Community Modelling & Construction as a predictive tool for determining probiotic efficacy in poultry.
Data/: Contains metagenomic datasets, as well as manifest files used for simulation.micom_script.py: Python script for running MiCOM simulations.data/: Directory containing input data files.- Metabolic agora models (https://github.com/Gibbons-Lab/isb_course_2023)
- CarveFungi metabolic models (https://zenodo.org/records/7413265)
Results/: Directory containing output files.
The code in this repository relies on the following dependencies:
- MiCOM (version 0.33.2)
- CarveFungi (https://github.com/SandraCastilloPriego/CarveFungi)
- AutoPACMEN https://github.com/klamt-lab/autopacmen
For questions or inquiries, please contact
- Montazar Al-Nijir ([email protected])
We would like to thank the University of Bath's Research Computing Group for their support in this work. We would also like to thank Sandra Castillo for her help and advice during the use of CarveFungi and Paula Jouhten for her valuable advice and support. Finally this repository contains code adapted from the notebook "MiCOM 2023" by Gibbons Lab, available at: [https://colab.research.google.com/github/Gibbons-Lab/isb_course_2023/blob/main/micom_2023.ipynb]