Software and Data

As part of our commitment to FAIR, open science principles, the software that we develop for our projects is open-sourced. Restrictions may apply (e.g. data privacy reasons) depending on the context of the project.

You can find our public repositories on GitLab.

Individual project pages may contain further links to datasets, project code, pre-trained models and other resources.

Here are some public-facing web apps that we developed, or helped develop, as part of our projects:

• Glyfix: an annotation correction tool for Papyrologists.
  • Developed in collaboration with Isabelle Marthot-Santaniello's group at the Department of Ancient Civilizations.
• Sleep-Wake Atlas: an exploration of mouse brain activation patterns across undisturbed circadian or sleep deprived experimental conditions.
  • Developed in collaboration with Alex Schier's group at the Biozentrum.

Here are some highlights of general-purpose tools and resources that we maintain:

• CeDA Project Copier: a template for scientific Python-centric projects, with automatic setup of some best practice tools for reproducibility, development, documentation, and testing.
• UniBas Docs Copier: a template for University of Basel groups that want a Zensical documentation site managed with Pixi and deployed via GitLab CI.
• data-annotations: a small Python package for attaching provenance and structured descriptions to the files and directories your workflows produce