EuroMix model to SBML

This repository contains a re-implementation of the EuroMix PBK model in Antimony and demonstrates how this Antimony model implementation is automatically converted to an annotated Systems Biology Markup Language (SBML) file using the SBML PBK workflow. The purpose of this re-implementation is to demonstrate how to create and publish interoperable PBK models using the EuroMix PBK model as example.

Reimplementation in Antimony

The model was re-implemented in Antimony, see file euromix.ant. Notebook validateantimonymodel.ipynb shows the results of the validation comparison with the results obtained by the R/MCSim/deSolve implementation. The results of the R simulation and the SBML simulation (using libroadrunner in Python) match.

Model annotation

Annotations of the model and its element are specified in the file euromix.annotations.csv. This annotations file links the different model elements (e.g., compartments and parameters) to ontological terms and specifies the units of measure. For the annotations of modelling terms, the PBPK ontology is used. For the annotation of the units of measure, the UCUM notation is adopted.

Note that the Antimony format also allows for specification of units and annotation of model elements directly in the Antimony file. However, it was decided to keep them in a separate csv file to keep the Antimony file cleaner/simpler/easier to read.

SBML conversion and SBML model annotation

Conversion to an annotated SBML file is done automatically using the SBML PBK workflow. This workflow follows several steps. It first converts the Antimony model implementation to SBML. Then, it annotates this SBML file using the annotations specified in the euromix.annotations.csv file. After this, it runs validation scripts on the generated SBML file to check for consistency and completeness (e.g, of the units). Finally, it publishes the generated SBML file (and log files) as build artifacts and adds/updates the generated/updated SBML file (euromix.sbml) in this repository.

Demonstration of use

The generated annotated SBML file is considered to be the interoperable digital object that can be used/re-used by others. Notebook getsbmlmodel_info.ipynb shows how information can be retrieved from the annotated SBML model file (e.g., units, differential equations, diagrams, semantic annotations). Notebook runsbmlmodel.ipynb demonstrates how to run the SBML model.

Running the notebooks

To run the Jupyter notebooks, install Jupyter notebook and the the required python packages. Install notebook and the required python packages using the command:

pip install -r requirements.txt