Self-study material for course "Metabolic Network modelling"

Project-based learning course on metabolic network modelling in computational systems biology

Thomas Sauter, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, Thomas Pfau, Patricia Martins Conde, Maria Pires Pacheco

Project-based learning (PBL) is a dynamic student-centred teaching method that encourages students to solve real-life problems while fostering engagement and critical thinking. Here, we report on a PBL course on metabolic network modelling that has been running for several years within the Master in Integrated Systems Biology (MISB) at the University of Luxembourg. This 2-week full-time block course comprises an introduction into the core concepts and methods of constraint-based modelling (CBM), applied to toy models and large-scale networks alongside the preparation of individual student projects in week 1 and, in week 2, the presentation and execution of these projects. We describe in detail the schedule and content of the course, exemplary student projects, and reflect on outcomes and lessons learned. PBL requires the full engagement of students and teachers and gives a rewarding teaching experience. The presented course can serve as a role model and inspiration for other similar courses.

For course concept and schedule see: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009711

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Suggested Plan

1. Setting Up: Start by setting up the necessary environment and tools.

   Directory: SettingUp

2. Basic Examples and Concepts: First approach based on the book 'Introduction to Systems Biology'.

   Directory: LecturesAndBasicExamples/BasicExample

3. Introduction to the COBRA Toolbox: Lectures and exercises introducing the COBRA Toolbox for computational biology.

   • Lectures Directory: LecturesAndBasicExamples/Cobra_Introduction/Lectures
   • Exercises Directory: LecturesAndBasicExamples/Cobra_Introduction/Exercises

4. Metabolic Modelling & Introduction to FASTCORMICS: Lectures and exercises covering metabolic modeling and an introduction to FASTCORMICS.

   • Lectures Directory: LecturesAndBasicExamples/MetabolicModelling_Fastcormics/Lectures
   • Exercises Directory: Contextualization/Reconstruction/Tutorial

5. Further Analysis: Explore advanced topics and additional resources to deepen your understanding.

   Directory: Contextualization, Analysis, DataProcessing & Visualisation