaple.omex')