You will be assessed through:
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).
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:
The deadlines (indicated below) are strict. You will send me your work by email (and I will systematically acknowledge receipt).
If you choose to work as a team of two students, both will get the same grade, with no exception. It is up to you to agree on the way you will work together (division of labor, logistics, etc). The instructor will not arbitrate conflicts between team members.
Each team is expected to produce its own work. Sharing work between teams as well as using code, text or data written or generated by someone else (or by a software) is strictly forbidden. One exception: you are allowed to use figures from the articles as well as other articles you find relevant, but they must be properly referenced. Ideas and information found in other works and used in your work must also be properly referenced.
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.
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:
The understanding and presentation of the scientific content, especially clearly highlighting the questions, hypotheses and conclusions (this was often missing) instead of just presenting the methods and the data (which was usually well done). Scientific articles are not just a collection of experiments and observations, but have a specific narrative where they aim at filling a black spot in our understanding of the evolutionary processes.
The connexion with the content of the class: some articles had a very strong connexion with material discussed in class, and this was not always identified
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.
Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution (Amicone et al, 2022), presentation on 2025-01-07
The evolution of stress-induced hypermutation in asexual populations (Ram and Hadany, 2012), presentation on 2025-01-14
Emergent cooperation in microbial metabolism (Wintermute and Silver, 2010), presentation on 2025-01-21