This repository pertains to the Chapter "Prediction of source nutrients for microorganisms using metabolic networks", in the book Computational Methods for Molecular Microbiology (Springer, upcoming).

It contains two files:

1. A zip file (seed_inference_tutorial.zip), which contains the necessary files for running the seed inference tutorial. This includes two python scripts, two bash scripts, four text files, and two SBML metabolic models, in the directory structure outlined below.

2. A docker image (docker-image-seeds.tar), which includes the contents the zip file, as well as the conditions and configurations for running the commands using docker. This can be loaded with the command docker load -i docker-image-seeds.tar

Tutorial directory structure:

. ├── LICENSE.md ├── objective │   ├── iCN718_target.txt │   └── toy-model_target.txt ├── README.txt ├── sbml │   ├── iCN718.xml │   └── toy-model.xml ├── scripts │   ├── cobra_seedsearch │   │   ├── cobra_seedsearch.py │   │   └── run_cobra_seedsearch.sh │   └── met_get │   ├── met_get.py │   └── run_met_get.sh └── target ├── iCN718_targets.txt └── toy-model_targets.txt