Orientating Biochemical reactions in metabolic pathways and Networks.

This is the repostitory for Zephyr Serret Verbist's bachelor's thesis.

This study proposes an approach that utilizes ILP optimization to obtain a solution to the problem of minimizing the number of external vertices in a hypergraph, using the context of Metabolic Pathways.

What's in this repository?

1. An easy to use UI to rapidly orient and visualize pathways from the KEGG database.
2. The thesis' memoir and the source latex for the memoir.
3. The slides that were used to present the thesis during the presentation.

Using and setting up our GUI python program :

Installing the requirements :

AMPL

This project revolves around the AMPL model created for the author's TFG (Bachelor's Thesis).

To run this program you will need to sign up and install AMPL.

venv and python dependencies

Creating and activating the venv.

On windows

python -m venv venv
venv\Scripts\activate.bat

On Linux

python3 -m venv venv
source venv/bin/activate

Your terminal should look like this

(venv) tfg_python>

Then install the depencies

pip install -r requirements.txt

Running the Program

python3 App.py

Built With

• Tkinter - Python GUI
• AMPL - Mathematical Programming Language
• LaTeX - Document Preparation System

Authors

- Zephyr Serret Verbist

Acknowledgments

This work was supervised by Gabriel Valiente Feruglio. A special thanks to him for his guidance and support throughout the project.