🔬 EMBOMicroCom2: Metabolite and species dynamics in microbial communities 🧬

💻 Metabolic modeling tutorial (Day 5)

📜 About

This repo hosts training materials for the second installment of EMBO's Practical Course Metabolite and species dynamics in microbial communities. 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.

Learning outcomes

Exercise 1

• 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
• 1.5: Run flux balance analysis (FBA)
• 1.6: Perform in-silico gene knockout experiments

Exercise 2

• 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

🚚 Software requirements

The following packages will already be installed on the provided machines:

• cobrapy
• matplotlib
• numpy
• notebook

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

Using the requirements.txt files:

$ pip install -r requirements.txt

Or from scratch:

$ pip install cobra matplotlib numpy notebook

🛠️ Usage

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.

Running locally

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

$ git clone https://github.com/franciscozorrilla/EMBOMicroCom2.git

Navigate into cloned repo folder:

$ cd EMBOMicroCom2

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.

Running on the cloud

Alternatively launch an interactive binder session by clicking below:

🧠 Further exercises

• metaGEM: Metagenomics-driven metabolic modelling tutorial using unseen bio samples
• SymbNET: From metagenomics to metabolic interactions
• EMBOMicroCom: Metabolite and species dynamics in microbial communities
• OLISSIPO: FBA and community simulations

👷 Contributors

• Updated by Francisco Zorrilla in September 2024
• Expanded by Francisco Zorrilla and Arianna Basile in January 2024
• Originally developed by Arianna Basile and Kiran Patil in January 2023

☎️ Contact

Feel free to get in touch with us by raising an issue or sending an e-mail to Francisco Zorrilla (fz274@cam.ac.uk).