Computational biology II: assessment

You will be assessed through:

Programming labs

To be done individually or in pair of students. Send a jupyter notebook to the lecturer (antoine.frenoy@univ-grenoble-alpes.fr) containing your code and graphs with comments before the deadline. Beyond programming, pay attention to the quality of the graphs and their interpretation (you must clearly describe them and conclude).

Common rules for project OR article presentation

You can work alone or in a team of two students. You will indicate here your choice of team and activity (project or one of the proposed articles), before 2024-12-20.

General rules:

Project

The goal is to design and implement simple individual-based simulations of evolution, and use it to study phenomena discussed during this course.

Suggested ingredients and design choices of the model:

Main question: you will then use this model to study the selection for (or against) mutator alleles (Chao and Cox, 1983, Taddei et al, 1997).

Additionally, you may if you want include the study of other factors and their effects on selection for / against mutator alleles, such as : - Effect of population size - Effect of environmental changes - Effect of spatial structure

You will send a short report, which should clearly describe your modeling choices as well as the obtained results (with relevant figures). Strict deadline: 2025-01-31.

Article presentation

You will choose an article among the list below (on a first come first served basis) and present it in front of the class (max 12 min presentation + 5 min questions). Your presentation should include a broad overview of the topic, explain the impact of the ideas and the connection with the class, and make the main ideas understandable by a non-specialist audience. The target audience is the other students of the class (math and cs students), not the lecturer.

Beware that presenting a research article is not an easy task, and the article presentation should not be considered as an easy alternative to the project. A substantial reading work is expected: it is likely that you will have to read further than the original article to be able to fully understand it and its scientific context.

FYI, the eval grid I use for the presentations is available here. In case this helps, here are the two main weak points that I saw in article presentations previous year:

Article list below. There is no flexibility in the choice of date for the presentations as they have to be synchronised with the advancement of the lectures. You will email me the slides for your presentation (as a pdf or html file) the day before your presentation at the latest.