Context-specific Reconstruction Pipeline

A generic pipeline to reconstruct context-specific models using Troppo.

Usage

To run the pipeline, run troppo_reconstruction_pipeline.py script. This pipeline requires some arguments to be passed to it, which can be adapted to the user's needs in three different files:

• utils/config_variables.py - contains the configuration of the pipeline.
• utils/medium_variables.py - contains the medium composition to be used by the model.
• utils/pipeline_paths.py - contains the paths to be using by the pipeline. Including, model files, data files, and output paths.

Author

• Alexandre Oliveira - Developer - ao60337