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Quantitative Viral Dynamics

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M2_E35_Quantitativeviraldynamics_schedule_2021_2022

PSL Master in Life Sciences - ENS IMaLiS
Bio-M2_E35 | Quantitative Viral Dynamics
Year and Semester : M2 | S1
Duration : 30 hours
First and last day of class : November 29th - December 3rd, 2021
Hours : 9am-12pm, 2pm-5pm
Venue : ENS Biology Department

Coordination

Joshua Weitz (ENS Chaire Blaise Pascal, Georgia Tech)
François Blanquart (CNRS & ENS Département de Biologie)

Credits

3 ECTS

Keywords

Viral life cycle | Viral life-history traits. Viral ecology (e.g., phage-bacteria) | Within-host dynamics (e.g., HIV) | Epidemic dynamics (e.g., SARS-CoV-2).

Course Prerequisites

The course is targeted to interdisciplinary audiences, including students with background in ecology, evolutionary biology, life sciences, physics, mathematics, engineering, and/or computing, with experience and interest in mathematical modeling. Participants are welcome given the following prerequisites :
• Introductory ecology : population dynamics, population regulation (density-dependence), exponential growth, logistic model, Lotka-Volterra model.
• Basic systems modeling : non-linear differential equations, equilibrium, stability analysis.
• Some experience in programming (Python, MATLAB or R).

Course objectives and description

The course presents a theoretical foundation from which to model and predict the ecological and evolutionary dynamics that result from the interaction between viruses and their hosts, both microbial and human. The course will present foundational principles and applications of viral ecology and evolution in bacteria populations, epidemiological dynamics of endemic and emerging viruses in human populations, and the models used to understand and control viral dynamics. Finally, the course will present how genomic data can give insights into the origins, epidemiological dynamics and spatial spread of pathogens. In doing so, students will learn more about how to link mechanisms of virus-host interactions across scales from cells to populations.

Organization : This is a one-week intensive course. Lecture-style presentations will be complemented by computer-based tutorials. In the tutorial sessions, students will work to implement the theory and numerically study model examples. This will involve the guided writing of simple code in Python.

This is a one-week intensive course. Lecture-style presentations will be complemented by computer-based tutorials. In the tutorial sessions, students will work to implement the theory via the numerically study of model examples. Tutorials will involve the guided development of simulations and analysis in Python and/or R. The course is targeted to interdisciplinary audiences, including students with background in the life sciences, physics, mathematics, engineering, and/or computing.

Assessment

Evaluation is based on the students presenting the work they carried out in the tutorial sessions. The presentations will take place at the end of the week.

Register

The course is open to selected non-IMaLis Master’s and PhD students. To apply, please send a 1-page CV and brief letter of motivation to François Blanquart no later than 31st October.

Course material

Readings, slides, computer simulation tutorial and video-recorded presentations will be made available to enrolled students.

Suggested readings

Weitz JS (2016) Quantitative Viral Ecology : Dynamics of Viruses and their Microbial Hosts. Monographs in Population Biology, Princeton University Press.