BIOENG-320 / 4 crédits

Enseignant(s): Hatzimanikatis Vassily, Barth Patrick Daniel

Langue: Anglais


Summary

This course will cover fundamentals and approaches at the interface of biology, chemistry, engineering and computer science for the design of biological systems at both theoretical and practical levels. The principal techniques used in diverse fields of synthetic biology will be introduced.

Content

Keywords

Gene networks, metabolic pathways, biological circuits, chemical biology engineering, protein design, cell engineering, genome engineering, computer simulation.

Learning Prerequisites

Recommended courses

Basic bachelor courses of Mathematics, Physics, Molecular Biology, Biochemistry, Chemical Biology, Computer programming

Important concepts to start the course

Gene expression & regulation, cell metabolism, chemical & structural biology of proteins, enzyme catalysis, biomolecular sensing, thermodynamics, kinetics, numerical analysis, informatics, signal processing

Learning Outcomes

By the end of the course, the student must be able to:

  • Understand and interpret the designs of natural cellular networks
  • Develop and apply softwares (e.g. Matlab, Cello) for modeling and designing genetic circuits and metabolic pathways
  • Use modern techniques in genome engineering for manipulating gene expression and rerouting cell programs
  • Devise and apply effective experimental/ computational protein design strategies for reprogramming and engineering cellular functions
  • Use modern chemical biology tools for selective reprogramming, perturbing, and probing cellular functions
  • Choose the appropriate method to tackle a problem
  • Design a synthetic biology project

Transversal skills

  • Set objectives and design an action plan to reach those objectives.
  • Assess one's own level of skill acquisition, and plan their on-going learning goals.
  • Continue to work through difficulties or initial failure to find optimal solutions.
  • Assess progress against the plan, and adapt the plan as appropriate.
  • Use both general and domain specific IT resources and tools
  • Write a scientific or technical report.

Teaching methods

Half of the course is based on lectures, while in the other half exercises, projects (computational) are provided to the students

Expected student activities

Attending lectures, completing exercises, reading assignments, presenting a scientific paper, doing a project, writing a report, presenting the results of a project

Assessment methods

Written exam during the exam session, exercises, (graded) mini project

Supervision

Office hours Yes
Assistants Yes
Forum Yes

Resources

Bibliography

Synthetic Biology: Parts, Devices and Applications (Eds: Christina Smolke Sang Yup Lee Jens Nielsen Gregory Stephanopoulos) 2018 Wiley‐VCH Verlag GmbH & Co. KGaA

Systems Biology: Simulation of Dynamic Network States 1st Edition (by Bernhard Palsson) 2011 Cambridge University Press

Systems Biology: A Textbook 2nd Edition (by Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald) Wiley-Blackwell; 2 edition (June 27, 2016)

Ressources en bibliothèque

Dans les plans d'études

  • Semestre: Printemps
  • Forme de l'examen: Ecrit (session d'été)
  • Matière examinée: Synthetic biology
  • Cours: 2 Heure(s) hebdo x 14 semaines
  • Exercices: 2 Heure(s) hebdo x 14 semaines
  • Semestre: Printemps
  • Forme de l'examen: Ecrit (session d'été)
  • Matière examinée: Synthetic biology
  • Cours: 2 Heure(s) hebdo x 14 semaines
  • Exercices: 2 Heure(s) hebdo x 14 semaines
  • Semestre: Printemps
  • Forme de l'examen: Ecrit (session d'été)
  • Matière examinée: Synthetic biology
  • Cours: 2 Heure(s) hebdo x 14 semaines
  • Exercices: 2 Heure(s) hebdo x 14 semaines

Semaine de référence

 LuMaMeJeVe
8-9     
9-10     
10-11     
11-12     
12-13     
13-14     
14-15     
15-16     
16-17     
17-18     
18-19     
19-20     
20-21     
21-22