Updates

• 24/02/22 (Adrien O) Added top_authors.csv file showing the 20 authors with the most publications in the given query. Also added other csv files acquired from the PubMed query page.

QLS600 reproducibility assignment

Reproducibility / reusability in life sciences is impacted by many factors. In particular, the availability of code or software on the one hand, and of data on the other, is a key component for the ability to reuse research and replicate results. In this collaborative exercise, you will assess the evolution of code and data availability over the past 12 years in a specific domain of cognitive neuroscience (memory studied with fMRI).

To do this, you will sample the literature in this specific domain (defined by the PubMed query below) and estimate for a number of articles (to be determined) the availability of code and data. Often, it will not be easy to determine from the publication if the code is really available, or if the data are truly accessible.

PubMed query:

(fMRI[Title/Abstract]) AND (memory[Title/Abstract] AND n-back) https://pubmed.ncbi.nlm.nih.gov/?term=%28fMRI%5BTitle%2FAbstract%5D%29+AND+%28memory%5BTitle%2FAbstract%5D+AND+n-back%29

The goals of this assignment are to:

1. Make you aware of the level of reusability of the literature in this specific domain
2. Acquire some experience with collaborative work using Git

Constraints:

• The time spent on this assignment should not exceed the normal amount of hours spent on an assignment.
• Procedure, code, results should be pushed to the Github organization. You may reuse the assignment repository if you wish.
• Discussions / organization can happen on a Slack space or using GitHub issues but should be open to all students and myself.

Presentation:

On Thursday March 10th, all results will be presented to the class. I suggest to present your work with the following sections:

• Design of the study (~15mn)
• Protocol for data acquisition, and organization of the work across collaborators (~15mn)
• Analysis of results and conclusions (~15mn)

Personal feedback

In addition, each student should write a paragraph to give some feedback on their personal experience (difficulties, lessons learnt, etc). Please email me the paragraph by March 18th.

Other

A few students asked to complete a specific reproducibility project. This project also needs to be presented (10-15mn) on March 10th.

Presentation Link

Our presentation can be found here (McGill University login required).