2. Reading and writing model files

A SKiMpy model can be saved and edited using YAML, allowing users to curate large model files in a human-readable fashion. Additionally we support importing and exporting models from and to SBML format.

Function to save and load YAML model are encoded in the skimpy.io.yaml module

# Loading a yml model
from skimpy.io.yaml import load_yaml_model
kmodel = load_yaml_model('/skimpy/models/kin_varma.yml')

# Exporting a SKiMpy model to yml
from skimpy.io.yaml import export_to_yaml
export_to_yaml(kmodel, 'test.yml')

Function to save and load SMBL model are encoded in the skimpy.io.yaml module

# Exporting a SKiMpy model to SBML
from skimpy.io.sbml import export_sbml
export_to_yaml(kmodel, 'test.sbml')

# Loading a SBML model
from skimpy.io.sbml import import_sbml
kmodel = import_sbml(kin_varma.sbml')

It should be noted here that the SMBL format does not permit to preserve the object oriented structure of the model. Thus a generic mechanism is used which cannot be exported into the prefered (Human readable) yaml format.