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# System prepended metadata

title: Hackathon on Python/R interoperability for single cell and spatial bioinformatics

---

*Last updated: 12th September 2023*

Two-day hackathon on Python/R interoperability for single cell and spatial bioinformatics.

Monday 18 and Tuesday 19 September 2023
Meeting room V114, Technologiepark-Zwijnaarde 71, 9052 Gent

Organised by [Saeys Lab](https://saeyslab.sites.vib.be/en) at [VIB-UGent Center for Inflammation Research](https://vib.be/en/research-and-impact/research-centers/center-inflammation-research#/).
For questions, send a message on the Zulip stream or email Louise.Deconinck@UGent.be and Benjamin.Rombaut@UGent.be.

Links to:
- [image.sc Zulip stream](https://imagesc.zulipchat.com/#narrow/stream/402390-Zzz.3A-.5B2023-09.5D-Ghent-Hackathon-Python.2FR)
- [GitHub repository](https://github.com/saeyslab/sc_hackathon_2023)
- [GitHub issues Kanban board](https://github.com/orgs/saeyslab/projects/2)

## Objectives

- **Python/R interoperability for single cell and spatial bio-informatics**
- Document and improve interoperability between scverse and bioconductor packages
- Find synergies and foster possible collaborations in an open setting
- Answer three user questions:
    1. **💾 data format: Data format and conversion**
How do I convert dataset in format X to format Y?
    2. **📚 multi support: Support for comparing multiple models or datasets**
    How do I organize and compare multiple models and/or datasets?
    3. **🔍 viz: Visualization of datasets**
How do I visualize a spatial dataset?
- Projects of interest
    - [anndata](https://github.com/scverse/anndata) / [anndataR](https://github.com/scverse/anndataR)
      - add to anndataR functionality
      - document latest functionality in converting spatial datasets
    - [SpatialData](https://spatialdata.scverse.org) / [SpatialData in R](https://github.com/HelenaLC/SpatialData)
      - multiple tables proposal ([#298](https://github.com/scverse/spatialdata/issues/298))
      - support more R functionality ([TODOs](https://github.com/HelenaLC/SpatialData#todos))
      - Make [Python SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) available in R
      - Make [R imcdatasets](https://bodenmillergroup.github.io/imcdatasets/articles/imcdatasets.html) available in Python
  - Visualize datasets using:
    - Python viz (spatialdata-plot, napari-spatialdata...)
    - R viz (cytomapper, cytoviewer, MoleculeExperiment...)

## Travel details

- Participation is free, but registration is mandatory and limited to ensure enough room capacity
- For activities and accommodation in Ghent, check out [visit.gent.be](https://visit.gent.be/en) and [vibconferences.be/host-city-ghent](https://www.vibconferences.be/host-city-ghent). Feel free to contact us with specific questions
- A free lunch will be provided for you on both days.
- A free 15min [shuttle service](http://www.techlane.be/park-services/shuttle-services/) is available with a visitor QR code between Gent-Sint-Pieters railway station and Tech Lane Park (first stop VIB-UGent).
- It is possible but not required to attend the European Bioconductor Conference in Ghent afterward on 20-22 September. For info and registration: https://eurobioc2023.bioconductor.org/. (Location is 15min from Gent-Sint-Pieters with Tram 2)

## Agenda
### Mon 18 September
9:00-10:00 Welcome, introduction, setup
10:00-11:00 Work out objectives and tasks
11:00-12:00 Hacking
12:00-13:00 Lunch
13:00-16:30 Hacking
16:30-17:00 Updates from participants and discussion

*18:30 Dinner and drinks in city center*
[Mosquito Coast](https://www.mosquitocoast.be/) - [Menu](https://www.resengo.com/Code/Webshop/Menu/index.asp?AID=1&CID=2533&SCID=0&WSCID=0&MFID=21145&LC=EN&LCSelected=1#menu-folder-21235) - Hoogpoort 28, 9000 Gent

### Tue 19 September
9:00-10:30 Hacking
10:30-11:00 Report on progress and issues
11:00-12:00 Discussion on future work and possible collaborations
12:00-13:00 Lunch
13:00-13:10 Group picture
13:10-16:00 Hacking
16:00-16:30 Updates from participants and discussion
16:30-17:00 Finish up final notes, issues and future work

### Wed 20 - Fri 22 September
European Bioconductor Conference in Ghent
https://eurobioc2023.bioconductor.org/

~~Submission of late poster abstracts is open until August 21.~~

