Introduction
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.
Prerequesites
Steps to follow
- So first, upload your model to the Databox.
- Then, create a new experiment.
- Import your resource
- Link it to the task available in the brick.
- Run your experiment
- Get your converted model on output into the JSON format


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