This is an example project page which serves as a template
By Samuel Guay, & Pierre Bellec
Published on May 16, 2020 | Last updated on September 7, 2023
Inspired by the Recurse Centre initiative (formally known as the “hacker school”), Brainhack School was established in 2018 with the mission to train students from multidisciplinary backgrounds to a panoply of reproducible tools for neural data science, using a project-based approach. Following an initial 3-weeks long pilot, a 4th week was added with an intensive bootcamp, so that students could choose what tools to learn more deeply in their projects. As the course became integrated in standard curriculum at different universities, the formula seemed to be working. In order to streamline the different stages of the project, some standard template and milestones needed to be incorporated in a github-based workflow. The “project template” project (which is also our first BHS meta-project) aims at establishing such a standardized template. You can check the following video where Pierre Bellec gives an overview of the Brainhack school.
The “project template” project will rely on the following technologies:
- Markdown, to structure the text.
- The Hugo website framework which is used by the BHS website. This makes it possible to easily add the markdown project description to the website.
- Adding the project to the website relies on github, through pull requests.
Ultimately, the project template will be used by all BHS participants. Data on the different projects will be aggregareted on the following page. This will serve as an additional example gallery in the years to come for future brainhack school students. Many reports from BHS 2019 already used this template.
At the end of this project, we will have:
- The current markdown document, completed and revised.
- A gallery of the student projects at Brainhack 2020.
- Instructions on the website about how to submit a pull request to the brainhack school website in order to add the project description to the website.
The project was swiftly initiated by P Bellec, based on the existing template created in 2019 by Tristan Glatard and improved by different students. It was really not that hard. Community feedback is expected to lead to rapid further improvements of this first version.
Tools I learned during this project
- Meta-project P Bellec learned how to do a meta project for the first time, which is developping a framework while using it at the same time. It felt really weird, but somehow quite fun as well.
- Github workflow- The successful use of this template approach will demonstrate that it is possible to incorporate dozens of students presentation on a website collaboratively over a few weeks.
- Project content Through the project reports generated using the template, it is possible to learn about what exactly the brainhack school students are working on.
Deliverable 1: report template
You are currently reading the report template! I will let you judge whether it is useful or not. If you think there is something that could be improved, please do not hesitate to open an issue here and let us know.
Deliverable 2: project gallery
There is not yet a project gallery, as BHS 2020 is the first edition that will incorporate it on the website. You can still check out the 2019 BHS github organization
ECG pupilometry pipeline by Marce Kauffmann
The repository of this project can be found here. The objective was to create a processing pipeline for ECG and pupillometry data. The motivation behind this task is that Marcel’s lab (MIST Lab @ Polytechnique Montreal) was conducting a Human-Robot-Interaction user study. The repo features:
- a video introduction to the project.
- a presentation made in a jupyter notebook on the results of the project.
- Notebooks for all analyses.
- Detailed requirements files, making it easy for others to replicate the environment of the notebook.
- An overview of the results in the markdown document.
Here are other good examples of repositories:
- Learning to manipulate biosignals with python by François Lespinasse
- Run multivariate anaylysis to relate behavioral and electropyhysiological data
- PET pipeline automation and structural MRI exploration by Rebekah Wickens
- Working with PSG [EEG] data from Parkinson’s patients by Cryomatrix
- Exploring Brain Functional Activation in Adolescents Who Attempted Suicide by Anthony Gifuni
Deliverable 3: Instructions
To be made available soon.
Conclusion and acknowledgement
The BHS team hope you will find this template helpful in documenting your project. Developping this template was a group effort, and benefitted from the feedback and ideas of all BHS students over the years.