Converting a SBML/Matlab metabolic model to BiGG JSON format

Maëva Beugin
May 5, 2023, 2:46 PM

Co-authors : 


Genome-scale metabolic modelling is the formalism for the reconstruction and use digital twins of cell metabolisms. It is a core technology embedded into Constellab. Today, several file formats exist to save genome-scale metabolic models (GEM).
The official format is the sbml (saved asxml file). An other commont format is the mat format create with Matlab. However, the json proposed by the BiGG database (http://bigg.ucsd.edu/) has recently gain more and more interests in the community because it is simpler (human readable) and easy to use with modern open programming languages.

You have a genome-scale metabolic model from a database in the the smbl or mat and you want to put it on Constellab?
You are in the right place!
Constellab is natively complaint with metabolic models in JSON format. Before you can take full advantage of Constellab, you will need to follow this tutorial to convert your smbl or mat model in JSON format.
If your model is in SBML format, first check that the model is valid (in terms of syntax and internal consistency) by uploading it to this site: Online SBML Validator


Check that the file extension of your model is xml or mat depending on whether the model is in SBML or Matlab format respectively.

Steps to follow

  1. Ensure that the "gws_gena" brick is loaded
  2. So first, upload your model to the Databox.
  3. Then, create a new experiment.
  4. Import your resource
  5. Link it to the "XML/Matlab to JSON" task available in the "gws_gena" brick.
  6. Run your experiment
  7. Get your converted model on output into the JSON format

This demonstration was done using task from the brick gws_gena in version 0.5.1.