https://github.com/scverse/202503_hackathon_owkin
Repository to organise the shared hackathon with Owkin in Paris
https://github.com/scverse/202503_hackathon_owkin
Last synced: 11 months ago
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Repository to organise the shared hackathon with Owkin in Paris
- Host: GitHub
- URL: https://github.com/scverse/202503_hackathon_owkin
- Owner: scverse
- Created: 2025-03-06T11:11:47.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-03-16T17:01:16.000Z (about 1 year ago)
- Last Synced: 2025-03-16T18:39:38.918Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 4.14 MB
- Stars: 2
- Watchers: 4
- Forks: 2
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
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README
# scverse x Owkin Hackathon 2025
Welcome to the scverse Hackathon 2025 organized in collaboration with [Owkin](https://www.owkin.com)! This repository is your central hub for all hackathon resources including workstreams, data tutorials, event details, and participation guidelines.
---
## Table of Contents
- [scverse x Owkin Hackathon 2025](#scverse-x-owkin-hackathon-2025)
- [Table of Contents](#table-of-contents)
- [Overview](#overview)
- [Event Details](#event-details)
- [Schedule](#schedule)
- [How to Participate](#how-to-participate)
- [Workstreams](#workstreams)
- [Data \& Tutorials](#data--tutorials)
- [Important Information](#important-information)
- [Communication](#communication)
- [Contact](#contact)
---
## Event Details
- **Dates:** Monday, 2025-03-17 09:00 to Wednesday, 2025-03-19 12:30
- **Location:** Owkin Office, 14/16 boulevard Poissonnière, Paris, France
- **Access:** Upon arrival, please check in at the reception.
- **What to Bring:**
- Your own laptop and charger (extension cords will be provided).
- Remember to bring an adapter if needed (France uses type E power sockets).
---
## Schedule
*Note: Schedule subject to minor adjustments.*
| Date | Time | Activity |
|----------------------------|-----------------|----------------------------------------|
| **Monday, March 17, 2025** | 09:00 – 09:30 | Breakfast on Owkin |
| | 09:30 – 10:00 | scverse Introduction |
| | 10:00 – 10:30 | Owkin Introduction |
| | 10:30 – 10:45 | Kick-off |
| | 10:45 – 12:00 | Hack Session |
| | 12:00 – 14:00 | Lunch on Owkin / Continued Hack |
| | 14:00 – 18:00 | Hack Session |
| | 18:00 – 20:00 | Afterwork @Owkin |
| | | |
| **Tuesday, March 18, 2025**| 09:00 – 09:30 | Breakfast on Owkin |
| | 09:30 – 12:00 | Hack Session |
| | 12:00 – 14:00 | Lunch on Owkin / Continued Hack |
| | 14:00 – 18:00 | Hack Session |
| | 18:00 – 20:00 | Afterwork @ [Bianca](https://maps.app.goo.gl/paTs1PoTaLMpGFsJ9) |
| | | |
| **Wednesday, March 19, 2025**| 09:00 – 09:30 | Breakfast on Owkin |
| | 09:30 – 11:00 | Hack Session |
| | 11:00 – 12:30 | Team Updates & End of Event |
---
## How to Participate
1. **Explore Workstreams:**
Check out the challenges (workstreams) detailed as [GitHub issues in this repository](https://github.com/scverse/202503_hackathon_owkin/issues).
2. **Claim a Workstream:**
Indicate on which project you want to work by writing your name in the respective column in this [Google Sheet](https://docs.google.com/spreadsheets/d/1f8i7c4cuFnUof2_-dPTYoTEVhK4i5flWGV2vGViLvsE/edit?gid=0#gid=0).
3. **Develop Your Solution:**
Use your preferred tools and techniques to bring your innovative ideas to life.
4. **Discuss with your peers and have fun:**
Hackathons are not purely about lines-of-code, but also intellectual exchange. We highly encourage you to discuss your ideas with your peers.
5. **Please abide by the [Code of Conduct](https://scverse.org/about/code_of_conduct).**
---
## Workstreams
Our GitHub Issues contain a variety of workstreams designed to challenge your skills in single-cell data analysis. Each issue includes a description, requirements, and expectations.
- **Workstream 1:** Unified scverse ecosystem plotting package – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/1)
- **Workstream 2:** Segger-SpatialData Integration – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/11)
- **Workstream 3:** Cross-sample comparisons with Squidpy – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/12)
- **Workstream 4:** Knowledge-driven identification of therapeutic spatial clusters – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/14)
- **Workstream 5:** Improve memory and runtime of spatialdata and spatialdata-io – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/10)
- **Workstream 6:** {Micro,Tile}JSON for SpatialData – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/4)
- **Workstream 7:** SpatialData: exploring ergonomics and speed improvements – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/6)
- **Workstream 8:** SpatialData-IO support for annotations from histology tools – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/9)
- **Workstream 9:** Exploring support for 2.5/3D shapes – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/8)
- **Workstream 10:** Housekeeping & Cookiecutter template maintenance – [View detallied description](https://github.com/scverse/202503_hackathon_owkin/issues/7)
*More workstreams might be added as task forces are confirmed.*
---
## Data & Tutorials
To help you get started quickly, we have prepared:
- **Data Access Instructions:**
Detailed guidelines on how to download and explore the datasets [scverse/202503_hackathon_owkin > data](https://github.com/scverse/202503_hackathon_owkin/tree/main/data).
- **Tutorials:**
Generally, we recommend to check out the following tutorials pages, depending on your project:
- [AnnData](https://anndata.readthedocs.io/en/stable/tutorials/index.html)
- [MuData](https://mudata.readthedocs.io/en/latest/notebooks/quickstart_mudata.html)
- [SpatialData](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html)
- [Scanpy](https://scanpy.readthedocs.io/en/stable/tutorials/index.html)
- [Squidpy](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/index.html)
---
## Important Information
- **Meals:**
- Breakfast and lunch are provided by Owkin (with vegetarian and vegan options).
- **Note:** Lunch will not be provided on Wednesday.
- **Afterworks:**
- **Monday:** Afterwork at Owkin
- **Tuesday:** Afterwork at [Bianca](https://maps.app.goo.gl/paTs1PoTaLMpGFsJ9) (with drinks and light food)
- **Emergency Contacts:**
- **Reception:** (+33) 6 07 95 41 38
- **Building Security:** (+33) 6 59 23 49 77
---
## Communication
Stay connected and be in the loop by [joining our Zulip](https://scverse.zulipchat.com) and look for the [2025-03 hackathon owkin](https://scverse.zulipchat.com/#narrow/channel/488601-2025-03-hackathon-owkin) channel.
If you have any questions or doubts, please reach out, either via Zulip or using the contact information below.
---
## Contact
For further inquiries or support, please contact us at:
- **Email:** [core@scverse.org](mailto:core@scverse.org)
---
We look forward to your innovative contributions and a dynamic hackathon experience at the Owkin office in Paris!
*Organized by the scverse team in collaboration with Owkin.*