Reproducible research through reusable code

Erasmus University Rotterdam

December 3, 2024

9:30 - 17:00

Instructors: Sven van der Burg, Eduard Klapwijk

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General Information

This workshop teaches you the skills to make your code reusable by others. You will practice these skills by directly applying them to your own project. Inevitably, this will make your research more reproducible.

Who:

This workshop is aimed at researchers who want to make their code reusable. You are able to write basic code in a programming language like R or Python. This can be a few simple lines of code or a larger piece of software.

Where: Polak Building, Burgemeester Oudlaan 50, 3062 PA Rotterdam. Get directions with OpenStreetMap or Google Maps.

When: December 3, 2024, 9:30 - 17:00.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They should bring their own coding project to the workshop. This can range from a few small scripts to an extensive piece of software.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

The room is wheelchair / scooter accessible.
Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Workshop files: You will find all slides, notebooks, archived collaborative documents, and other relevant files in the files folder of the workshop website repository after the workshop.

Contact: Please email training@esciencecenter.nl for more information.

Code of Conduct

Participants are expected to follow these guidelines:

Use welcoming and inclusive language
Be respectful of different viewpoints and experiences
Gracefully accept constructive criticism
Focus on what is best for the community
Show courtesy and respect towards other community members

Syllabus

Why is reproducibility important?
How do I share my code with others using GitHub?
What is the minimal documentation required for others to be able to run my code?
- Writing a good README file
- Dealing with dependencies
What makes code readable and reusable?
Code conventions and modular coding

Schedule

09:30 Welcome & icebreaker
09:45 Workshop introduction: why is reproducibility important?
10:00 Uploading a coding project to GitHub
10:30 break
10:40 Software dependencies
11:00 Software documentation
11:30 break
11:40 Code conventions and modular coding
12:30 Lunch
13:30 Next steps: how to make your code reusable?
13:45 Work on your own project
15:30 Reusability check
16:15 Wrap-up
16:30 END

Setup

To participate in this workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Software setup

Software

To participate in this workshop, you will need to prepare the following (if you haven’t already):

Create a GitHub account. Please refer to this page for instructions.
Make sure you can edit the code of your project during the day of the workshop.