Simple OMEX example¶

This notebook an example for creating a COMBINE archive. A COMBINE archive is a bundled package containing all the necessary documents and relevant information for a modeling and simulation project, ensuring that all components are conveniently stored together. The archive is encoded using the Open Modeling EXchange format (OMEX).

1) Including libraries¶

Note: Please change the colab flag to True if you are using Google Colab.

In [2]:

colab = False
if colab:
  !pip install git+https://github.com/combine-org/combine-notebooks
  !git clone https://github.com/combine-org/combine-notebooks
  %cd /content/combine-notebooks/notebooks

In [38]:

from pathlib import Path

from pymetadata.console import console
from pymetadata.omex import EntryFormat, ManifestEntry, Omex

from combine_notebooks import RESULTS_DIR

2) Creating a COMBINE archieve¶

Creating an empty archive and adding entry for SBML.

In [39]:

# Create OMEX archive of resources.
omex = Omex()

Get the file location of our results files. These were generated by other notebooks in this repositiory. The files we will be adding to our OMEX file include:

hello_world_sbml.xml - a simple SBML model
hello_world_cellml.cellml - a simple CellML model
hello_world_sbgn.png - a diagram showing a simple reacton that has been generated using SBGN
hello_world_sbgn.sbgn - correponding SBGN used to generate the .png file
hello_world_sedml.sedml - a simple simulation experiment described using SED-ML

In [40]:

# Path to our results
results_dir =  Path(RESULTS_DIR.stem)

First, lets add our simple SBML file into the COMBINE archieve.

In [41]:

# Add entry for the SBML model
omex.add_entry(
    entry=ManifestEntry(
        location="./sbml/hello_world_sbml.xml",
        format=EntryFormat.SBML_L3V2,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sbml.xml",
)

Now we'll add our simple CellML model.

In [42]:

# Add entry for the CellML model
omex.add_entry(
    entry=ManifestEntry(
        location="./cellml/hello_world_cellml.cellml",
        format=EntryFormat.CELLML,
        master=False,
    ),
    entry_path=results_dir / "hello_world_cellml.cellml",
)

Next lets add entries for both our SBGN file and the png that it generated.

In [43]:

# Add entry for SBGN file
omex.add_entry(
    entry=ManifestEntry(
        location="./sbgn/hello_world_sbgn.sbgn",
        format=EntryFormat.SBGN,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sbgn.sbgn",
)

# Add entry for corresponding png file generated from the SBGN
omex.add_entry(
    entry=ManifestEntry(
        location="./sbgn/hello_world_sbgn.png",
        format=EntryFormat.PNG,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sbgn.png",
)

Finally, we will add a SED-ML file to the COMBINE archieve.

In [44]:

# Add entry for the SEDML simulation experiment
omex.add_entry(
    entry=ManifestEntry(
        location="./sedml/hello_world_sedml.sedml",
        format=EntryFormat.SEDML,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sedml.sedml"
)

3) Write and print the COMBINE archieve¶

And we're done creating the OMEX file. Now lets save it.

In [45]:

RESULTS_DIR.mkdir(parents=True, exist_ok=True)
omex_path = RESULTS_DIR / "combine_hello_world.omex"
omex.to_omex(omex_path)

We can also use the console.print function to display the comtent of the OMEX file.

In [46]:

console.print(omex)

[   ManifestEntry(location='.', format='http://identifiers.org/combine.specifications:omex', master=False),
    ManifestEntry(location='./manifest.xml', format='http://identifiers.org/combine.specifications:omex-manifest', 
master=False),
    ManifestEntry(location='./sbml/hello_world_sbml.xml', 
format='http://identifiers.org/combine.specifications:sbml.level-3.version-2', master=False),
    ManifestEntry(location='./cellml/hello_world_cellml.cellml', 
format='http://identifiers.org/combine.specifications:cellml', master=False),
    ManifestEntry(location='./sbgn/hello_world_sbgn.sbgn', 
format='http://identifiers.org/combine.specifications:sbgn', master=False),
    ManifestEntry(location='./sbgn/hello_world_sbgn.png', format='https://purl.org/NET/mediatypes/image/png', 
master=False),
    ManifestEntry(location='./sedml/hello_world_sedml.sedml', 
format='http://identifiers.org/combine.specifications:sed-ml', master=False)]