Computational Bioengineering

Instructors

Practical information

The course will be given in English. The sessions will take place on Monday from 1:15pm to 5:30pm Paris time at ENS Paris-Saclay in room TBA, and online for remote participants. Classes start on September 15, 2025.

Important: This is a flipped class. Pre-reading of the lecture notes will be expected before each session.

Registration

For on-campus partication, please register through your department or contact us. For online participation, please fill out the registration form.

Prerequisites

No previous knowledge of biology or chemistry is required. The following will be helpful, however:

basic algorithmics and programming (we'll program in Python)
basic graph theory definitions
basic circuit theory (notions like NAND, NOR shouldn't scare you)
basic probability theory
vocabulary of ordinary differential equations

Motivations and main objectives

Bioengineering is a rising discipline with applications in bioproduction, pharma, environmental sciences, and medicine. It inherently requires skills from biology, computer science, control theory, and other fields of engineering. The course will feature experimental data from spectroscopy and microscopy, mathematical modeling, compilation, control, and optimization of an example process.

Related courses

Bibiography

Uri Alon, An Introduction to Systems Biology, 2nd edition, CRC Press, Boca Raton, 2019.
Bruce Alberts et al., Molecular Biology of the Cell, 7th edition, W. W. Norton & Company, New York, 2022.
Jennifer A. N. Brophy and Christopher A. Voigt, Principles of genetic circuit design, Nature Methods 11(5):508-520, 2014.
Alec A. Nielsen et al., Genetic circuit design automation, Science 352(6281), 2016.
M. Omar Din et al., Synchronized cycles of bacterial lysis for in vivo delivery, Nature 536:81-85, 2017.
Michael J. Diao, M. Omar Din, Lev Tsimring, and Jeff Hasty, Rock-paper-scissors: engineered population dynamics increase genetic stability, Science 365(6457):1045-1049, 2019.

session	date	topic	notebook
1	September 15, 2025	Introduction	(html) (ipynb) (zip)
2	September 22, 2025	Chemical Reaction Networks	(html) (ipynb) (zip)
3	September 29, 2025	Distributed Algorithms, Majority Consensus	(html) (ipynb) (zip)
4	October 6, 2025	Genetic Control	(html) (ipynb) (zip)
5	October 13, 2025	Logic Gates	(html) (ipynb) (zip)
6	October 20, 2025	Oscillators	(html) (ipynb) (zip)
7	November 3, 2025	CRN Modeling with MobsPy	(html) (ipynb) (zip)
8	November 10, 2025	Stochastic Simulation	(html) (ipynb) (zip)
9	November 17, 2025	Plasmid Design	(html) (ipynb) (zip)
10	November 24, 2025	Parameter Estimation	(html) (ipynb) (zip)
11	December 1, 2025	Measurements	(html) (ipynb) (zip)
12	December 8, 2025	Computer Vision for Microscopy	(html) (ipynb) (zip)
13	December 15, 2025	TBA	(html) (ipynb) (zip)

session	problem	notes
1	Modeling	(html) (ipynb) (zip)
2	Birth-Death Processes	(html) (ipynb) (zip)
3	Majority Consensus	(html) (ipynb) (zip)
4	Genetic Control	(html) (ipynb)
5	Logic Gates	(html) (ipynb)
6	Oscillators	(html) (ipynb) (zip)
7	CRN Modeling with MobsPy	(html) (ipynb) (zip)
9	Plasmid Design	(html) (ipynb) (zip)
10	Parameter Estimation	(html) (ipynb) (zip)
11	Measurements	(html) (ipynb) (zip)

number	due date	notes