FUnctionality Sharing In Open eNvironments
Heinz Nixdorf Chair for Distributed Information Systems

Reproducibility of Jupyter Notebooks from publications


Reproducibility is vital in science. Reproducibility of published results is one of the challenges faced in science in the present era. We provide several thesis topics on this and related areas.

The task is to explore reproducibility and study which features of the publications correlate with reproducibility. The work is developed on top of the existing solution developed in our group. The task involves developing a solution to implement the recommendations to improve reproducibility.

We provide some thesis topics which can be explored further. If interested in any of these topics, please feel free to contact us.

What are the topics?

  • Develop solutions for practitioners with the implementation of our recommendations for reproducibility.
  • Study how certain features of the articles (e.g. data availability, ethics statement, journal, etc.) correlate with reproducibility
  • Zoom in on reproducibility by subject, e.g. cell lines or invasive species
  • Incorporate feedback from stakeholders
  • Build a validator to assess the fit of some workflow with the recommendations
  • Also consider the integration of computational and non-computational steps (e.g. biospecimens) in reproducibility workflows
  • timeline/ continuous service, including visualizations
  • Environmental footprint

What do we expect?

  • Programming knowledge in Python
  • Any bio knowledge is a plus

Start: May or later

Supervisor: Sheeba Samuel (sheeba.samuel@uni-jena.de), Daniel Mietchen, Birgitta König-Ries

Please contact Sheeba Samuel (sheeba.samuel@uni-jena.de) or Birgitta König-Ries (birgitta.koenig-ries@uni-jena.de) to discuss more on the topic.