Command Line Interface

This notebook shows the command line interface of yaml2sbml, using the “Lotka Volterra” example. For details on * the definition of the .yaml file * simulation of the SBML model using AMICI (Python) * fitting the PEtab problem using pyPESTO (Python),

see the corresponding notebook

YAML validation:

yaml2sbml allows to validate the input YAML via

yaml2sbml_validate <yaml_inout_file>

!yaml2sbml_validate ../Lotka_Volterra_python/Lotka_Volterra_basic.yml

Path to yaml file: ../Lotka_Volterra_python/Lotka_Volterra_basic.yml
Validating...
YAML file is valid ✅

SBML generation

yaml2sbml generates an **SBML** via

yaml2sbml <yaml_input_file> <sbml_output_file>

!yaml2sbml ../Lotka_Volterra_python/Lotka_Volterra_basic.yml Lotka_Volterra_basic.xml

Path to yaml file: ../Lotka_Volterra_python/Lotka_Volterra_basic.yml
Path to sbml file: Lotka_Volterra_basic.xml
Converting...

PEtab generation:

The basic way of generating **PEtab** tables is given by

yaml2petab <yaml_input_file> <petab_output_directory> <model_name>

# create target directory, if it doesn't exist yet
!mkdir -p ./Lotka_Volterra_PEtab/
# needed .yml /measurement files in current directory.
!cp ../Lotka_Volterra_python/Lotka_Volterra_PEtab/measurement_table.tsv ./Lotka_Volterra_PEtab/
!cp ../Lotka_Volterra_python/Lotka_Volterra_PEtab.yml .

# This is the actual command
!yaml2petab Lotka_Volterra_PEtab.yml ./Lotka_Volterra_PEtab Lotka_Volterra

Path to yaml file: Lotka_Volterra_PEtab.yml
Output directory: ./Lotka_Volterra_PEtab
Path to sbml/petab files: Lotka_Volterra
Converting...

Further Options:

Two further optional arguments to the yaml2petab command allow to create a PEtab yaml file and a measurement table. A PEtab yaml allows for a easier input of a PEtab problem to some toolboxes: * In the directory , given by --petab_yaml, a yaml file, that groups the PEtab problem, will be created. * --measurement_table allows to specify the measurement table. This option is only possible in combination with --petab_yaml.

# now generate the PEtab table:
!yaml2petab Lotka_Volterra_PEtab.yml ./Lotka_Volterra_PEtab Lotka_Volterra --petab_yaml petab_problem.yml --measurement_table measurement_table.tsv

Path to yaml file: Lotka_Volterra_PEtab.yml
Output directory: ./Lotka_Volterra_PEtab
Path to sbml/petab files: Lotka_Volterra
Converting...

Checking the PEtab files

Finally, PEtab offers a PEtab-linter (no output = no error found). (This is a feature of the PEtab python library, not of yaml2sbml.)

!petablint -vy Lotka_Volterra_PEtab/petab_problem.yml

Checking SBML model...
Checking measurement table...
Checking condition table...
Checking observable table...
Checking parameter table...
OK