This repo hosts training materials for the OLISSIPO Winter School Mathematical modelling of inter-cell and communities’ interactions with a focus on metabolism. More specifically, these are practical exercises for the computational session on flux balance analysis (FBA) using genome-scale metabolic models (GEMs). Some of the text and code chunks in the following exercises are based on selected portions of the cobrapy documentation.

• 1.1: Import a metabolic reconstruction
• 1.2: Inspect the reactions of your model
• 1.3: Inspect the metabolites in your model
• 1.4: Inspect the genes in your model
• 1.4.1: Perform in-silico gene knockout experiments

• 2.1: Modify growth medium of your reconstruction
• 2.2: Perform gene essentiality analysis under different conditions
• 2.3: Case study, simulate the Crabtree effect in yeast

• 3.1: Build a 2 members community
• 3.2: Perform community-based simulations
• 3.3: Basics of pandas to analyse exchanges
• 3.4: Modify growth medium of your community

Please install these packages on your own laptop if required:

• cobrapy
• matplotlib
• numpy
• notebook
• micom
• pandas
• os

To install on your own computers use the pip package manager.

Using the requirements.txt files:

$ pip install -r requirements.txt

You will find everything you need for these practical exercises under the /notebooks folder. Each tutorial is uploaded as .html, .md, .tex, and .ipynb files. As you carry out the exercises using the the python notebooks, you will find the original text and results in the html, markdown, and latex files.

You may run these exercises on your local machine by cloning this repo:

$ git clone https://github.com/arianccbasile/FBA_OLISSIPO_Winter_School/tree/main

Navigate into cloned repo folder:

$ cd FBA_OLISSIPO_Winter_School

Launch interactive jupyter notebook session:

$ jupyter notebook

This should launch a browser window, where you can click on the /notebooks folder and start the exercises.

• SymbNET: From metagenomics to metabolic Interactions
• EMBOMicroCom: Metabolite and species dynamics in microbial communities

• Originally developed by Arianna Basile and Kiran Patil in 2023
• Updated by Francisco Zorrilla and Arianna Basile in 2024
• Community modelling added by Arianna Basile in 2024

Feel free to get in touch with us by raising an issue or sending an e-mail to Arianna Basile ([email protected])