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👋 BHG2023-OMERO-ARC

License: CC BY 4.0

🚧 Under construction. 🚧

This repository is still growing.
For some preparatory work for this topic from another hackathon, please see this repository or the respective publication at Zenodo.


Repository for documentation during the 2nd de.NBI BioHackathon Germany - 11.-15.12.2023 - OMERO-ARC project (in short: BHG2023-OMERO-ARC)

Code of Conduct

Please also adhere here to the ELIXIR Germany Code of Conduct.

Task_Groups

Initially prepared and suggested based on defined task of participants.

Branch protection

  • The main branch is protected. For merging a branch into main you need a PR with at least one approving review.
  • @andreaschrader only initially bypasses this in order to set up the repository for the participants for the Hackathon.

.gitignore

  • currently selected: Visual Studio
  • Prep_stage/
    • You can create this directroy inside your cloned BHG2023-OMERO-ARC repo and use it when you want to prepare files or place data in this repo locally but do not want to push these to this repo.

Overview of the content in this repository

.
├── .zenodo.json
├── CITATION.cff
├── CONTRIBUTING.md
├── LICENSE
├── README.md
├── Reporting
│   ├── BioHack_2023_Final_OMERO_ARC.pdf
│   └── BioHack_2023_Intro_OMERO_ARC.pdf
├── Task_Groups
│   ├── 01_Roadmap
│   │   ├── README.md
│   │   └── arc-omero-roundtrip-proposal.md
│   ├── 02_Use_Cases
│   │   └── README.md
│   ├── 03_RDMcompliant_Metadata
│   │   ├── IDRtemplates-2-ARC
│   │   ├── IDRtemplates-2-ARC.md
│   │   ├── README.md
│   │   ├── REMBI-2-ARC
│   │   ├── REMBI-2-ARC.md
│   │   ├── REMBI_Templates
│   │   │   └── RGC_Ca2+_imaging.csv
│   │   └── REMBI_Templates.md
│   ├── 04_Metadata_Transfer
│   │   └── README.md
│   ├── 05_OMERO-2-ARC
│   │   └── README.md
│   ├── 06_ARC-2-OMERO
│   │   ├── README.md
│   │   ├── metadata_filler.py
│   │   ├── requirements.txt
│   │   ├── transfer.xml
│   │   └── workflow.sh
│   ├── 07_Test_Tools
│   │   ├── README.md
│   │   ├── omero-cli-transfer-arc-installation.md
│   │   └── omero-cli-transfer-arc-report.md
│   ├── 08_Teaching_Material
│   │   └── README.md
│   ├── 09_Documentation
│   │   └── README.md
│   └── README.md
└── images
    └── rat-brain-ls.png

21-01-2024 (created using tree v2.1.1 © 1996 - 2023 by Steve Baker, Thomas Moore, Francesc Rocher, Florian Sesser, Kyosuke Tokoro)


Contributions

Notes on contributions during the Hackathon are here.


🙌 Thank you for any contribution to the BHG2023-OMERO-ARC repository!!!

When contributing, please consider that (parts of) this repository might be used by people with various background and intentions including teaching in the future. Therefore, it is appreciated if you can provide a brief non-specialist targeted introduction / summary preceding your content and work on Hackathon tasks.

Contributors

🤝 Participants contributing to the BHG2023-OMERO-ARC project can provide their name, GitHub handle, ORCID iD and ROR here - if you like.

Suggestion: alphabetical order (surname):

name GitHub ORCID ROR
Mohamed Abdrabbou @MM-abdrabbou https://orcid.org/0000-0003-2778-7483
Michele Bortolomeazzi @MicheleBortol https://orcid.org/0000-0001-5805-5774
Jean-Marie Burel @jburel https://orcid.org/0000-0002-1789-1861 https://ror.org/03h2bxq36
Niraj Kandpal @Nirkan https://orcid.org/0009-0007-5101-4786 https://ror.org/00rcxh774
https://ror.org/04c4bwh63
Josh Moore @joshmoore https://orcid.org/0000-0003-4028-811X https://ror.org/05tpnw772
Andrea Schrader @andreaschrader https://orcid.org/0000-0002-3879-7057 https://ror.org/034waa237
https://ror.org/00rcxh774
Peter Zentis @pzentis https://orcid.org/0000-0002-6999-132X https://ror.org/00rcxh774
https://ror.org/04c4bwh63

Acknowledgement

🚧 Under construction. 🚧

To be filled after the Hackathon.

Funding enabling project leads organization and Hackathon participation

DataPLANT and NFDI4BIOIMAGE

We acknowledge the support of DataPLANT and NFDI4BIOIMAGE, both funded by the German Research Foundation (DFG) within the framework of the NFDI – project numbers: 442077441 and 501864659.

Other Organisations

CEPLAS

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within Germany’s Excellence Strategy – EXC-2048/1 – project number 390686111.

CECAD

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy - EXC 2030 - 390661388.

CRC TRR341

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 456082119.