Synthetic biology
Summary
This advanced Bachelor/Master level course will cover fundamentals and approaches at the interface of biology, chemistry, engineering and computer science for diverse fields of synthetic biology. This class requires critical and analytical thinking at the frontiers of multiple disciplines
Content
- Gene network engineering: Methods for reconstructing gene networks from genome annotation. Computational approaches for synthetic gene circuits.
- Protein engineering: state of the art computational and experimental approaches to protein design, their application to the engineering of novel molecular tools for synthetic biology (e.g. biocatalysts) and biomedicine (e.g. biosensors for cancer immunotherapies) will be covered.
- Chemical biology engineering: this component will focus on cutting-edge chemical biology tools that address pressing problems in human health, €”from identifying druggable molecular targets and novel mechanism-of-action, to engineering modern small-molecule-based targeted therapies.
- Signalling pathways and cell engineering: recent progress and challenges in the rational design of signaling pathways toward the reprogramming of cellular functions in diverse cell types including bacteria, yeast and vertebrate cells will be discussed.
Keywords
Gene networks, metabolic pathways, biological circuits, chemical biology engineering, protein design, cell engineering, computer simulation.
Learning Prerequisites
Required courses
Basic bachelor courses of Mathematics, Physics, Molecular Biology, Biological Chemistry, Computer programming, and for SV Bachelor students the following specific class: Dynamical systems in Biology (BIO-341)
Recommended courses
Genetics & Genomics (BIO-373) and Cell and Developmental biology for engineers (BIO-221)
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
- Apply softwares for modeling and designing genetic circuits and metabolic pathways
- Devise and apply effective experimental/ computational protein design strategies for reprogramming and engineering cellular functions
- Understand modern chemical biology tools for selective reprogramming, perturbing, and probing cellular functions
- Choose the appropriate method to tackle a problem
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
Assessment methods
Written exam during the exam session
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 Wileyâ€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)
Papers assigned during the course
Ressources en bibliothèque
- Systems Biology: Simulation of Dynamic Network States
- Synthetic Biology: Parts, Devices and Applications (
- Systems Biology: A Textbook
Moodle Link
In the programs
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Synthetic biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional