Welcome

Join us for the scverse Hackathon taking place from Wednesday, April 26th, 12:00 PM to Friday, April 28th, afternoon at BioQuant (Neuenheimer Feld 267, 69120 Heidelberg, Germany).

The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Event Schedule

  • Wednesday, April 26th (SR041)

    • 13:30 – 14:00 — PI introductions (Julio Saez-Rodriguez, Wolfgang Huber)
    • 14:00 – 14:30 — Hackathon introduction
    • 14:30 – 15:00 — State of the scverse + Q&A
    • 15:00 – 15:30 — Coffee break
    • 15:30 – 18:30 — Split into groups and hack
    • 18:30 – 19:00 — Short updates from teams

  • Thursday, April 27th (SR042 & SR044)

    • 08:30 – 09:00 — Coffee in the morning
    • 09:00 – 12:00 — Hack
    • 12:00 – 13:00 — Lunch + group photo
    • 13:00 – 15:30 — Hack + short updates
    • 15:30 – 16:00 — Coffee break
    • 16:00 – 18:30 — Hack + short updates
    • 19:30 — Group dinner

  • Friday, April 28th (SR042 & SR043)

    • 08:30 – 09:00 — Coffee in the morning
    • 09:00 – 12:00 — Hack
    • 12:00 – 13:00 — Lunch
    • 13:00 – 15:00 — Hack
    • 15:30 – 16:00 — Updates from teams
    • 16:00 — Coffee / departure
    • 16:30 — Feedback and brainstorming session
    • 19:00 — Self-organized going out

Hackathon Focus Areas

  1. Interoperability - Improve compatibility with other languages and tools.
  2. Biological Knowledge Representation - Enhance the integration of biological information in the scverse ecosystem.
  3. House keeping - Solve the issues that were forgotten about

Interoperability Tasks

  • Develop AnnData/MuData reader for Julia.
  • Develop AnnData/MuData reader for Bioconductor/R.
  • Create OME-ZARR reader and writer in R using Rarr.
  • Establish a test suite of scverse data files for various implementations.

Knowledge Representation Tasks

  • Develop a backend for BioCypher output and frontend Python package for annotating AnnData.
  • Enable access to genomic annotations through Bioconductor AnnotationHub.
  • Implement knowledge-guided sparsity for factor models.

House keeping Tasks

  • Integrating scverse tutorials
  • Implement scverse example datasets package
  • Improve cookiecutter template
  • Generate scverse branding content
  • Add events page to scverse website

See this hackmd for more information.

Hackathon checklist

  • Check that you agree with the scverse code of conduct.
  • Ensure that you have a Github account.
  • Join our zulip where you’ll be added to the hackathon stream. Say hi if this is your first time on the scverse zulip!
  • Have python and any scverse package that you might work on installed.